Curriculum Vitae
Goran Neshich
Last General Update: Jauary 14, 2009
1. Personal Data
2. Professional Qualifications
3. Education History
4. Professional Experience
5. Membership To
6. Language Competence
7. Publications (Abstracts from Entrez)
8. Work Presentend At Scientific Meetings
9. Thesis Committee Participation
10. Software Packages Published
11. Seminars & Lectures given
12. Courses
13. Projects
14. Professional References
1. PERSONAL DATA
1.1. Name: Goran Nesic
Original name writing (Serbian): Goran Nešić
U.S. documents anotation: Goran Neshich
Portuguese pronunciation: Góran Neshitch
(born in Beograd, Yugoslavia)
1.2. Professional:
Embrapa Informática Agropecuária
Caixa Postal: 6041
Av. Dr. André Tosello No: 209
Barão Geraldo, Cidade Universitária "Zeferino Vaz"
CEP: 13083-886 Campinas (SP) - Brazil
Telefone: 55-19-3211-5774
FAX: 55-19-3211-5754
E-mail: neshich@cnptia.embrapa.br
Website: http://www.cbi.cnptia.embrapa.br/~neshich
2. PROFESSIONAL QUALIFICATIONS
Laboratory Management, Network Management, Software Design, Experiment Design,
Supervising and Teaching,
Scientific Society Managment, Scientific Meeting Organization.
TECHNICAL AREAS AND SKILLS USED:
Computational Biology, BioInformatics, Structural Bioinformatics, Protein Engineering and
Molecular Modeling;
Computational Biology & BioInformatics:
-In Silico Chemogenomics
- Macromolecular Structure analysis, Macromolecular Surface analysis, Macromolecular
Complexes and their Interfaces
-Sequence analysis, Multiple Sequence Alignment, Structure Alignment
-Phylogenetic trees and Evaluation of Multiple Sequence and Structure Alignments Based on
Phylogenetic trees
-Software Manufacturing for Sequence, Structure and Surface Analysis
-Large Scale Automated Data-Base Consulting, Data Manipulation and Data Generation,
Relational Database of protein descriptors
Protein:
-Purification (including isolation from the membranes)
-Characterization
-Sequence analysis (including DNA sequences), data-bases
-Structure prediction and determination
-Structural analysis
-Molecular modeling, Homology modeling and Computer graphics
-Molecular mechanics and molecular dynamics calculations
-Protein design (Molecular Genetics, Site-directed mutagenesis)
-Protein stability: kinetic and thermodynamic analysis
-Modification and expression of proteins
Biochemistry:
-HPLC
-SDS/PAGE
-Ion-exchange chromatography
-Peptide and protein sequencing
Biophysics, Bioenergetics and Photosynthesis:
-Experimental studies on electron transport in photosynthesis, Flash photolysis; Laser
spectroscopy; Electronics; Quantum statistical mechanics
-EPR (spin labeling; membrane fluidity)
-Fluorescence (including quenching)
-electrochemical measurements
-cryogenics
Protein-DNA interactions
-Simulation of Protein-DNA interactions (Molecular modeling; Sequence recognition)
Computer Networking, Data analysis, Statistics and Instrument interfacing:
-Networking (WAN and LAN), InterNet, TCP/IP, FTP
-WWW/Gopher document editing, organization and distribution
-UNIX, VMS and MS-DOS, MS-Windows and MS-Windows-NT operating systems
-software design (using Fortran, Forth, Basic, C++, Pearl, JAVA, JavaScript)
-molecular presentation software
-GPIB and RS-232 interfacing to instruments
3. EDUCATION HISTORY
3.1. Post-graduation:
Post Doctorate: Biophisics - (1997-1998) University of
Columbia
Prof. Barry Honig - Dept. Biochemistry & Molecular Biophysics, New York, USA
Subject: Development of algorithms to describe macromolecular interfaces.
3.1.1. Ph.D.:
Biophysics - University of Illinois at Urbana Champaign, Illinois, USA (1989)
Title of the thesis: "Biophysical Investigation of Electron Transfer between High
Potential Hemes in C Subunit and Special Pair
of Reaction Center Protein of Photosynthetic Bacteria Rhodopseudomonas viridis".
3.1.2. M.S.:
Plant Bio-physics - Center for Multidisciplinary Studies, University of Belgrade,
Yugoslavia (1981).
Title of the thesis: "Influence of the Temperature on some Aspects of the
Photosynthetic Process and Membranes in
Maize (Zea mays L.)
3.2. B.S.:
3.2.1. Theoretical Physical-Chemistry Faculty of Life Science and Mathematics, University of
Belgrade, Yugoslavia (1978)
Title of the thesis: "The Computation of the Energies and the Wave Functions for the Bending
Vibrations of Three-atomic
Molecules using Variation Method".
3.3. Other courses:
3.3.1. United Nations Environment Programme (UNEP) course "Studies on Photosynthesis in
Relation to Bioproductivity", chief
coordinator Dr. David 0. Hall, King's College, University of London, U.K., conducted in the
Laboratory of Biophysics, Maize
Research Institute, Belgrade, Yugoslavia, July.15 August.5.1981.
3.4. Professional Contacts:
3.4.1. European Molecular Biology Laboratory (EMBL), The EMBL data Library and Protein Design
Group. Heidelberg - Germany.
3.4.2. RIKEN Life Science Center, The RIKEN Data Library, Tsukuba - city, Japan.
3.4.3. University of Illinois at Urbana-Champaign, Department of Biophysics and Beckman Institute.
U.S.A.
3.4.4. National Center of Biotechnology Information (NCBI) Washington D.C., U.S.A.
3.4.5. International Center for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy
3.4.6. Broohaven National Laboratory, Protein Data Bank, Upton, New York, U.S.A.
3.4.7. Scripps Institute, San Diego, U.S.A.
3.4.8. University of Columbia, New York, New York, U.S.A.
3.4.9. Research Collaboratory for Structural Bioinformatics (RCSB) PDB, SDSC, UCSD, U.S.A.
3.4.10. CNB Madrid, Spain
3.4.11. Kyushu Institute of Technology, Japan
3.4.12. Scuola Normale Superiore, Pisa, Italy
3.4.13. H. Poincare University, Nancy, France
3.4.14. Zentrum für Bioinformatik, Universität Hamburg, Germany
3.4.15. Facultad de Ciencias Exactas, UNLP, Calles 49 y 115, 1900 La Plata, Argentina
3.4.16. Facultad de Ingeniería y Tecnologías, Universidad Católica del Uruguay, Montevideo,
Uruguay
3.4.17. Center for Biological Sequence Analysis - DTU - Copenhagen - Denmark
3.4.18. Center for Multidisciplinary Studies, University of Belgrade, Serbia
4. PROFESSIONAL EXPERIENCE
4.1. 1979-1985: Maize Research Institute, Zemun Polje, Belgrade, Yugoslavia.
4.1.1. Department of Physiology, Laboratory of Biophysics
4.1.2. Position: Research Associate
4.1.3. Project: "Computer Modeling of the Cell Membrane Response to Environmental Stress"
4.2. 1983-1989: University of Illinois at Urbana-Champaign, Illinois, U.S.A..
4.2.1. Department of Biophysics, Laboratory of Molecular Biophysics
4.2.2. Position: Research Assistant
4.2.3. Project: Bioenergetics of the photosynthetic processes.
4.3. 1988-1992: IICA/ (CENARGEN)/ EMBRAPA, Brasília, D.F., Brazil
4.3.1. Department of Molecular Biology, Laboratory for Protein Engineering and Biophysics
4.3.2. Position: International Consultant for EMBRAPA/CENARGEN through the Inter American
Institute for Cooperation on Agriculture (IICA)
4.3.3. Project:
a) "Determination of the structure and the function of the storage protein 2S from Bertholletia
excelsa H.B.K. with parallel introduction of tryptophan to satisfy
nutritional requirement in human diet”
b) "Molecular Genetics and Biophysical Studies on Reaction Center Protein from
Rhodopseudomonas viridis".
4.4. 1993-1994: National Research Council (CNPQ) - National Computer Research Network (RNP)
and CENARGEN/EMBRAPA Brasilia, DF, Brazil
4.4.1. Department of Molecular Biology, Laboratory for Protein Engineering and Bioinfomatics
4.4.2. Position: Group Leader and Chief Coordinator
4.4.3. Project:
a) Protein modeling
b) Establishment and coordination on the national level of the Brazilian Molecular Biology and
Biotechnology Network (BMBBNet) and its principal node Brazilian Bioinformatics Resource
Center (BBRC).
4.5. 1994 -1996 CENARGEN/EMBRAPA - Brasília, DF, Brazil
4.5.1. Department of Molecular Biology, Laboratory for Protein Engineering and Department of
Bioinformatics
4.5.2. Position: Researcher/level III; Group Leader and Chief Coordinator
4.5.3. Project:
a) Protein modeling, DNA/Protein interaction studies
b) Coordination on the national level of the Brazilian Molecular Biology and Biotechnology
Network (BMBBNet) and its principal node Brazilian Bioinformatics Resource Center
(BBRC).
4.6. 1997-1998 : Columbia University, New York, U.S.A. -Barry Honig's Lab
4.7. 1998 -2000 CENARGEN/EMBRAPA - Brasília, DF, Brazil
4.7.1. Bioinformatics Laboratory
4.7.2. Position: Researcher/level III; Group Leader
4.8.- 2000 - Embrapa Informática Agropecuária -Campinas, SP, Brazil
4.8.1 Structural BioInformatics Center
4.8.2 Group Leader
5. MEMBERSHIP TO
5.1. Associação Brasileira da Bioinformatica e Biologia Computacional (AB3C) - Brazil.
5.2. Sociedade Brasileira da Bioquímica e Biologia Molecular (SBBq) - Brazil.
5.3. Biophysical Society, U.S.A..
5.4. Biophysical Society, Yugoslavia.
5.5. Protein Society - International
5.6. International Society for Computational Biology (ISCB) - Member of the ISCB Board of
Directors (2002-2005)
6. LANGUAGE COMPETENCE
6.1. Serbian, English, Russian and Portuguese (conversation, reading and writing competence).
6.2. Spanish and Italian (reading competence).
7. PUBLICATIONS
This Section Updated: JANUARY 14, 2009
Web of Science:
Total of 33 papers
Total of 198 citations
H Factor H10
(Neshich G OR Nesic G OR Neschich G)
Date: January 07, 2009
7.1.
Goran Neshich, Milan Schara, Marijeta Sentjurc, Zeljko Vucinic:
"An EPR study of temperature dependent changes in fluidity of isolated maize thylakoid."
Periodicum Biologorum, Vol.84, Nº2. 166-169, 1982, Zagreb, Yugoslavia.
This article was cited: [ISI: 2]
Listed in:
7.2.
Zeljko Vucinic, Goran Neshich and Cedomir Radenovic:
"Delayed fluorescence as an in situ probe of fluidity changes in maize photosynthetic membranes."
Periodicum Biologorum, Vol. 84, Nº 2. 221-226, 1982, Zagreb, Yugoslavia.
This article was cited: [ISI: 5]
Listed in:
7.3.
I.C. Bezerra, L.A.B. de Castro, G. Neshich and D.C. Monte- Neshich:
"A corm-specific gene encodes tarin, a major globulin of taro (Colacasia esculenta L. Schott)."
Plant Molecular Biology, 28: 137-144, 1995.
This article was cited: [ISI: 14] [Google Scholar: 8] [Scopus:14]
Journal ISI Impact Index for 2006: 3,577
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7.4.
P.G.B. Carvalho, C. Bloch Jr., L. Morhy, Maria C.M. da Silva, Luciane V. de Mello, and Goran Neshich:
"Amino Acid Sequence of the Phaseolus vulgaris Var. "Fogo na serra" Inhibitor and Interactive
Surface Modeling for the enzyme-Inhibitor Complex."
Journal of Protein Chemistry, Vol. 15, Nº 6, 1996 591-598.
This article was cited: [ISI: 1] [Google Scholar: 1] [Scopus:1]
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7.5.
L.H. Marcellino, G. Neshich, M.F. Grossi de Sa, E. Krebbers and E. Gander:
“Mutagenized 2S Albumins with improved tryptophan content are correctly expressed in
transgenic tobacco plants.”
FEBS Letters 385 (1996) 154-158.
This article was cited: [ISI: 10] [Google Scholar: 12] [Scopus:12]
Journal ISI Impact Index for 2006: 3,372
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7.6.
M. Vincentz, . Leite, L. Barros, D. Weinberg, E. de Almeida, M. Paes de Carvalho, F. Aragão, E. Gander
and G. Neshich:
“ACGT and Vicilin core sequences in a promoter domain required for seed specific expression of a
2S storage protein gene are recognized by the Opaque-2 regulatory protein."
Plant Molecular Biology vol. 34, 1997 879-889.
This article was cited: [ISI: 11] [Google Scholar: 18] [Scopus:14]
Journal ISI Impact Index for 2006: 3,577
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7.7.
S.M. de Freitas, L.V. de Mello, M.C.M. da Silva, G. Vriend,G. Neshich and M.M. Ventura:
“Analysis of the Black-eyed Pea Trypsin and Chymotrypsin Inhibitor-alpha-chymotrypsin
complex."
FEBS Letters 409 (1997) 121-127.
This article was cited: [ISI: 10] [Google Scholar: 19] [Scopus:22]
Journal ISI Impact Index for 2006: 3,372
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7.8.
T.B. Cavalcante, A Rezende, R. Togawa, Patricia Rodrigues, Luciano Magalhaes and G. Neshich:
"A new field-tested electronic system for data gathering, recording, transfer and dissemination via
the World Wide Web."
Taxon 47, May (1998), 381-386.
Journal ISI Impact Index for 2006: 2,519
Listed in:
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7.9.
G. Neshich, Roberto Togawa and Barry Honig:
"Sequence To and withIN Graphics PDB Viewer (STING -PDB viewer)."
PDB Quarterly NewsLetter, July 1998, page 6.
This article was cited: [Google Scholar: 6]
7.10.
G. Neshich, Roberto Togawa, Jaime Prilusky, Joel Suussman and Barry Honig:
"Searching for the Right PDB File with the 3DB Browser and Displaying Structure and Sequence
Data with STING."
PDB Quarterly NewsLetter, July 1998, page 7.
7.11.
Da Silva M.C.M., Grossi de Sá M.F., Chrispeels M.J., Togawa R.C. and G. Neshich:
"Analysis of Structural and Physico-chemical Parameters Involved in the Specificity of Binding
between Alpha-Amylases and their Inhibitors."
Protein Engineering, Vol. 13, Nº 3, 167-177, March 2000.
This article was cited: [ISI: 12] [Google Scholar: 10] [Scopus:20]
Journal ISI Impact Index for 2006: 2,718
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7.12.
Caldas, C.A., Coelho, V.P.C.V., Rigden, D., G. Neshich, Moro, A.M. and Brigido, M.:
"Design and synthesis of germline-based hemi-humanized single chain Fv against the CD18 surface
antigen."
Protein Engineering Vol. 13, Nº5, 353-360, May 2000.
This article was cited: [ISI: 13] [Google Scholar: 16] [Scopus:11]
Journal ISI Impact Index for 2006: 2,718
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7.13.
G. Neshich, Roberto Togawa, Adauto L. Mancini, Paula R. Kuser, Michel E. B. Yamagishi, Georgios
Pappas Jr., Wellington V. Torres, Tharsis Fonseca e Campos, Leonardo L. Ferreira, Fabio M. Luna,
Adilton G. Oliveira, Ronald T. Miura, Marcus K. Inoue, Luiz G. Horita, Dimas F. de Souza, Fabiana
Dominiquini, Alexandre Álvaro, Cleber S. Lima, Fabio O. Ogawa, Gabriel B. Gomes, Juliana C. F.
Palandrani, Gabriela F. dos Santos, Esther M. de Freitas, Amanda R. Mattiuz, Ivan C. Costa, Celso L. de
Almeida, Savio Souza, Christian Baudet and Roberto H. Higa:
"STING Millennium: a Web based suite of programs for comprehensive and simultaneous analysis
of protein structure and sequence."
Nucleic Acids Research Vol. 31, Nº 13, page 3386 - 3392, 2003.
This article was cited: [ISI: 28] [Google Scholar: 39] [Scopus: 27]
Journal ISI Impact Index for 2006: 6,317
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7.14.
Fernandez J. H., Hayashi M.A.F., Camargo A.C.M. 1 and G. Neshich:
"Structural basis of the lisinopril binding specificity in N and C domains of human somatic ACE."
BBRC: Biochemical and Biophysical Research Communications 308 (2003)219-226.
This article was cited: [ISI: 7] [Google Scholar: 8] [Scopus: 8]
Journal ISI Impact Index for 2006: 2,855
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7.15.
Paula Kuser Falcão, Michel Yamagishi, Roberto Higa e Goran Neshich:
"Sting Millennium Suite: ferramentas para análise estrutural de proteínas."
Com Ciência, August, 2003.
7.16.
R. C. Togawa, P. R. Kuser, R. H. Higa, M. E. B. Yamagishi, A. L. Mancini, and G. Neshich*:
"STING Millennium Suite: integrated software for extensive analyses of 3d structures of proteins
and their complexes."
BMC Bioinformatics. 2004 Aug 09;5(1):107.
This article was cited: [ISI: 12] [Google Scholar: 10] [Scopus:8]
Journal ISI Impact Index for 2006: 3,617
BMC-BI total downloads: 2685 (August 09, 2004 to January 14, 2009)
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7.17.
R.H. Higa, A.G. Oliveira1, L.G. Horita1, R.T. Miura1, M.K. Inoue1 P.R. Kuser, A.L. Mancini, M.E.B.
Yamagishi, R. Togawa1, and G. Neshich*:
"Defining 3D residue environment in protein structures using SCORPION and FORMIGA."
Bioinformatics. 2004 Aug 12;20(12):1989-1991. Epub 2004 Mar 25.
This article was cited: [ISI: 2] [Google Scholar: 2] [Scopus: 2]
Journal ISI Impact Index for 2006: 4,894
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7.18.
R. H. Higa, R. C. Togawa2, P. R. Kuser, M. E. B. Yamagishi, A. L. Mancini, G. Pappas Jr.3, R. T.
Miura2, L. G. Horita2, andG. Neshich*: "ConSSeq: a web-based application for analysis of amino
acid conservation based on HSSP database and within context of structure."
Bioinformatics. 2004 Aug 12;20(12):1983-5. Epub 2004 Mar 25.
This article was cited: [ISI: 4] [Google Scholar: 6][Scopus: 4]
Journal ISI Impact Index for 2006: 4,894
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7.19.
R. C. Togawa2, P. R. Kuser, R. H. Higa, M. E. B. Yamagishi, A. L. Mancini, and G. Neshich*:
"STING Contacts: a web-based application for identification and analysis of amino acid contacts
within protein structure and across protein interfaces."
Bioinformatics. 2004 Sep 1;20(13):2145-7. Epub 2004 Apr 08.
This article was cited: [ISI: 8] [Google Scholar: 10] [Scopus: 8]
Journal ISI Impact Index for 2006: 4,894
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7.20.
Goran Neshich, Walter Rocchia, Adauto L. Mancini, Michel E. B. Yamagishi, Paula R. Kuser, Renato
Fileto, Christian Baudet, Ivan P. Pinto, Arnaldo J. Montagner, Juliana F. Palandrani, Joao N. Krauchenco,
Renato C. Torres, Savio Souza, Roberto C. Togawa and Roberto H. Higa:
"JavaProtein Dossier: a novel web-based data visualization tool for comprehensive analysis of
protein structure."
Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W595-601.
This article was cited: [ISI: 13] [Google Scholar: 16][Scopus: 15]
Journal ISI Impact Index for 2006: 6,317
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7.21.
Marcellino LH, Neshich G, Neto AF, Gander ES.:
"An opaque-2-like transcription factor from pearl millet."
Protein Pept Lett. 2004 Aug;11(4):345-52.
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Journal ISI Impact Index for 2006: 1,130
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7.22.
SILVA, Maria Cristina Mattar da; MELLO, Luciane V de; COUTINHO, Marise Ventura; RIGDEN,
Daniel John; Goran Neshich; CHRISPEELS, Maarten John; GROSSI DE SA, Maria Fatima:
"Mutants of common bean alpha-amylase inhibitor-2 as an approach to investigate binding
specificity to alpha-amylases."
Pesquisa Agropecuária Brasileira, Brazil, v. 39, n. 3, p. 201-208, 2004.
This article was cited: [ISI: 1] [Google Scholar: 2] [Scopus:2]
Journal ISI Impact Index for 2006: 0,286
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7.23.
Goran Neshich, Adauto L. Mancini, Michel E. B. Yamagishi, Paula R. Kuser, Renato Fileto, Ivan P.
Pinto, Juliana F. Palandrani, João N. Krauchenco, Christian Baudet, Arnaldo J. Montagner and Roberto
H. Higa:
" STING Report: convenient web-based application for graphic and tabular presentations of
protein sequence, structure and function descriptors from the STING database."
Nucleic Acids Res. 2005 Jan 1;33 (Database Issue):D269-74.
This article was cited: [ISI: 9] [Google Scholar: 14] [Scopus: 9]
Journal ISI Impact Index for 2006: 6,317
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7.24.
NESHICH, Goran; BORRO, Luiz C; HIGA, Roberto; KUSER, Paula; YAMAGISHI, Michel; FRANCO,
Eduardo H; KRAUCHENCO, Joao; FILETO, Renato; RIBEIRO, Andre; BEZERRA, George;
VELLUDO, Thiago; JIMENEZ, Tomas; FURUKAWA, Noburo; TESHIMA, Hirofumi; KITAJIMA,
Koji; BAVA, Abdulla; SARAI, Akinori; TOGAWA, Roberto; MANCINI, Adauto:
" Diamond STING Server."
Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W29-35.
This article was cited: [ISI: 10] [Google Scholar: 21] [Scopus: 10]
Journal ISI Impact Index for 2006: 6,317
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7.25.
HERNANDEZ, Jorge Fernandez; NESHICH, Goran; ACM, Camargo:
"USING BRADYKININ POTENTIATING PEPTIDE (BPP) STRUCTURES TO DEVELOP NEW
ANTIHIPERTENSIVE DRUGS."
Genet. Mol. Res, Riberao Preto, v. 3, n. 4, p. 554-563, 2005.
This article was cited: [Google Scholar: 6] [Scopus:9]
This article was cited: [Google Scholar: 6]
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7.26.
Yamagishi ME, Martins NF, Neshich G, Cai W, Shao X, Beautrait A, Maigret B.:
"A fast surface matching procedure for protein-ligand docking."
J Mol Model (Online). 2006 May 4.
This article was cited: [ISI: 2] [Google Scholar: 2] [Scopus: 2]
Journal ISI Impact Index for 2006: 1,384
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7.27.
HIGA, Roberto; KUSER, Paula; MICHEL, Yamagishi; MANCINI, Adauto; NESHICH, Goran:
" Building Multiple Sequence Alignments with a flavour of HSSP alignments."
Genet. Mol. Res. 5 (1), p: 127-137, 2006.
This article was cited:[ISI: 2] [Google Scholar: 2] [Scopus:2]
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7.28.
Luiz C. Borro, Stanley R.M. Oliveira, Michel E.B. Yamagishi, Adaulto L. Mancini, José G. Jardine, Ivan
Mazoni, Edgard H. dos Santos, Roberto H. Higa, Paula R. Kuser and Goran Neshich:
"Predicting enzyme class from protein structure using Bayesian classification."
Genet. Mol. Res. 5 (1), p:193-202, 2006.
This article was cited:[ISI: 6] [Google Scholar: 6] [Scopus:4]
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7.29.
Renato Fileto, Paula R. Kuser, Michel E. B. Yamagishi, André A. Ribeiro, Thiago G. Quinalia, Eduardo
H. Franco, Adauto L. Mancini, Roberto H. Higa, Stanley R. M. Oliveira, Edgard H. Santos, Fabio D.
Vieira, Ivan Mazoni, Sergio A. B. Cruz, Goran Neshich:
"PDB-metrics: a web tool for exploring the PDB contents."
Genet. Mol. Res. 5 (2), p:333-341, 2006.
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7.30.
Goran Neshich, Ivan Mazoni, Stanley R. M. Oliveira, Michel E. B. Yamagishi, Paula R. Kuser-Falcão,
Luiz C. Borro, Douglas U. Morita, Kassyus R. R. Souza, Gustavo V. Almeida, Diego N. Rodrigues, José
G. Jardine, Roberto C. Togawa, Adauto L. Mancini, Roberto H. Higa, Sérgio A. B. Cruz, Fábio D. Vieira,
Edgard H. dos Santos, Raquel C. de Melo and Marcelo M. Santoro:
"The Star STING server: A multiplatform environment for protein structure analysis."
Genet. Mol. Res. 5 (4), 717-722, 2006.
This article was cited:[ISI: 6] [ Google Scholar: 10] [Scopus: 7]
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7.31.
NESHICH, G, Bourne PE, Brunak, S.:
" ISMB 2006."
PLoS Comput Biol. Feb;2(2), 2006.
Journal ISI Impact Index for 2006: 4,914
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7.32.
M.C. Simões; D. Bahia; A.Z. Neto; K. Torres; F. Artiguenave; G. Neshich; P.R. Kuser, G.C. Oliveira:
"Single nucleotide polymorphisms identification in expressed genes of Schistosoma mansoni."
Molecular and Biochemical Parasitology, 154 134-140, 2007.
This article was cited: [Google Scholar: 1] [Scopus:2]
Journal ISI Impact Index for 2006: 2,641
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7.33.
Jorge H. Fernandez, Marcia O. Mello, Leticia Galgaro, Aparecida S. Tanaka, Marcio C. SilvaFilho, Goran Neshich:
"PROTEINASE INHIBITION USING SMALL BOWMAN-BIRK TYPE STRUCTURES."
Genet. Mol. Res. 6 (4): 846-858 (2007)
This article was cited: [Scopus:1]
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7.34.
R.C. Melo, C. Ribeiro, C.S. Murray, C.J.M. Veloso, C.H.. da Silveira, Goran Neshich, W. Meira Jr, R.L.
Carceroni and M.M. Santoro:
"Finding protein-protein interactions by contact-maps matching."
Genet. Mol. Res. 6 (4): 946-963 (2007)
This article was cited: [Google Scholar: 1] [Scopus:1]
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7.35.
Walter Rocchia and Goran Neshich:
"Electrostatic Potential Calculation for biomolecules - creating a database of pre-calculated values
reported on a per residue basis for all PDB protein structures."
Genet. Mol. Res. 6 (4): 923-936 (2007)
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7.36 .
Stanley R. M. Oliveira, Gustavo V. Almeida, Kassyus R. R. Souza, Diego N. Rodrigues, Paula R. KuserFalcão, Michel E. B.Yamagishi, Edgard H. Santos, Fábio D. Vieira, José G. Jardine and Goran Neshich:
"STING_RDB: A relational database of structural parameters for protein analysis with support for
Data Warehousing and Data Mining."
Genet. Mol. Res. 6 (4): 911-922 (2007)
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7.37.
NESHICH, G:
"Computational Biology in Brazil."
PLoS Comput Biol. Oct; v3 (issue 10, e185), 2007.
This article was cited: [ISI: 1] [Google Scholar:1] [Scopus: 1]
Journal ISI Impact Index for 2006: 4,914
Listed in:
and
,
7.38.
MOUTRAN, Alexandre; BALAN, Andrea; PEREZ, Carolina Santacruz; FERREIRA, Rita Café;
RAMOS, Carlos; FERREIRA, Luís Carlos Souza; NESHICH, Goran:
"Crystallographic structure and substrate-binding interactions of the 3 molybdate-binding
protein of the phytopathogen 4 Xanthomonas axonopodis pv. citri.”
Biochim Biophys Acta. 2008 Feb;1784(2):393-9.
Listed in:
and
,
7.39.
R. C. Togawa, C. Ribeiro, I. Mazoni, T. Pelligrinelli, and NESHICH, Goran:
" The Table of Interface Forming Residues as the Specificity Indicator for Serine Proteases Bound
to Different Inhibitors "
Accepted: BIOCOMP 08, 2008.
Listed in:
7.40.
Carlos H. da Silveira, Douglas E. V. Pires , Raquel C. Melo , Cristina Ribeiro , Caio J. M. Veloso , Julio
C. D. Lopes , Wagner Meira Jr , Goran Neshich , Carlos H. I. Ramos , Raul Habesch, Marcelo M.
Santoro:
" Protein cutoff scanning: A comparative analysis of cutoff dependent and cutoff free methods for
prospecting contacts in proteins. "
PROTEINS: Structure, Function, and Bioinformatics,2008 Aug 14;74(3):727-743. 2008
Listed in:
7.41.
Janaina Gomide ; Raquel Melo Minardi ; Marcos Augusto dos Santos ; Wagner Meira Jr. ; Julio Cesar
Dias Lopes ; SANTORO, Marcelo ; NESHICH, Goran:
" Using Linear Algebra for Protein Structural Comparison and Classification."
Accepted: Genet. Mol. Res., 2009.
Journal ISI Impact Index for 2006: 3,617
7.42.
Luiz Cesar Borro, Ivan Mazoni, Jose G. Jardine, Edgard H. Santos, Daniel de Alvarenga Campos,
Mauri Carvalho, Thais Vital Pelligrinelli; NESHICH, Goran:
" BlueStar STING environment for protein structure analysis: expanded fetures and compatibility
with remediated PDB format"
Submitted: BMC Bioinformatics, 2009.
Journal ISI Impact Index for 2006: 3,617
7.43.
Luiz Cesar Borro, Ivan Mazoni, Jose G. Jardine, Edgard H. Santos, Daniel de Alvarenga Campos,
Mauri Carvalho, Thais Vital Pelligrinelli; NESHICH, Goran:
" The signals for initiation of secondary structure element nucleation in protein structures"
To be submitted: Plos Computational Biology, in progress, 2009
Journal ISI Impact Index for 2006: 4,914.
7.44.
Luiz Cesar Borro, Ivan Mazoni, Jose G. Jardine, Edgard H. Santos, Daniel de Alvarenga Campos,
Mauri Carvalho, Thais Vital Pelligrinelli; NESHICH, Goran:
" Java Secondary Structure Dossier: environment for analysis of protein secondary structure"
To be submitted: Bioinformatics, in progress, 2009.
Journal ISI Impact Index for 2006: 4,894
7.45.
Luiz Cesar Borro, Ivan Mazoni, Jose G. Jardine, Edgard H. Santos, Daniel de Alvarenga Campos,
Mauri Carvalho, Thais Vital Pelligrinelli; NESHICH, Goran:
" Chameleon sequences: secondary structure fidelity to a primary amino-acid sequence"
To be submitted: Journal of Molecular Biology, in progress, 2009.
Journal ISI Impact Index for 2006: 4,890
7.46.
Luiz Cesar Borro, Ivan Mazoni, Jose G. Jardine, Edgard H. Santos, Daniel de Alvarenga Campos,
Mauri Carvalho, Thais Vital Pelligrinelli; NESHICH, Goran:
" STING_RDB: the database containing 730 parameters describing protein structure, function,
sequence and stability"
To be submitted: Nucleic Acid Research - Database issue, in progress, 2009.
Journal ISI Impact Index for 2006: 6,317
8. WORK PRESENTED AT SCIENTIFIC MEETINGS
8.1. Z. Vucinic, G. Neshich, C. Radenovic:
"Influence of temperature at photosynthetic process: Photo-induced bioluminescence as an in
situ method to monitor changes of the thylakoid membranes". XI Yugoslav Biophysics
Symposium, pp 101, Donji Milanovac, 11-14 October,1981, Yugoslavia.
8.2. G. Neshich, M. Schara, M. Sentjurc, Z. Vucinic:
"Studies on conformational changes in thylakoid membranes of the chloroplasts from different
maize genotypes using EPR spectroscopy". XI Yugoslav Biophysics Symposium, pp 102, Donji
Milanovac, 11-14 October, 1981, Yugoslavia.
8.3. Z. Vucinic, G. Neshich, C. Radenovic:
"Photoinduced bioluminescence as in situ method for monitoring state of fluidity in thylakoid
membranes". - Book of abstracts, problems in biophysics, SEP meeting, 1982, pp. III-33,
Puschino, USSR.
8.4. Z. Vucinic, G.Neshich:
"Possible application of the fluorescence methods for photosynthesis research in maize
breeding program". - Second seminar of Yugoslav Society for plant physiology, Serbian
Academy of Science, SANU, in Belgrade,March 27-29. 1983, Yugoslavia.
8.5. Z. Vucinic, G. Neshich, J. Svetek, M. Schara:
"Proline effects on maize thylakoid membrane fluidity and water structure ordering". - Book of
abstracts of XII Yugoslav biophysics symposium, p. 51, Sept. 29 - Oct. 01. 1983. Opatija,
Yugoslavia.
8.6. G. Neshich, D. DeVault and C. Wraight:
"Kinetics of Electron Transfer from high potential Cytochrome c hemes to P+
functionally associated to photochemical reaction center in Rhodopseudomonas viridis" Biophysical Society meeting, Cincinnati, OH, USA, February.05- 12. 1989.
8.7. F.X.S. Scares, M.C.M. da Silva, T.L. Rocha, L.H. Marcellino, N.S. Paes, I. Caracelli, M.
Carneiro, E. Gander, M-J.A.M. Sampaio, L-A.B. De Castro and G. Neshich:
"Theoretical model of the secondary and tertiary structure of Brazil nut 2s storage albumins" in
Abstracts of the First International Symposium on Crystallography and Molecular Biology,
November 1990, Guaruja, SP, Brazil.
8.8. L.H.Marcellino, M.C.M. da Silva, T.L. Rocha, N.S. Paes, M. Carneiro, E. Gander, M-J.A.M.
Sampaio, L-A.B. De Castro and G. Neshich:
"Introduction of tryptophan in the brazil nut 2s storage albumins by site- directed mutagenesis"
in Abstracts of the First International Symposium on Crystallography and Molecular
Biology, November 1990, Guaruja, SP, Brazil.
8.9. M.C.M. da Silva, T.L. Rocha, L.H. Marcellino, N.S. Paes, I. Caracelli, M. Carneiro, E. Gander,
M-J.A.M. Sampaio, LA.B. De Castro and G. Neshich:
"Brazil nut 2s storage albumin isoform purification and circular dichroism assisted secondary
structure confirmation" in Abstracts of the First International Symposium on Crystallography
and Molecular Biology, November 1990, Guaruja, SP, Brazil.
8.10. M.C.M. da Silva, L.V. de Mello, C. Bloch Jr., L. Morhy and G. Neshich:
"Disulphide bridges determination in a 2S albumin storage protein from Brazil
nut (Bertholetia excelsa H.B.K.) Preliminary studies". In "Resumos da XXI Reunião Anual da
Sociedade Brasileira de bioquímica e biologia molecular” Caxambu, MG, Brazil 16-19 May,
1992.
8.11. I.C. Bezerra, L.A.B. De Castro, G. Neshich, E.R. Almeida and D.C. Monte-Neshich:
"Structure of the gene coding for a major protein from taro tuber (Colocasia esculents)". In
"Programa e Resumos da XXII Reunião Anual da Sociedade Brasileira de bioquímica e
biologia molecular" Caxambu, MG, Brazil 1-4 May, 1993.
8.12. P.G.B. Carvalho, C. Bloch Jr. and L. Morhy in collaboration with G. Neshich:
"The complete amino-acid sequence of a Bowman-Birk inhibitor from seeds of Phaseolus
vulgaris Var. "Fogo na serra"." In "Programa e Resumos da XXII Reunião Anual da Sociedade
Brasileira de bioquímica e biologia molecular" Caxambu, MG, Brazil 1-4 May, 1993.
8.13. M.C.M. da Silva, L.V. de Mello, C. Bloch Jr., L Morhy, J.B. Aragão and G. Neshich:
"Determination of the disulphide bridges in 2S albumin from Brazil nut (Bertholetia excelsa
H.B.K.) ". In "Programa e Resumos da XXII Reunião Anual da Sociedade Brasileira de
bioquimica e biologia molecular” Caxambu, MG, Brazil 1-4 May, 1993.
8.14. L.H.Marcellino, E. Gander, A.S. Conceicao, E. Krebers and G. Neshich:
"Introduction of tryptophan in the brazil nut 2s protein". In "Programa e Resumos da XXII
Reuniao Anual da Sociedade Brasileira de bioquimica e biologia molecular" Caxambu, MG,
Brazil 1-4 May, 1993.
8.15. S.M.Freitas, L.V.Mello, M.C.M.Silva, M.M.Ventura and G.Neshich:
"The Binding Surface Identification Through The Homology Modeling For The System Black
Eyed Pea Trypsin And Chymotrypsin Inhibitor (BTCI)/Chymotrypsin". Caxambu, MG, Brazil,
May 14-17, 1994.
8.16. P.G.B.Carvalho, C.Bloch Jr. L.V.Mello, M.C.M. Silva, G.Neshich :
"Calculation of Electrostatic Potential Around The Active Site Region For The System:
Bowman-Birk Inhibitor From Seeds of Phaseolus vulgares Var. “Fogo na Serra” (PFSI)
/Chymotrypsin". Caxambu, MG, Brazil, May 4-17, 1994.
8.17. E. Gander, M. Vicentz, A. Leite, M.C. Mattar de Silva, G. Vriend, L. Barros, D. Weinberg, E. R.
de Almeida, M. Pais de Carvalho, F. Aragão and. G. Neshich:
"The opaque-2 regulatory protein recognizes acgt and vicilin core sequences in an essential
seed specific promoter region from a brazil nut albumin gen." The Protein Society - Ninth
Symposium, Boston, MA - USA, July 8-12, 1995. PROGRAM & ABSTRACTS: 180 (672-M)
8.18. T.B. Cavalcante, A Rezende, R. Togawa and G. Neshich:
" Field data collection, relational data-base data formating, printing of the data on the selfadhesive labels and data distribution through World Wide Web". XLVII Congresso Nacional de
Botanica, Nova Friburgo/RJ, Brazil, 21-26 de Julho de 1996.
8.19. M.C. Mattar da Silva, G. Neshich, R. Togawa, M.Crispeels and M. F. Grossi de Sa:
"Molecular Modeling of Plant alpha-amylase inhibitors and insect alpha-amylases complexes".
III Encontro Latino Americano De Biotecnologia Vegetal, La Havana, Cuba, June 1-5, 1998
8.20. Da Silva MCM, G. Neshich, Ghrispeels M., Roberto Togawa and Grossi de Sa, M.F:
"Molecular Basis of the Interactions Between InsectAlpha-Amylases and Inhibitors". XXVIII
Reuniao Anual da Sociedade Brasileira de Bioquimica e Biologia Molecular - SBBq Caxambu, MG, Brazil,May 22-25, 1999.
8.21. Fonseca, A.S., G. Neshich, Brigido M.M.:
"Design and Construction of a Humanized Version for the Ant-CD2 Fv through a New
Strategy." XXVIII Reuniao Anual da Sociedade Brasileira de Bioquimica e Biologia Molecular SBBq - Caxambu, MG, Brazil, May 22-25, 1999.
8.22. Goran Neshich, Roberto C. Togawa, Wellington Vilella Torres, Tharsis Fonseca e Campos,
Leonardo Lima Ferreira, Adilton Guedes Oliveira, Ronald Tetsuo Miura, Marcus Kiyoshi Inoue,
Luiz Gustavo Horita, Georgios Pappas Jr.,Barry Honig:
"STING Millennium: Web based suite of programs for comprehensive and simultaneous
analysis of structure and sequence", ISMB 2001, Denmark, abstract#87
8.23. Adauto L. Mancini, Roberto H. Higa, Paula R. Kuser, Michel E. B. Yamagishi and Goran
Neshich:
"STING MILLENNIUM SUITE (SMS): a Web tool for identification and visualization of protein
intra and inter chain contacts", Resumo número: 301595. XXXII Reuniao Anual da Sociedade
Brasileira de Bioquimica e Biologia Molecular - SBBq - Caxambu, MG, Brazil, May 17-20,
2003.
8.24. Michel E. B. Yamagishi, Adauto Mancini, Roberto H. Higa, Paula R. Kuser and Goran Neshich:
"In Silico Filtering of Successful Protein-Ligand Binding", Resumo numero: 300345. XXXII
Reuniao Anual da Sociedade Brasileira de Bioquimica e Biologia Molecular - SBBq - Caxambu,
MG, Brazil, May 17-20, 2003.
8.25. Roberto H. Higa, Christian Baudet, Paula R. Kuser, Adauto L. Mancini, Michel E. B. Yamagishi
and Goran Neshich:
"Java Protein Dossier – a java tool for analyzing stability and potential function of proteins with
known structure", Resumo número: 300592. XXXII Reuniao Anual da Sociedade Brasileira
de Bioquimica e Biologia Molecular - SBBq - Caxambu, MG, Brazil, May 17-20, 2003.
8.26. Paula R. Kuser, Roberto H. Higa, Christian Baudet, Adauto L. Mancini, Michel E. B. Yamagishi
and Goran Neshich:
"STING MILLENNIUM - Suite of software tools for analysis of protein structures and summary
of structure/function parameters", Resumo número: 300538. XXXII Reuniao Anual da
Sociedade Brasileira de Bioquimica e Biologia Molecular - SBBq - Caxambu, MG, Brazil, May
17-20, 2003.
8.27. Goran Neshich, Roberto Togawa, Walter Rocchia, Adauto L. Mancini, Paula R. Kuser, Michel
E. B. Yamagishi, Alexandre 301lvaro, Christian Baudet and Roberto H. Higa:
"STING MILLENNIUM SUITE v.3 and JAVA PROTEIN DOSSIER: a novel concept in data
visualization and analysis of the protein structure/function relationship" has been accepted for
presentation at ISMB2003, Brisbane, Australia, 29th June - 3rd July, 2003.
8.28. Guelfi, A., Molina, S. M. G., Neshich, G.:
"Structural alignment: A clue for enzyme function?", 49º Congresso Nacional de Genética SBG - Águas de Lindóia, SP, Brazil, September 16 - 19, 2003.
8.29. Hernandez, J.F.1, Hayashi, M.A.F.2, Neshich, G., and Camargo, A.C.M.2 : " “in silico” model
for human sACE substrate binding : structural parameters defining N- and C-domain substrate
specificity", I São Paulo Research Conference : Molecular Medicine. Sao Paulo, Brazil, 2003.
8.30. Neshich, G. GRID Computing at EMBRAPA:
"Searching for the best shape match between the potential drug targets at the protein surfaces
and small chemicals"In: Workshop de Grade Computacional e Aplicações, LNCC, 2003. v.1.
p.97 - 102, Petrópolis, RJ, Brazil, 2003.
8.31. Hernandez, J.F.1, Hayashi, M.A.F.2, Neshich, G.1, and Camargo, A.C.M.2:
" Comparative Modelling of the N-terminal Domain of the Human Somatic ACE-Lisinopril
Complex" - V Reunião Científica Anual do Instituto Butantan, Sã Paulo, Brazil, December 0105, 2003.
8.32. Neshich, Goran; Fernandez JH; Hayashi MAF; Camargo ACM:
“IN SILICO” MODEL FOR HUMAN sACE SUBSTRATE BINDING: STRUCTURAL
PARAMETERS DEFINING N- AND C- DOMAIN SUBSTRATE SPECIFICITY". In: I SÃO
PAULO RESEARCH CONFERENCE : MOLECULAR MEDICINE., 2003, SP. Anais de I São
Paulo Research Conference : Molecular Medicine.. Brazil, 2003.
2004.
8.33. Neshich, Goran; GUELFI, Andrea; G, Molina S M:
"Structural alignment: a clue for enzyme function". In: II ESCOLA DE MODELAGEM
MOLECULAR EM SISTEMAS BIOLOGICOS, 2004, Petropolis: LNCC, Brazil, 2004.
8.34. Neshich, Goran; MANCINI, Adauto;
HIGA, Roberto Hiroshi; KUSER, Paula; MICHEL, Yamagishi "Gold STING: the new DB and
concept in protein structure/function data visualisation/analysis". In: SBBQ XXXIII, 2004,
Caxambu. Brazil, 2004.
8.35. Neshich, Goran; MANCINI, Adauto; KUSER, Paula; FILETO, Renato; MICHEL, Yamagishi;
HIGA, Roberto Hiroshi:
"Gold STING: studying protein stability and folding by looking at an extensive DB of the
structure descriptors". In: ISMB 2004, 2004, Glasgow. ISMB 2004. Scotland, 2004.
8.36. Neshich, Goran; MANCINI, Adauto; KUSER, Paula; FILETO, Renato; MICHEL, Yamagishi;
HIGA, Roberto Hiroshi:
"Selecting a set of the protein structure descriptors uniquely defining the active site residues".
In: 3D-SIG: ISMB 2004, 2004, Glasgow. ISMB 2004. Scotland, 2004.
8.37. HERNANDEZ, Jorge Fernandez; NESHICH, Goran; CM, Camargo Antonio.:
"USING BRADYKININ POTENTIATING PEPTIDE (BPP) STRUCTURES TO DEVELOP NEW
ANTIHIPERTENSIVE DRUGS". In: ICOBICOBI, 2004, Angra dos Reis. Brazil. 2004.
8.38. NESHICH, Goran; KUSER, Paula; JESUS, Katia Regina Evaristo de; MANCINI, Adauto;
MICHEL, Yamagishi; RENATO, Fileto; ROBERTO, Higa.:
"The signals hidden in a set of protein structure descriptors: in silico identifying a protein active
site". In: 1ST LATIN AMERICAN PROTEIN SOCIETY MEETING, 2004, Angra dos Reis.
Brazil. 2004.
8.39. NESHICH, Goran; JESUS, Katia Regina Evaristo de; KUSER, Paula; MICHEL, Yamagishi;
MANCINI, Adauto; RENATO, Fileto; ROBERTO, Higa.:
"Identifying a protein active site in silico by selecting for the signals hidden in a set of protein
structure descriptors". In: ICOBICOBI, 2004, Angra dos Reis. Brazil. 2004.
8.40. NESHICH, Goran; MANCINI, Adauto; HIGA, Roberto Hiroshi; KUSER, Paula; MICHEL,
Yamagishi.:
Gold STING: the new DB and concept in protein structure/function data visualisation/analysis.
In: SBBQ XXXIII, Brazil, Caxambu. 2004.
8.41. NESHICH, Goran; YAMAGISHI, M. E. B. ; ROCCHIA, Walter ; MANCINI, Adauto ; FALCÃO,
Paula Regina Kuser ; FILETO, Renato ; BAUDET, Christian ; PINTO, Ivan ; MONTAGNER ,
Arnaldo ; PALANDRANI, Juliana ; KRAUCHENKO, João ; TORRES, Renato Cristiano ;
BEZERRA, George Barreto Pereira ; SOUZA, Sávio ;TOGAWA, Roberto C. ; HIGA, Roberto
Hiroshi .:
" Protein Structure Analysis and Visualization Using Java Protein Dossier". In: International
Conference on Chemometrics and Bioinformatics in Asia, 2004, Shanghai. Proceedings of
International Conference on Chemometrics and Bioinformatics in Asia, China, ,p. 128128.2004
2005.
8.42. KUSER, Paula; YAMAGISHI, Michel; MANCINI, Adauto; HIGA, Roberto; BORRO, Luiz C;
NESHICH, Goran.:
"STING - A web server for comprehensive analysis of protein structure and sequence". In:
ISMB 2005, 2005, Detroit. USA ISMB proceedings. 2005
8.43. KUSER, Paula; YAMAGISHI, Michel; MANCINI, Adauto; BORRO, Luiz C; NESHICH, Goran.:
"Identification of folding essential residues by looking at an extensive DB of the structure
descriptors in Diamond STING". In: ISMB 2005, Detroit. USA ISMB 2005 proceedings. 2005.
8.44. Marcelo G. Narciso, Michel E. B. Yamagishi, Thiago Quinalia, George B. P. Bezerra, Goran
Neshich.:
"2D Maps of Protein Interface Surfaces". In: X-Meeting Brazil, Caxambu. 2005
8.45. Michel E. B. Yamagishi, George B. P. Bezerra, Thiago Quinalia, Paula R. Kuser, Roberto H.
Higa, Adauto L. Mancini, José G. Jardine, Ivan Mazoni, Edgard H. dos Santos, Sérgio A. B.
Cruz, Stanley R. M. Oliveira, Goran Neshich.:
"An Interative Protein Interface Surface Java Viewer". In: X-Meeting, Brazil, Caxambu. 2005
8.46. Roberto Hiroshi Higa, Sergio Aparecido Braga da Cruz, Paula Regine Kuser, Michel Eduardo
Beleza Yamagishi, Renato Fileto, Adauto Luiz Mancini and Goran Neshich.:
"Building Multiple Sequence Alignments with a flavour of HSSP alignments". In: X-Meeting,
Brazil, Caxambu. 2005
8.47. Sergio A. B. da Cruz, Ivan Mazoni, Stanley R. M. Oliveira, Michel E. B. Yamagishi, Paula R.
Kuser, Edgard H. Santos, Fabio D. Vieira, Roberto H. Higa, Adauto L. Mancini, Goran
Neshich.:
"JMOL and STING integration: a STING for multiple plataform". In: X-Meeting, Brazil,
Caxambu. 2005
8.48. Guelfi, A.; Chabregas, S. M.; Falco, M. C., Falcão, P. K., Neshich, G.; Azevedo R. A.;
"Molecular Dynamics Analysis of Glutathione Transferases Sugarcane Mutants and Their
Interactions With Atrazine". In: X-Meeting, Brazil, Caxambu. 2005
8.49. José G. Jardine, Goran Neshich, Paula R. K. Falcão, Michel E. B. Yamagishi, Stanley R. M.
Oliveira, Sérgio Marangoni, Daniel Martins, Flavia V. Winck,José C. Novello.:
"Molecular Modeling of the Protein Twitching Motility of Xylella fastidiosa". In: X-Meeting,
Brazil, Caxambu. 2005
8.50. Mariana Simões, Diana Bahia, Kleider Torres, Adhemar Zerlotini Neto, François Artiguenave,
Paula Kuser, Goran Neshich, Guilherme Oliveira.:
"SNP Identification in Schistosoma mansoni Expressed Genes". In: X-Meeting, Brazil,
Caxambu. 2005
8.51. Stanley R. M. Oliveira, Daniel S. Pavanelli, Gustavo V. Almeida, Michel E. B. Yamagishi, Paula
. Kuser, Edgard H. Santos, Fabio D. Vieira, Ivan Mazoni, Sergio A. B. da Cruz, Roberto H.
Higa, Adauto L. Mancini, Goran Neshich.:
"STING_DB: A relational database of structural parameters of protein analysis". In: XMeeting, Brazil, Caxambu. 2005
8.52. Katia Regina Evaristo de Jesus, Paula Kuser Falcão, Goran Neshich. "Structural Analyses of
Cry 1Ac Protein from Bacillus thuringiensis". In: X-Meeting, Brazil, Caxambu. 2005
8.53. Goran Neshich, Paula Kuser, Michel Yamagishi, Stanley Oliveira, Ivan Mazoni, Edgard Santos,
Favio Vieira, Sergio Cruz, Adauto Mancini, Jose Gilberto Jardine, Roberto Higa.:
"What makes the active site amino acids so different from the others: defining the structural
descriptors specific for activity". In: X-Meeting, Brazil, Caxambu. 2005
8.54. Noboru Furukawa, Yuko Takeno, Goran Neshich and Akinori Sarai.:
" Systematic Analysis of Structure-Stability Relationship for Proteins and Mutants".
In: The 16th International Conference on Genome Informatics, held at PACIFICO YOKOHAMA,
December 19-21, 2005., JAPAN, 2005.
8.55. Paula R. Kuser, Michel E. B. Yamagishi, Luiz C. Borro, Adauto Mancini, Roberto Higa and
Goran Neshich.:
"Identification of folding essential residues by looking at an extensive DB of the structure
descriptors in Diamond STING". In: ISMB 2005, Detroit, USA. 2005
2006.
8.56. Stanley R. M. Oliveira, Diego N. Rodrigues , Kassyus R. R. Souza, Ivan, Gustavo V. Almeida,
Paula R. K. Falcão, Michel E. B.Yamagishi, Edgard H. Santos, Fábio D. Vieira, José G. Jardine
and Goran Neshich;
"STING Database Quality Assessment". In: ISMB 2006, Fortaleza. Brazil ISMB 2006
proceedings, Poster B-33. 2006
8.57. R.C. Melo, I. Mazoni, G. Neshich, M.M. Santoro and W. Meira Jr;
"Contacts as the key elements for comparing two protein structures". In: ISMB 2006, Fortaleza.
Brazil ISMB 2006 proceedings - Poster I-6. 2006
8.58. R.C. Melo, I. Mazoni, G. Neshich, M.M. Santoro and W. Meira Jr;
"Protein structure topology comparison based on contact maps". In: ISMB 2006, Fortaleza.
Brazil ISMB 2006 proceedings, Poster I-5. 2006
8.59. Michel E. B. Yamagishi, Paula R. Kuser1, Luiz C. Borro, Stanley Oliveira, Edgar H. Santos,
José G. Jardine, Fábio D. Vieira, Ivan Mazoni and Goran Neshich;
"Analysing Protein-Protein Interface using the STING JPIV". In: ISMB 2006, Fortaleza. Brazil
ISMB 2006 proceedings, Poster I-14. 2006
8.60. Michel E. B. Yamagishi, Stanley Oliveira, Luiz C. Borro , Edgar H. Santos, José G. Jardine,
Fábio D. Vieira, Ivan Mazoni, Paula R. Kuserand Goran Neshich;
"Predicting Enzyme Class From Protein Structural Parameters Using STING_DB parameters
and Bagging Predictors". In: ISMB 2006, Fortaleza. Brazil ISMB 2006proceedings, Poster I13. 2006.
8.61. José G. Jardine, Goran Neshich; Paula R. K. Falcão, Michel E. B.Yamagishi, Stanley R. M.
Oliveira, Juliana M. Papine, Mariana S. Vieira;
"Structural Analysis of proplasmepsin from the human malarial pathogen plasmodium vivax".
In: ISMB 2006, Fortaleza. Brazil ISMB 2006 proceedings, Poster I-34. 2006
8.62. Jorge Hernandez Fernandez, Vanessa Rioli, Emer S.Ferro, Fernanda C. Portaro, Antonio
Carlos M. Camargo;
"Dynamics of catalysis and inhibition in oligopeptidases: Natural peptide structures as
promising antihypertensive agents". In: ISMB 2006, Fortaleza. Brazil ISMB 2006 proceedings,
Poster E-8 . 2006
8.63.Paula R. Kuser, Michel E. B. Yamagishi, Stanley R. M. Oliveira, Ivan Mazoni Edgard H.
Santos, Fábio D. Vieira, José G. Jardine Luiz C. Borro and Goran Neshich;
"BlueStar STING - A multiplatform environment for protein structure analysis". In: ISMB 2006,
Fortaleza. Brazil ISMB 2006 proceedings, Poster I-22. 2006
8.64. José G. Jardine, Goran Neshich; Paula R. K. Falcão, Michel E. B.Yamagishi, Stanley R. M.
Oliveira, Ivan Mazoni, Edgard H. Santos, Fábio D. Vieira, Sérgio Marangoni; Daniel Martins;
Flavia V. Winck; José C. Novello;
"Structural Analysis of the Protein Twitching Motility of Xylella fastidiosa". In: ISMB 2006,
Fortaleza. Brazil ISMB 2006 proceedings, Poster I-35. 2006
8.65. Stanley R. M. Oliveira, Diego N. Rodrigues , Kassyus R. R. Souza, Gustavo V. Almeida, Goran
Neshich, Paula R. K. Falcão, Michel E. B.Yamagishi, Edgard H. Santos, Fábio D. Vieira, José
G. Jardine;
"An Integrated database of structural parameters for protein analysis". In: ISMB 2006,
Fortaleza. Brazil ISMB 2006 proceedings, Poster B-44. 2006
8.66. Katia Regina Evaristo de Jesus, Paula Kuser Falcão, Goran Neshich;
"The Cry 1Ac Protein from Bacillus thuringiensis and its structure stability centers".
In: ISMB 2006, Fortaleza. Brazil ISMB 2006 proceedings, Poster I-47. 2006
8.67. Cristina Ribeiro, M.M. Santoro, Goran Neshich;
"Serine Proteases analisys based on phylogenetic trees constructed from the sequence and
structure alignments". In: ISMB 2006, Fortaleza. Brazil ISMB 2006 proceedings, Poster LB-39
and I-48. 2006
8.68. Ivan Mazoni, Paula R. Kuser-Falcão, Michel E. B. Yamagishi, Luiz C. Borro, José G. Jardine,
Edgard H. dos Santos, Stanley R. M. Oliveira, Goran Neshich;
"MSSP: simultaneous comparison of the same structure descriptor for different protein
structures". In: ISMB 2006, Fortaleza. Brazil ISMB 2006 proceedings, Poster I- 50. 2006
8.69. Luiz C. Borro, Ivan Mazoni, Paula R. Kuser-Falcão, Michel E. B.Yamagishi, José G. Jardine,
Edgard H. dos Santos, Stanley R. M. Oliveira, Goran Neshich;
"Protein Ligand Contacts Analysed In An Integrated Environment With Other Structure And
Sequence Related Parameters". In: ISMB 2006, Fortaleza. Brazil ISMB 2006 proceedings,
Poster I49. 2006
8.70. Marcelo Narciso, Ivan Mazoni, Paula R. Kuser-Falcão, Michel E. B. Yamagishi, José G.
Jardine, Edgard H. dos Santos, Stanley R. M. Oliveira, Goran Neshich;
"Comparisson of AA co-evolution and correlated structure descriptors". In: ISMB 2006,
Fortaleza. Brazil ISMB 2006 proceedings, Poster I-51. 2006
8.71. Stanley R. M. Oliveira, Diego N. Rodrigues, Kassyus R. R. Souza, Gustavo V. Almeida, Goran
Neshich, Paula R. K. Falcão, Michel E. B.Yamagishi, Edgard H. Santos, Fábio D. Vieira, José
G. Jardine;
"Sting_RDB: A Relational Database of Structural Parameters for Protein Analysis". In: ISMB
2006, Fortaleza. Brazil ISMB 2006 proceedings, Demo. 2006
8.72. Marcelo G. Narciso, Michel E. B.Yamagishi, Paula R. K. Falcão and Goran Neshich,:
"2D Maps of Protein Surface". in: ISMB 2006, Fortaleza. Brazil ISMB 2006 proceedings,
Poster B-63. 2006
8.73. Maria Cristina Mattar da Silva, Fabíola Rodrigues Teixeira, Cleiton C.M, da Cruz, Roberto
Togawa, Goran Neshich and Maria Fatimaosé Grosse de Sá;
"In vitro Molecular Expression of Bean Alpha-Amulase Inhibitors -Investigating Specificity of
Binding to Alpha Amylases". In: ISMB 2006, Fortaleza. Brazil ISMB 2006 proceedings, Poster
LB-28. 2006
8.74. Marcelo Mendes Brandão, Paula R. K. Falcão and Goran Neshich,
"Structural Parameters to Filter Crucial Catalytic Site Amino Acids from Fructose 1,6Biphosphate Aldolase". In: ISMB 2006, Fortaleza. Brazil ISMB 2006 proceedings, Poster I-21.
8.75. Marcos Tadeu Santos, Lucio Fabio Caldas Ferraz, Fernanda de Castro Reis, Ana Paula
Felicio, Paula R. K. Falcão, Maria Teresa marques Novo, Goran Neshich, Oswaldo Garcia Jr,
Laura Maria Mariscal Ottoboni;
"Sequence Analysis of the Riboflavin Biosythesis Genes from Acidithiobacillus ferrooxidans".
In: ISMB 2006,Fortaleza. Brazil ISMB 2006 proceedings, poster H-76. 2006
8.76. Lucio Fabio Caldas Ferraz, Fernanda de Castro Reis, Marcos Tadeu Santos,Ana Paula Felicio,
Paula R. K. Falcão, Maria Teresa marques Novo, Goran Neshich, Oswaldo Garcia Jr, Laura
Maria Mariscal Ottoboni;
"Molecular Modelling of the Riboflavin Genes from Acidithiobacillus ferrooxidans" In: ISMB
2006, Fortaleza. Brazil ISMB 2006 proceedings, Poster I-90. 2006
8.77. Fernanda de Castro Reis, Lucio Fabio Caldas Ferraz, Marcos Tadeu Santos, Paula R. K.
Falcão, Goran Neshich and Laura Maria Mariscal Ottoboni;
"Molecular Modelling of polypeptide deformylase from Acidithiobacillus ferrooxidans". In: ISMB
2006, Fortaleza. Brazil ISMB 2006 proceedings, Poster I-95. 2006
8.78.Lucio Fabio Caldas Ferraz, Fernanda de Castro Reis, Paula R. K. Falcão, Goran Neshich and
Maricilda Palandi de Melloi;
"Molecular Homologous Modelling of 3B-HSD2 Mutant Enzyme: Structure-Function Aspects of
PRO222GLN Mutation Correlates with the Experimental data from a Patient with Congenital
Adrenal Hyperplasia". In: ISMB 2006, Fortaleza. Brazil ISMB 2006 proceedings, Poster D-12.
2006
8.79. Marcelo G. Narciso; Goran Neshich; Michel B.Yamagishi; Paula Falcão; Edgar Henrique; Fábio
D.Vieira; José G.Jardine; Ivan Mazoni
" Aspectos computacionais da análise da co-evolução de aminoácidos que pertencem a uma
proteína qualquer usando o software Sting". II Congresso de Computação do Sul de Mato
Grosso - COMPSULMT2006 16 a 20 de outubro de 2006 Rondonópolis, MT
8.80. Marcelo G. Narciso;Michel B.Yamagishi;Goran Neshich; Paula Falcão; Edgar Henrique; Fábio
D. Vieira; José G. Jardine; Ivan Mazoni
"Transformação de imagens 3D para 2D para análise de proteínas usando o software Sting".
II Congresso de Computação do Sul de Mato Grosso - COMPSULMT2006 16 a 20 de outubro
de 2006 Rondonópolis, MT
2007.
8.81.Luiz César Borro, Ivan Mazoni, Daniel Alvarenga, Thais Vital Pelligrinelli, Mauri Carvalho, José
Gilberto Jardine and Goran Neshich; "Chameleon sequences seen under a prism of structure
descriptors". In: X-meeting 2007, São Paulo. Brazil. X-meeting proceedings, Poster XP190.
2007
8.82. Ivan Mazoni, Luiz César Borro, Daniel Alvarenga, José Gilberto Jardine and Goran Neshich;
"JavaSecondary Structure Dossier". In: X-meeting 2007, São Paulo. Brazil. X-meeting
proceedings, Poster XP48. 2007
8.83.José Gilberto Jardine, Goran Neshich, Ivan Mazoni, Daniel Martins, Sérgio Marangoni, José
Camillo Novello, Wagner F. Gattaz, Emmanuel Dias-Neto; "Molecular Homologous Modelling of
3B-HSD2 Mutant Enzyme: Structure-Function Aspects of PRO222GLN Mutation Correlates with
the Experimental data from a Patient with Congenital Adrenal Hyperplasia". In: X-meeting 2007,
São Paulo. Brazil. X-meeting proceedings, Poster XP40. 2007
8.84.Cristina Ribeiro, Marcelo Santoro, Goran Neshich; "Protein Dossier and Protein Fingerprints
produce Surface Signatures: A simple and powerful technique for coding and comparing
compound and receptor shape information". In: X-meeting 2007, São Paulo. Brazil. X-meeting
proceedings, Poster XP 220. 2007
8.85.Raquel Melo, Janaína Gomide, Wagner Meira Jr., Júlio Lopes, Goran Neshich, Marcelo
Santoro; "Mining Structural Signatures in Proteins using Intrachain Interactions". In: X-meeting
2007, São Paulo. Brazil. X-meeting proceedings, Poster XP15. 2007
2008.
8.86.
Ivan Mazoni, Luiz César Borro, Daniel Alvarenga, Pablo Lira Cecilio, José Gilberto Jardine, Adauto
Mancini and Goran Neshich; “Dossier of Secondary Structure Elements Amino Acid Properties”. In:
ISMB 2008 July 18 to 23, Toronto. Canada.
8.87.
Mazoni I., Borro L.C., Alvarenga D., Jardine J.G., Goran Neshich; “STUDYING STRUCTURE
FUNCTION RELATIONSHIP OF PROTEINS USING “REMEDIATED” PDB FILES ”. In:
SBBq 2008 May 17 to 20, Águas de Lindóia. Brazil.
8.88. Mazoni I., Jardine J.G, Borro L.C., Alvarenga D., Goran Neshich; “ELECTROSTATIC
POTENTIAL AT THE ALPHA CARBON ATOMS ALONG THE ALPHA HELICES AND BETA
STRANDS ”. In: SBBq 2008 May 17 to 20, Águas de Lindóia. Brazil.
8.89. Jardine J.G., Mazoni I., Borro L.C., Alvarenga D., Goran Neshich; “SIGNATURE CONTACT
COORDINATION PATTERNS FOR SECONDARY STRUCTURE ELEMENTS IN PROTEIN
STRUCTURES ”. In: SBBq 2008 May 17 to 20, Águas de Lindóia. Brazil.
8.90. Jardine J.G., Mazoni I., Mancini A., Borro L.C., Alvarenga D., Cecilio P.L, Pelligrinelli T.V.
and Goran Neshich; “HOW DID THE STRUCTURE FUNCTION DESCRIPTORS OF PROTEINS
CHANGE WITH INTRODUCTION OF "REMEDIATED" PDB FILES”. In: RIB 2008 October 15 to
17, Santiago. Chile.
8.91. Mancini A., Jardine J.G., Mazoni I., Borro L.C., Alvarenga D., Cecilio P.L, Pelligrinelli T.V.
and Goran Neshich; “Structure Descriptors of Chameleon Sequences ”. In: RIB 2008 October 15 to 17,
Santiago. Chile.
8.92. Borro L.C., Mazoni I., Alvarenga D., Cecilio P., Grassi, J.A., Mancini A., Jardine J.G. and Goran
Neshich; “CONTACT COORDINATION PATTERNS AND ELECTROSTATIC POTENTIAL AT
ALPHA CARBON ATOMS: A DOSSIER OF PROTEIN SECONDARY STRUCTURE ELEMENTS”.
In: EMBnet Conference 2008: 20th Anniversary Celebration,2008 September 18 - 20, Martina Franca
(Puglia), Italy.
8.93. Izabella Pena ; MANCINI, Adauto L. ; MAZONI, Ivan ; JARDINE, Jose Gilberto ; Neshich,
Goran ; José Miguel ortega . "Identification of phylogenetic relationship between GDPD and SMaseD
proteins based on active site amino acid physical chemical properties". In: x-meeting, 2008, Salvador,
BA. x-maating 2008, 2008, Brazil.
9. THESIS COMMITTEE PARTICIPATION
This Section Updated: JANUARY 14, 2009
9.1.1. "Disulphide bridge determination in 2S albumin from Brazil nut (Bertholetia excelsa H.B.K.)
9.1.2. author: Maria Cristina Mattar da Silva
9.1.3. degree: Msc, UnB - Brasilia, Brazil
9.1.4. participation: thesis adviser
9.1.5. Finalized: 1993
9.2.1. "Purification and the partial amino-acid sequence of the tripsin- chymotripsin inhibitor from the
Dolichos labiab cv albiflorus seeds"
9.2.2. author: Marcelo Silveira de Alcantra
9.2.3. degree: Msc, UnB - Brasilia, Brazil
9.2.4. participation: committee member
9.2.5. Finalized: 1994
9.3.1. "Secondary structure prediction of the globular proteins: structure prediction software design COMBO, and its utilization for the analysis of the C-terminal region of the proteins binding to poly-A
(PABP)”
9.3.2. author: Antonio Francisco Pereira de Araújo
9.3.3. degree: Msc, UnB - Brasilia, Brazil
9.3.4. participation: committee member
9.3.5. Finalized: 1994
9.4.1. "Structural analysis of Piruvate Decarboxilase from Saccharomyces cerevisiae"
9.4.2. author: Maria Angela Lopes de Almeida Arrazonas
9.4.3. degree: Ph.D., UNICAMP - Campinas, Brazil
9.4.4. participation: committee member
9.4.5. Finalized: 1994
9.5.1. "Trypsine and Chymotrypsine inhibitor from Vigna unguiculata (L.) Walp: Modeling of three
dimensional structure by homology, Thermodynamics and Kinetics of the interaction with aChymotrypsine"
9.5.2. author: Sonia Maria de Freitas
9.5.3. degree: PhD., UnB - Brasilia, Brazil
9.5.4. participation: committee member
9.5.5. Finalized: 1995
9.6.1. "Inibidores de Proteinase do Tipo Bowman-Birk: Evolução Molecular, Expressão na Superfície de
Fagos Filamentosos e seu Papel na Interação Planta-Inseto"
9.6.2. author: Marcia Ometto de Mello Alves José
9.6.3. degree: PhD., ESALQ/USP, Piracicaba, Brazil
9.6.4. participation: committee member
9.6.5. Finalized: 2002
9.7.1. "Structure Function Relationship for Glutationa S transferase proteins "
9.7.2. author: Andrea Guelfi
9.7.3. degree: PhD., ESALQ/USP, Piracicaba, Brazil
9.7.4. participation: committee member
9.7.5. Finalized: 2006
9.8.1. "In Silico analysis of the patterns in interactions established between the serion proteases and their
inhibitors"
9.8.2. author: Cristina Ribeiro
9.8.3. degree: PhD., UFMG, Belo Horizonte, Brazil
9.8.4. participation: co-advisor
9.8.5. Finalized: in progress
9.9.1. "Globulins and their internal contact motifs analysed togather with other structure descriptors"
9.9.2. author: Carlos Henrique da Silveira
9.9.3. degree: PhD., UFMG, Belo Horizonte, Brazil
9.9.4. participation: co-advisor
9.9.5. Finalized: 2008
9.10.1. "Predicting hydrogen atom positions in proteins using neural networks"
9.10.2. author: Adauto Luiz Mancini
9.10.3. degree: MSc., UFSCAR, Sao Carlos, Sao Paulo, Brazil
9.10.4. participation: co-advisor
9.10.5. Finalized: 2008
9.11.1. "Protein classification based on internal contact patterns"
9.11.2. author: Raquel Melo
9.11.3. degree: PhD., UFMG, Belo Horizonte, Brazil
9.11.4. participation: co-advisor
9.11.5. Finalized: 2008
9.12.1. "TargetsDB - Base de dados de alvos terapêuticosvalidados"
9.12.2. author: Eduardo Campos dos Santos
9.12.3. degree: PhD., UFMG, Belo Horizonte, Brazil
9.12.4. participation: co-advisor
9.12.5. Finalized: in progress
9.13.1. "Meio ambiente dos elementos da estrutura secondaria em proteinas."
9.13.2. author: Ivan Mazoni
9.13.3. degree: MSc., UNICAMP, Campinas, Brazil
9.13.4. participation: advisor
9.13.5. Finalized: in progress
9.14.1. "Predição de epitopos em LiD1, proteína dermonecrotica do veneno da aranha marrom Loxosceles
intermédia por bioinformática e Imonologia molecular"
9.14.2. author: Ricardo Andrez Machado de Ávila
9.14.3. degree: PhD., UFMG, Belo Horizonte, Brazil
9.14.4. participation: co-advisor
9.14.5. Finalized: in progress
9.15.1. "Desenvolvimento de Interface Web para Docking Automático de Consenso. "
9.15.2. author: Andrelly Martins Jose
9.15.3. degree: PhD., UFMG, Belo Horizonte, Brazil
9.15.4. participation: co-advisor
9.15.5. Finalized: in progress
9.16.1. "Estudos de comunicação entre as macromoleculas em homo e hetero complexos atraves das
interfaces. "
9.16.2. author: Fábio Rogéio de Moraes
9.16.3. degree:PhD., UNICAMP, Campinas, Brazil
9.16.4. participation: advisor
9.16.5. Finalized: in progress
9.17.1. "Produção de um inibidor para Quinase de Adesão Focal (FAK) estudos estruturais"
9.17.2. author: João Eustáquio Antunes
9.17.3. degree:PhD., UNICAMP, Campinas, Brazil
9.17.4. participation: co-advisor
9.17.5. Finalized: in progress
9.18.1. "Produção de um compsto quimico simples, substituto de peptídeo natriurético, o inibidor de
receptores do tipo Guanilato Ciclase."
9.18.2. author: Álisson Campos Cardoso
9.18.3. degree:PhD., UNICAMP, Campinas, Brazil
9.18.4. participation: co-advisor
9.18.5. Finalized: in progress
9.19.1. "Analise dos aspectos estruturais dos inibidores vegetais de enzymas proteoliticas."
9.19.2. author: Vanessa da Silveira Ramos
9.19.3. degree:PhD., UNICAMP, Campinas, Brazil
9.19.4. participation: co-advisor
9.19.5. Finalized: in progress
9.20.1. "Aspectos estruturais da atividade de um inibidor do tipo Kunitz de Adenanthera pavonina
(APTI)"
9.20.2. author: Desiree Soares da Silva.
9.20.3. degree:PhD., UNICAMP, Campinas, Brazil
9.20.4. participation: co-advisor
9.20.5. Finalized: in progress
10. SOFTWARE PACKAGES PUBLISHED
All packages are available at:
Country
Home (Embrapa/CNPTIA, Campinas - Brazil)
USA: PDB/RCSB at SCSD-UCSD
USA: Columbia University
Spain: CNB-Madrid
Japan: Kyushu Institute of Technology (KIT)
Argentina: La Plata
Brazil: Embrapa-Cenargen-Brasilia
www address
http://www.cbi.cnptia.embrapa.br
http://mirrors.rcsb.org/SMS
http://trantor.bioc.columbia.edu/SMS/
http://www.es.embnet.org/SMS/
http://gibk26.bse.kyutech.ac.jp/SMS/
http://www.ar.embnet.org/SMS/
http://asparagin.cenargen.embrapa.br/SMS
10.1.
STING---STING is a WWW tool for the simultaneous display of information about macromolecular
structure (in STING's Graphics Frame) and sequence (in STING's Sequence Frame). Special
attention is given to MacroMolecular INTERFACE analysis. (1998)
10.2.
STING_PAINT---STINGpaint is WWW tool for - sequence and multiple sequence alignment coloring
- residue/nucleotide within_the_sequence_number identification - characterization of the immediate
environment for any residue/nucleotide within the sequence. (1998)
10.3.
HORNET---HORNET Specifically shows Hydrogen Bond Net formed between two protein chains (or
protein and DNA). HORNET also shows exact listing of the Interface Forming Residues (IFR), based
on calculated buried surface area. (1998)
10.4.
MDB_MINING---Molecular Data Base - MDBMining: is a compilation of a variety of algorithms for
retrieving specific data from Protein Databank (PDB), SwissProt and GenEMBL. Total
Residue/Nucleotide occurrence in each database, keyword search, file sizes, number of chains,
resolution of 3D data, protein families classification are all available in MDBMining. (1999)
10.5.
PDB_MINING---Protein Data Base - PDBMining: is a compilation of a variety of algorithms for
retrieving specific data from Protein Databank (PDB). Total Residue occurrence in whole PDB,
keyword search, file sizes, number of chains, resolution of 3D data, protein families classification are
all available in PDBMining. (1999)
10.6.
SCORPION---SCORPION is the WWW tool for analysis of the amino acid frequences within protein
chain(s) (of given pdb file or group of pdb files) as well as foranalysis of 3D contacts of C-alpha
and/or Last Hevy Atoms in the residue side chain (LHA). Convinient Graphical presentation can be
used for identification of specific interactions for given family of the proteins or given domains. (1999)
10.7.
FORMIGA---FORMIGA is a program that evoluted from SCORPION and is a WWW tool for analysis
of PROTEIN INTERFACES with respect to amino acid residue frequences (of given pdb file or group
of pdb files) as well as for analysis of 3D contacts of C-alpha and/or Last Hevy Atoms in the residue
side chain (LHA) for Interface Forming Residues (IFR). Convinient graphical presentation of
calculated parameters makes possible to see specific interactions on the Protein Interfaces. (1999)
10.8.
HESPER---HESPER: A tool for the analysis of homologous protein families derived from the HSSP
database. (2000)
10.9.
SPIDER---Serine Protease super-family Interface Data Resource (SPIDER) is an expanding
collection of sequence, structural and functional information about the Serine Proteases Interface
Forming Residues located around Active Site. (2000)
10.10.
EMA---Evaluation of Multiple Alignments: A Comparison of Phylogenetic trees based on sequence
alignments and structure alignments. EMA is a Data Resource available over WWW. (2000)
10.11.
Ramachandran Plot -- Intelligent graphical presentation of the Ramachandran Plot using all
advantages of Java programming language; Options allow inter connection of data in dihedral angle
plot with 3D structure of the molecule. A number of subsets among amino acids can be highlighted
for better correlation among 3D structure position and Psi/Pfi spot. (2000)
10.12.
Protein Dossier -- This service provides a graphical report of several important structural
characteristics of the PDB entry. It offers a plot from PDB cartoon annotated with color coded scales
representing for each amino acid the corresponding temperature factor, solvent accessibility of the
chain in isolation and in complex with the other present chains in PDB file, sequence conservation in
a multiple alignment (relative sequence entropy) and histograms representing the atomic contacts
(as in the Graphical contacts module), as well as IFR residue identification and IFR contacts. In
addition, comparison of the Secondary Structure annotated by PDB and by DSSP is presented.
(2000)
10.13.
PDB_Cartoon -- Image of the amino acid sequence along with the secondary structure elements
rendered as cartoons. (2000)
10.14.
Contacts -- The atomic contacts between amino acids in a PDB entry received a special attention.
The complete profile of the interactions can be analyzed in the graphical contacts window, which
displays the primary sequence of a chain and below it a histogram containing the number of contacts
made by the respective residue. Virtual contact line connects residue of interest with other ones in
contact with it, in a form of fan. This presentation is very intuitive and user can easily grasp contact
parameters along the protein sequence. In case of IFR contacts, IFR are underlined with red line for
easy identification. (2000)
10.15.
ConSSeq -- This service presents PDB file sequence and consensus sequence (as found in HSSP)
colored by conservation, color coded graphic bars of relative entropy, information about residues
present in other homologous sequences, with their respective frequency. For fast visualization, this
program generates the sequence logo. (2000)
10.16.
Java Ca-Ca Distance plot -- is a diagram where the distances between the alfa carbon of one
residue and all alfa carbon atoms of other residues, within a single chain of the PDB file, are
represented by colored squares in a symmetrical plot. (2001)
10.17.
Java Cb-Cb Distance plot -- is a diagram where the distances between the beta carbon of one
residue and all beta carbon atoms of other residues, within a single chain of the PDB file, are
represented by colored squares in a symmetrical plot. (2001)
10.18.
Java MSA -- SMS_MSA stands for the new SMS component: Multiple Sequence Alignment. Those
sequences are extracted both from HSSP and from our own SH2Qs (Sequences Homologue to the
Query [Structure-having] Sequence). The latter one is designed so that we can benefit from the
possibility of making a choice of the number of sequences that we want to consider in the relative
entropy calculation. SMS_MSA will use standard MSA viewer package: SeaView. (2001)
10.19.
Java Protein Dossier -- is a interactive presentation of important physical-chemical characteristics
of the macromolecular structure described in PDB file. With a few mouse clicks the user can access
data about chosen parameter, call other SMS modules or refine the search for a specific
characteristics. By using color code scales for each residue of the sequence, JPD shows
corresponding: temperature factor, solvent accessibility of the single chain (and also in complex with
the other present chains in given PDB file), hydrophobicity, sequence conservation in a multiple
alignment (relative entropy), double ocupancy, reliability and histograms representing the atomic
contacts. JPD also shows the identification of Interface Forming Residue (IFR) and their internal
contacts. JPD offers information about electrostatic potential and curvature on protein surface. In
addition, comparison of the Secondary Structure annotated by PDB, by DSSP and by Stride is
presented. (2002)
10.20.
Java Table of Contacts -- is a interactive tool for listing contacts between residues of one protein
and dividing them in specific classes. JTC shows all contacts for a specified residue, IFR Contacts
and also Protein-DNA Contacts (the latter one starting from SMS version 3.1). This interactive tool
allows user to access other SMS components or have physical-chemical parameters already
"painted" within the table, such as: relative entropy, accessibility, secondary structure and the
distance for the identified contacts. The user can make a choice of the resudes important for his
consideration, make them appropriately displayed and then print the table of publication quality.
(2002)
10.21.
Protein DNA Contacts -- This SMS component demosntrates relevant contacts being established
across the interface formed by protein and DNA chain. Similar logistics is used here as in IFR
Graphical Contacts. (2003)
10.22.
SMS_P3 -- SMS_P3 sands for SMS Phylogenetic Tree component. Phylogenetic tree is generated
starting from either HSSP or SH2Qs multiple sequence alignments. TreeView standard viewer
package is used to present to a user calculated phylogenetic trees. (2003)
10.23.
SMS 2.2 -- STING Millennium is a new Java-based WWW tool for the simultaneous display of
information about macromolecular structure (in STING Millennium Graphics Window) and sequence
(in STING Millennium Sequence Window). Includes graphical amino acid Contacts, Ramachandran
plot, Surfaces, Sequence neighbors and other features. Parsing of data from relevant Data Bases
(HSSP and SwissProt) is one of the key features of this integrated environment for structure/function
analysis of the proteins, DNA and their complexes. To see the 3D structure you need to download
and install the CHIME plugin. (2003)
10.24.
Gold STING-- STING Millennium is a new Java-based WWW tool for the simultaneous display of
information about macromolecular structure (in STING Millennium Graphics Window) and sequence
(in STING Millennium Sequence Window). Includes graphical amino acid Contacts, Ramachandran
plot, Surfaces, Sequence neighbors and other features. Parsing of data from relevant Data Bases
(HSSP and SwissProt) is one of the key features of this integrated environment for structure/function
analysis of the proteins, DNA and their complexes. To see the 3D structure you need to download
and install the CHIME plugin. (2003)
10.25.
STING Report -- GOLD STING Report is a web based application for extracting concise and
focused information from the GOLD STING Data Base on specific amino acids within the structures
described in PDB files. The extracted information is presented to a user through a series of GIF
images and a table of numerical values for the set of structure/function descriptors/parameters,
generated by the GOLD STING components. The resulting HTML page with the GIF images and the
table is ready to be printed and most importantly, it can be visualize at platforms with the most
elementary configurations (no java, chime, plug-ins etc.). Below is a schematic view of GIF image
panels which are generally produced by the GOLD STING Report. We have used 1cho.pdb, chain E,
residue HIS_57 to generate GOLD STING Report for this help. Other panels will be added with the
time, making GOLD STING Report GIF image collection more extensive. (2003)
10.26.
Diamond STING -- Diamond STING is a new version of the STING suite of programs for
comprehensive analysis of a relationship between protein sequence, structure, function and stability.
We have added number of new functionalities by both providing more structure parameters to the
STING Database and by improving/expanding the interface for enhanced data handling. The
integration among the STING components has also been improved. A new key feature is the ability
of the STING server to handle local files containing protein structures (either modeled or not yet
deposited to the PDB) so that they can be used by the principal STING components: JavaProtein
Dossier and STING Report. (2004)
10.27.
Multiple Structure - Single Parameter (MSSP) 2D Plot - The Multiple Structures - Single
Parameter 2D module allows the user to compare, in a graphical manner, any one of the 150
different parameters in different protein structures in a simple yet intuitive plot. The plot shows the
numerical values in the Y-axis and the sequence residue numbers in the X-axis. (2006)
10.28.
Contact Distance Map - Contact Distance Map (CDM) is a STING's module. It is designed to
display graphically all the protein's contacts. Moreover, the Secondary Structure (SS) elements are
also shown in a single line, facilitating theirs visualization for each residue, and contour curves
distances maps involving a carbon, ß carbon and LHA-LHA (Least Heavy Atom) are presented in a
Java interactive interface. (2006)
10.29.
Protein Contacts Difference - In STING_PCD users can obtain a complete comparison report of
the intrachain interactions for any two chains described in the PDB format file. The user must supply
any two PDB ids and corresponding chain ids for the analysis. At the output, a user will receive a list
of interactions which were preserved in both chains as well as the list of those which are present in
only one of them. Users can also analyse a wild type protein and a corresponding mutant structure
with a single point mutantion; in this case a user needs to supply at the input, the mutated amino
acid name and the number. (2006)
10.30.
Topology Similarity Map (TopSiMap) - STING_TopSiMap is a module which makes possible to
compare the contact maps of two chains in terms of the preserved interactions as well as the ones
which are present in only one of the two chains analysed. Users can see / print the images of the
maps and also view the contacts in a JMol window where STING presents two structurally aligned
chains. Users can also compare the chains in terms of the contacts classification (hydrophobic,
aromatic stacking, hydrogen bonds, salt bridges and cysteine bridges) and corresponding energies.
(2006)
10.31.
STING_DB QA - This module is designed for checking the quality of STING_DB, the STING_DB
Quality Assessment (STING_DB QA). With this new module, a user can perform the tracking of the
PDB files which contains the insufficient information clarity for a specific structure descriptor
calculation. Also, the overall quality of the STING_DB is much easier to assess now, setting this
STING version apart from other products in this area. (2006)
10.32.
STING_TGZ - STING_TGZ module generates a compressed file containing all the files used by
several STING's modules, for example, JPD (Java Protein Dossier). These files are saved in
different directories within the compressed file. If your research project needs to analyze the same
pdb file very often, the best way to save time (in downloading data from internet) is to use
STING_TGZ module. (2006)
10.33.
3D Java Protein Interface Viewer - JPIV - JPIV is a module of STING suite. It is designed to
visualize and analyze the proteins' interfaces. In order to accomplish this, the interfaces are
displayed separately, and over each one of them is painted a common physical-chemical property,
available from STING_DB, that could be important in the complex formation. The contact interfaces
are generated using weighted Delaunay triangulation and marching tetrahedra algorithms from the
CGAL library, afterwards they and rendered in an Interactive Java Viewer based on JavaView library.
(2006)
10.34.
PDB_Metrics - PDB Metrics can retrieve specific data from the Protein Data Bank (PDB). It provides
residues occurrences in the whole PDB repository, keywords search, PDB sorted by file size, PDB
sorted by number of chains, PDB sorted by resolution of 3D data, protein families classification,
among other facilities. (2006)
10.35.
Star STING - Star STING is the February, 2006 version of the STING suite of programs and
corresponding database. Five important aspects of this package that acquired some new
characteristics, designed to add key advantages to the whole suite: 1) Availability for most popular
platforms and browsers, 2) Introduction of the STING_DB quality assessment, 3) Improvement in
algorithms for calculation of three STING parameters, 4) Introduction of five new STING modules,
and 5) expansion of the existing modules.
The Star STING is freely accessible at: http://sms.cbi.cnptia.embrapa.br/SMS/ and
http://trantor.bioc.columbia.edu/SMS. (2006)
10.36.
2-Dimensional Interface Maps - 2DIM - Designed to visualize separately the protein interfaces and
analyze the main forces involved in protein complex formation. The 2DIM uses Floater's shape
preserving algorithm to project the 3D protein interfaces into 2D, where it is then possible to
superimpose the surfaces and estimate the interaction area between them. (2006)
10.37.
Sting Enzyme Classification - Module dealing with a protein classification based on STING_DB
parameters. (2006)
10.38.
Topologs 100 - In this module, users can obtain the index for a toplogy similarity for a list of up to
100 structures. By submitting the STING TGZ file (containing all STING_DB parameters,
precalcualated, corresponding to certain public or local structure) and a text file containing the list of
up to 99 public PDB files, user can start the procedure which calculates the similarity index among
selected (up to) 100 structures. This index is a reliable measure of the changes in the pattern of the
intrachain interactions and can be used to analyse the topology similarities. (2006)
10.39.
Topologs Astral 40 - This is a database of homologous PDB chains based on their interactions
(contacts) pattern. For each of the "ASTRAL 40" ensamble chains, we computed a list of the most
similar chains based on their contact maps. The database is searchable and for each chain, the list
of the topologs is presented. (2006)
10.40.
Multiple Parameter Aligment 3D Plot - Deals with the presentation of a single parameter for
multiple structures or multiple parameters for a singles structure. (2006)
10.41.
Amino Acid Co-evolution - The AA Co-evolution is the STING component which permits a user to
examine co-evolution parameter of residues in a simple, yet intuitive 3D plot. A user may confirm
which amino acid positions were identified by STING, within the previously confirmed amino acid
conserved set, as evolved in concert. (2006)
10.42.
Protein Ligand COntacts - This STING module can analyze the interatomic contacts in protein ligand complexes. The contacts shown by this STING module include those mediated by chargecharge interactions, hydrogen bonds and hydrophobic contacts. (2006)
10.43.
BlueStar STING - BlueStar STING is the July, 2006 version of the STING suite of programs and
corresponding database. Five important aspects of this package that acquired some new
characteristics, designed to add key advantages to the whole suite: 1) Relational Database of STING
parameters, 2) Amino acid co-evolving residues identified, 3) protein ligand contacts now available,
4) Sting Report now available in PDF format, and 5) improoved cross-talk among existing STING
modules .
The BlueStar STING is freely accessible at: http://sms.cbi.cnptia.embrapa.br/SMS/ and
http://trantor.bioc.columbia.edu/SMS. (2006)
10.44.
Java Secondary Structure Dossier (JSSD) - With this STING module a user may visually and
numerically observe and analyze per residue reported structure descriptors for the SSE: alpha
helices and beta strands. (2007)
11. SEMINARS & LECTURES GIVEN
1993
11.1."Bioinformatics: Databases and Computer Networks in Biology", 13 - 17 December 1993,
REDBIO, Brasília, DF, Brazil.
1994
11.2."Bioinformatics: Databases and Computer Networks in Biology", 30 May - 03 June 1994,
Held at the Fundação Tropical de Pesquisas e Tecnologia "André Tosello", Campinas, SP,
Brazil.
1995
11.3.1. "Aperfeiçoamento em Biossegurança", 25 September - 25 Octuber 1995, Fundação
Oswald Cruz FIOCRUZ, Rio de Janeiro, Brazil.
11.3.2. "Workshop Internacional sobre Redes de Informação para Recursos Genéticos
utilizando a Internet", 06 - 10 November 1995, Centro Nacional de Pesquisa de
Recursos Genéticos e Biotecnologia - CENARGEN/EMBRAPA, Brasília, DF, Brazil.
11.3.3. "Ecoturismo Científico mostrado pela Internet", November, 16 1995, Seminário da
Amazônia 95, Manaus, AM, Brazil.
1999
11.4.1. "Pragas quarentenárias: detecção e identificação", 07 - 11 June 1999, Centro Nacional
de Pesquisa de Recursos Genéticos e Biotecnologia CENARGEN/EMBRAPA, Brasília,
DF, Brazil.
2001
11.5.1. "Bringing Genome Into Three Dimensions", March, 29 2001, Centro de Biologia
Molecular do Laboratório Nacional de Luz Síncrotron, Campinas, SP Brazil.
11.5.2. "Bringing Genome Into Three Dimensions", June, 26 2001, Instituto de Química da USP,
São Paulo, Brazil.
11.5.3. "Bringing Genome Into Three Dimensions", August, 30 2001, Centro de Biologia
Molecular e Engenharia Genética da UNICAMP, Campinas, SP, Brazil.
11.5.4. "Bringing Genome Into Three Dimensions", September, 27 2001, Instituto Nacional de
Pesquisas Espaciais, São José dos Campos, SP, Brazil.
11.5.5. "Bioinformática - Experiências nos Últimos Meses", Octuber, 09 2001, Centro Nacional
de Pesquisa Tecnológica em Informática para a Agropecuária CNPTIA, Campinas, SP,
Brazil.
11.5.6. "Bioinformática: Bringing Genome Into Three Dimensions", November, 20 2001, Centro
de Informática da UFPE, Recife, PE, Brazil.
11.5.7. "Bioinformática: Definição, Limites e Oportunidades", Octuber, 08 2001, Centro Superior
de Educação Tecnológica, Limeira, SP, Brazil.
11.5.8. "Bioinformática: Bringing Genome Into Three Dimensions", November, 11 2001,
Laboratório de Computação Científica - LNCC/MCT, Petrópolis, RJ, Brazil.
11.5.9. "Bringing Genome Into Three Dimensions", 03 - 08 December 2001, Instituto de
Ciências Matemáticas e de Computação da USP, São Carlos, SP, Brazil.
2002
11.6.1. "Bringing Genome Into Three Dimensions", April, 02 2002, Pontifícia Universidade
Católica do Rio de Janeiro PUC-Rio, Rio de Janeiro, Brazil.
11.6.2. "Recognition at macromolecular interfaces: Protein Dossier and Protein Fingerprints
produce Surface Signatures, a simple and powerful technique for coding and comparing
compound and receptor shape information", April, 17 2002, NCBI: Department of
Health& Human Services, USA.
11.6.3. "Recognition at macromolecular interfaces: Protein Dossier and Protein Fingerprints
produce Surface Signatures, a simple and powerful technique for coding and comparing
compound and receptor shape information", April, 26 2002, Columbia University, New
York, NY, USA.
11.6.4. "Recognition at macromolecular interfaces: Protein Dossier and Protein Fingerprints
produce Surface Signatures, a simple and powerful technique for coding and comparing
compound and receptor shape information", May, 01 2002, University of California, San
Diego, USA.
11.6.5. "Recognition at macromolecular interfaces: Protein Dossier and Protein Fingerprints
produce Surface Signatures, a simple and powerful technique for coding and comparing
compound and receptor shape information", June, 04 2002, Laboratório de
Computação Científica - LNCC/MCT, Petrópolis, RJ,Brazil.
11.6.6. "Recognition at macromolecular interfaces: Protein Dossier and Protein Fingerprints
produce Surface Signatures, a simple and powerful technique for coding and comparing
compound and receptor shape information", May, 28 2002, Instituto Butantan, São
Paulo, SP, Brazil.
11.6.7. "Recognition at macromolecular interfaces: Protein Dossier and Protein Fingerprints
produce Surface Signatures, a simple and powerful technique for coding and comparing
compound and receptor shape information", June, 14 2002, Instituto de Biologia
Molecular do Paraná, Curitiba, PR, Brazil.
11.6.8. "Recognition at macromolecular interfaces: Protein Dossier and Protein Fingerprints
produce Surface Signatures, a simple and powerful technique for coding and comparing
compound and receptor shape information", June, 07 2002, Centro de Informática da
UFPE, Recife, PE, Brazil.
11.6.9. "Recognition at macromolecular interfaces: Protein Dossier and Protein Fingerprints
produce Surface Signatures, a simple and powerful technique for coding and comparing
compound and receptor shape information", August, 30 2002, Departamento de
Genética ESALQ/USP, Piracicaba, SP, Brazil.
11.6.10. "Recognition at macromolecular interfaces: Protein Dossier and Protein Fingerprints
produce Surface Signatures, a simple and powerful technique for coding and
comparing compound and receptor shape information", September, 16 2002,
Universidade Federal de São Paulo UNIFESP/EPM, São Paulo,SP, Brazil.
11.6.11. "Recognition at macromolecular interfaces: Protein Dossier and Protein Fingerprints
produce Surface Signatures, a simple and powerful technique for coding and
comparing compound and receptor shape information", September, 19 2002, Instituto
de Química de São Carlos da USP, São Carlos, SP, Brazil.
11.6.12. "Recognition at macromolecular interfaces: Protein Dossier and Protein Fingerprints
produce Surface Signatures, a simple and powerful technique for coding and
comparing compound and receptor shape information", November, 21 2002,
Faculdade de Ciências Farmacêuticas de Ribeirão Preto- USP,Ribeirão Preto, SP,
Brazil.
11.6.13. "Trazendo o Genoma em Terceira Dimensão", November, 29 2002, Instituto de
Biologia da UNICAMP, Campinas, SP, Brazil.
11.6.14. "Recognition at Macromolecular Interfaces", November, 26 2002, Centro Nacional de
Pesquisa Tecnológica em Informática para a Agropecuaria CNPTIA, Campinas, SP,
Brazil.
2003
11.7.1. "Grid Computing and Chemogenomics", 27 - 31 January, in Workshop de Grade
Computacional & Aplicações - LNCC, Rio de Janeiro, RJ, Brazil.
11.7.2. "Structural Bioinformatics and The ISCB and de ISMB 2006 in Fortaleza", 17 - 19 March
2003, Reunión Preparatoria Red Iberoamericana de Bioinformática - SeCyT, Buenos
Aires, Argentina.
11.7.3. "STING" at "Introdução à Biologia Computacional", 13 May 2003, Centro BrasileiroArgentino de Biotecnologia - Hemocentro de Ribeirão Preto, Ribeirão Preto, SP, Brazil.
11.7.4. "Bioinformatics from Genoms to Drugs", Simpósio 14 - 04, "Recognition at
Macromolecular Interfaces: Protein Dossier Maps Surface Signatures and Physico
Chemical Parameters Defining Binding Specifithy", 19 May 2003, SBBq 2003,
Caxambu, MG, Brazil.
11.7.5. "New features of SMS v.3 and Java Protein Dossier", PDB, 23 June 2003, San Diego,
USA.
11.7.6. "STING Millennium Suite structure and function descriptors: a new addition to the
existing jazz", 26 August 2003, Alellyx - Applied Genomics, Campinas, SP, Brazil.
11.7.7. "Estudo de Relação entre Sequência e Estrutura das Proteínas e DNA", 30 September
2003, Faculdade de Informática Biomédica - USP, Ribeirão Preto, SP,Brazil.
11.7.8. "Sting Millennium Suite", 06 - 10 Octuber 2003, CNRS, Nancy, France.
11.7.9. "Structural Bioinformatics", 27 Octuber 2003, Universidad de Talca - Facultad de
Ingenieria, Chile.
11.7.10."Opportunities and Challenges for Structural Bioinformatics", 30 Octuber 2003,
Universidad de Talca - Facultad de Ingenieria, Chile.
11.7.11."Tasks While Establishing Structural Bioinformatics Laboratory", 30 Octuber 2003,
Universidad de Talca - Facultad de Ingenieria, Chile.
11.7.12."High Performance Computing at Embrapa: searching for the best shape match
between the potential drug targets at the protein surface and the small chemical
compunds" Forum de Technologias e Aplicações de Sistemas de Alto Desempenho
(FSAD2003), São Paulo, Brazil, November 10-12, 2003.
11.7.13. "Opportunities and Challenges in Structural Bioinformatics - Searching for New Drugs"
CAT-CEPID, Instituto Butantan, São Paulo, Brazil, November 19, 2003.
2004
11.8.1. "Drug design and structural Bioinformatics", Knowledge Discovery in Genomic
Databases, Pan American Advanced Studies Institute (PASI), February 12, 2004,
Montevideo, Uruguay.
11.8.2. "New features of Gold STING and JavaProtein Dossier" Knowledge Discovery in Genomic
Databases, Pan American Advanced Studies Institute (PASI), February 12, 2004,
Montevideo, Uruguay.
11.8.3. "Drug specific applications for the Gold STING, JavaProtein Dossier, and STING Report:
case study - serine proteases" Knowledge Discovery in Genomic Databases, Pan
American Advanced Studies Institute (PASI), February 16, 2004, Montevideo, Uruguay.
11.8.4. "New Challanges and Opportunities for Structural Bioinformatics" Knowledge Discovery
in Genomic Databases, Pan American Advanced Studies Institute (PASI), February 16,
2004, Montevideo, Uruguay.
11.8.5. " Gold STING: Studying protein stability and folding by looking at an extensive DB of the
Structure Descriptors" Programma de Seminarios em Biologia
Computacional;Faculdade de Ciencias Farmaceuticas Riberao Preto USP, Brazil, Abril,
2004.
11.8.6. " Gold and DIamond STING: The volume and quality of results 3 and 1/2 years after
initiating the activities"; EMBRAPA Technical Meeting;Campinas, SãoPaulo, Brazil,
May,
2004.
11.8.7. "Protein Dossier - a Data Base of Physical-Chemical Parameters Describing Protein
Function. 2004. Caxambu;Brazil, XXXIII SBBq; May, 2004
11.8.8. "GOLD STING - data base of protein structure and function describing parameters".
Instituto de Biosciencias; Sao Jose do Rio Preto- Brazil; I Semana da Pos-Graduação
em Biofisica Molecular; UNESP, June, 2004.
11.8.9. " Opportunities and Challenges for Structural Bioinformatics". ; São Paulo-Brazil;
Instituto de Quimica - USP. June, 2004
11.8.10. "Challages and Opportunities for Structural Bioinformatics". . Fortaleza - Brazil:
WORKSHOP INTERNACIONAL DE NANOTECNOLOGIA APLICADA ÀS CIÊNCIAS
BIOLÓGICAS;: UFCE. June, 2004
11.8.11. " Protein structure / function /binding descriptors: Gold STING". ; CNB - Madrid Spain;July, 2004 .
11.8.12. "Protein structure / function /binding descriptors: Gold STING". Scuola Normale
Superiore. Pisa- Italy; July, 2004.
11.8.13. "Protein structure / function /binding descriptors: Gold STING". ; ISMB-2004,Glasgow Scotland; August, 2004.
11.8.14. "Protein structure / function /binding descriptors: Gold STING". ; CNRS, Nancy France; August, 2004.
11.8.15. "Protein structure / function /binding descriptors: Gold STING". ;ZBH Zentrum für
Bioinformatik, Hamburg -Germany; August, 2004.
11.8.16. "Protein structure / function /binding descriptors: Gold STING".Technical University of
Denmark,Center for Biological Sequence Analysis, Biocentrum-DTU ;Copenhagen Denmark; August, 2004.
11.8.17. "Protein structure / function /binding descriptors: Gold STING". Center for
Multidisciplinary Studies; Beograd -Yugoslavia; August, 2004.
11.8.18. "Genoma e Bioinformatica". In : 2a semana de atividades integradas do CEATEC;
Local: PUC Campinas; Brazil, 2004.
11.8.19. "Protein Dossier and STING Report: the database and user interface of the physicalchemical parameters describing the protein structure, function an
binding".INRIA/CNRS Nancy, France; 2004
2005
11.9.1. "Ferramentas da Bioinformática Estrutural". Centro Nacional de Pesquisa Tecnológica
em Informáticapara a Agricultura - CNPTIA. Campinas, Brazil.
11.9.2. "Proteoma e Recursos da Bioinformática". Centro Nacional de Pesquisa Tecnológica
em Informáticapara a Agricultura - CNPTIA. Campinas, Brazil. April.
11.9.3. "O que os 306 descritores de estrutura e função do STING_DB poderiam ensinar sobre
a relação entre a sequência/estrutura/função das proteínas". Doutorado Bioinformática
Universidade Federal de Minas Gerais. Belo Horizonte, Brazil. June.
11.9.4. "ISMB 2006 to be held in Fortaleza, Ceara, Brazil". ISMB 2005. Detroit, USA. June.
11.9.5. "STING - A Web Server for Comprehensive Analysis of Protein Structure and
Sequence". ISMB 2005. Detroit, USA. June.
11.9.6. "The Identification of the Folding Essential Residues and Active Site Residues by
looking at an extensive DB of the Structure Descriptors
in Diamond STING". Beckman Institute, University of Illinois. Urbana-Champaign, USA.
July.
11.9.7. "The identification of the folding essential residues and active site residues by looking at
an extensive DB of the structure descriptors in Diamond STING". Department of
Biochemistry and Molecular Biophysics, Columbia University, USA. July.
11.9.8. "The Identification of the Folding Essential Residues and Active Site Residues by
looking at an extensive DB of the Structure Descriptors in Diamond STING".Beckman
Institute for Advanced Science and Technology. USA. June.
11.9.9. "Como a bioinformática pode impulsionar o campo de saúde". Instituto de Pesquisa e
Desenvolvimento da UNIVAP. São José dos Campos, Brazil. September.
11.9.10. "How high performance computing can drive agriculture and health realted research". II
Fórum de Tecnologia e Aplicações de Sistemas de Alto Desempenho. Rio de Janeiro,
Brazil. October.
11.9.11. "Diamond STING". NANOGEN - II Workshop de Nanotecnologia Aplicada às Ciências
Biológicas e Genética. Universidade Estadual do Ceará. December.
2006
11.10.1."Bioinformatics (Computational Biology) at Embrapa: 1989-2006 and beyond". Centro
Nacional de Pesquisa Tecnológica em Informáticapara a Agricultura - CNPTIA.
Campinas, Brazil.
11.10.2. "Studying the amino acid co-evolution in terms of protein stability and functionality".
Segundas Jornadas Iberoamericanas de Bioinformatica,Buenos Aires, December, 2-5 ,
Buenos Aires, Argentina.
2007
11.11.1. "Computational Biology and Bioinformatics". 6. Congresso Brasileiro de Agroinformática
- SBIAgro 2007 São Paulo, Brazil.
11.11.2. "Protein Folding Seen Through the Secondary Structure Element Dossier and
Chameleon Sequences". 2d Latin American Protein Society Meeting (2LAPSM),
Acapulco, Mexico.
2008
11.12.1. "The architecture of Proteins, nano and macro Engines and of the Software". - Regional Architect
Forum 2008, Microsoft Brazil, São Paulo, Brazil.
11.12.2.“The Table of Interface Forming Residues as the Specificity Indicator for Serine Proteases Bound
to Different Inhibitors “ BIOCOMP 2008, Las Vegas, NE, (July 2008) USA
11.12.3. “Dossier of Secondary Structure Elemnts Amino Acid Properties “ISMB 2008, toronto, (July,
2008) Canda
11.12.4. “Contact coordination patterns and electrostatic potential at alpha carbon atoms: a dossier of
protein secondary structure elements“ Embnet 2008, Bari,(Sptember, 2008) Italia
11.12.5. ““Embnet activities at the Campinas Node, SP – Brazil“ Embnet 2008, Bari,(Sptember, 2008) Italia
11.12.6“Structure Descriptors of Chameleon Sequences “ RIB 2008, Santiago de Chile (October
2008), Chile
11.12.7 “How did the structure function descriptors of proteins change with introduction of “remediated”
pdb files - large scale db maintanance“ RIB 2008, Santiago de Chile (October 2008), Chile
12. COURSES
This Section Updated: JANUARY 14, 2009
12.1.
"Drug design and structural Bioinformatics", 29 January - 08 February / 04 March - 08 March 2002, Centro
Nacional de Pesquisa Tecnológica em Informática para a Agropecuária CNPTIA, Campinas, SP, Brazil.
12.2.
"Fisrt Sting Millennium Suite (SMS): tools to Analyze Macromolecular Structures and Applications in
Chemogenomics", 29 - 30 October 2002, Centro Nacional de Pesquisa Tecnológica em Informática para a
Agropecuária CNPTIA, Campinas, SP, Brazil.
12.3.
"Bioinformática Estrutural", 07 - 17 April 2003, Centro Nacional de Pesquisa Tecnológica em Informática para a
Agropecuária CNPTIA, Campinas, SP, Brazil.
12.4.
"Pan American Advanced Studies Institute - Knowledge Discovery in Genomic Databases"; 07 - 17 February
2004, Biotec Plaza Zona America;Montevideo Uruguay.
12.5.
"WORKSHOP INTERNACIONAL DE NANOTECNOLOGIA APLICADA ÀS CIÊNCIAS BIOLÓGICAS E
GENÉTICA" June 2004, FVA/CNPq; Fortaleza -Ceara, Brazil.
12.6.
"BIOINFORMÁTICA APLICADA À PROTEÔMICA".Septemeber - 2004, LNCC - Petropolis - Brazil.
12.7.
"Algorithms and Computational Methods for Biochemical and Evolutionary Networks (CompBioNets'04)".
December - 2004. Universidade de Pernanbuco, Recife - Brazil;
12.8.
"Diamond STING: suite of software for comprehensive protein structure/stability/function analysis" {80 hours}
March 2005, La PLata - Argentina.
12.9.
"Bioinformática Estrutural - NG250A", August/September 2005, Centro Nacional de Pesquisa Tecnológica em
Informática para a Agropecuária CNPTIA, Campinas, SP, Brazil.
12.10.
"Structural Bioinformatics" - {80 hours} September 2006, Embrapa Informatica Agropecuaria, Embrapa
Bioinformatics Network, Campinas, SP, Brazil.
12.11.
"Structural Computational Biology - using STING_DB to study protein structures " - {80 hours} February 2008,
Embrapa Informatica Agropecuaria, Campinas, SP, Brazil.
12.12.
"Structural Bioinformatics" - {120 hours} October/November 2008, Embrapa Informatica Agropecuaria and
UNICAMP, Campinas, SP, Brazil.
13. PROJECTS
This Section Updated: January, 2009
Year
Supporting
Agency
US$
1
1990
IICA
120.000,00
2
1994
FAPDF
3
1994
SGI
30.000,00
Computational Structural Biology in service of agrobusiness
4
1997/8
NSF
50.000,00
Sequente To and withIN Graphics - STING
5
198/9
FAPDF
100.000,00
Computer visualisation of quarantene pests
6
2001
FAPSP
285.741,10
7
2001
8
R$
Project title
Computer Modelling and visualisation
210.000,00
Bioinformatics in service of molecular biology and
biotechnology
185.731,72
Structural BioInformatics Research and Service Center
(CBI)
CNPq
240.000,00
Bioinformatics: From Gene Annotation to Development of
Drugs - Implementation of new Computational Tools,
Proprietary Data Banks and Metacomputing Concept
2002
FINEP
381.444,16
Structural Bioinformatics Applications with high demand for
available CPU time in post-genomic era
9
2002
CNPq
55.581,26
Expanding STING_DB
10
2004
SUN
Computers
11
2006
FAPSP
12
2007
SUN
Computers
150.000,00
13
2007
EmbrapaMP1
-
14
2008
CNPq
15
2008
CENAPAD
16
2008
FAPBA
Total
Per
Year
17 years total
150.000,00
STING_RDB
80.000,00
-
ISMB 2006 and X-meeting 2006 support
GenoProt PLUS - pipline for deciphering function of
proteins identified by Brazilian genomes projects
(2.300.000,00)
Co-participation: Functional Foods and Nutrigenomics Computational Biology - structure analysis
(55.000,00)
Co-participation: Nanotecnology Impacts
-
STING_DB update
Catalisadores e processos enzimáticos para produção de
biodiesel
885.741,10
1.152.757,14
52.102,42
67.809,24
Values are cited for the date received (consequently should be indexed for both currency fluctuations)
14. PROFESSIONAL REFERENCES
14.1.
Antony Crofts, Professor and Head, Dept. of Physiology and Biophysics, University of Illinois at
Urbana-Champaign 524 Burrill Hall, 407 S. Goodwin Avenue, Urbana, Il, 61801 USA
phone: (217) 333-2043
e-mail:Crofts@pop.life.uiuc.edu
or: a-crofts@uiuc.edu
http://www.life.uiuc.edu/~crofts
14.2.
Colin Wraight, Associate Professor, Dept. of Physiology and Biophysics, University of Illinois at
Urbana-Champaign 524 Burrill Hall, 407 S. Goodwin Avenue, Urbana, Il, 61801USA
phone: (217) 333-3245
e-mail: cwraight@pop.life.uiuc.edu
14.3.
Eduardo Tadao Takahashi, Coordenador - Geral Adjunto, Rede Nacional de Pesquisa, CNPq/SCT PR, Rua Dr. Antonio Augusto de Almeida, 334, Cidade Universitária, CEP 13083 CAMPINAS/SP Brazil.
phone: +55 192 39.4141
fax: +55 192 39.3070
e-Mail: tadao@na-cp.rnp.br
14.4.
Barry Honig, Professor, Dept of Biochemistry & Molecular Biophysics - Columbia University, New
York , USA
phone: (212) 305-7970
fax: (212) 305-6926
e-Mail: honig@bass.bioc.columbia.edu
or: bh6@columbia.edu