Dror Tobi
Curriculum Vitae
Department of Computer Sciences and Mathematics
Ariel University Center of Samaria
Ariel 40700
Israel
phone: +972 3 907 6547
fax:
+972 3 937 1422
email: drorto@ariel.ac.il
EDUCATION
Ph.D. in Biochemistry, 2003,
Hebrew University, Jerusalem, Israel
Adviser: Prof. Ron Elber
Thesis: “Enhancements and Applications of Theoretical Approaches to Predict
Protein Structures.”
M.S. in Biochemistry, 1996, Magna Cum Laude, Hebrew University, Jerusalem, Israel
Adviser: Prof. Daphne Atlas
Thesis: “Interactions of Synaptic Proteins with Calcium Channels.”
B.S. in Biology, 1994, Magna Cum Laude, Hebrew University, Jerusalem, Israel
PROFESSIONAL APPOINTMENTS
2009 – Present
Senior Lecturer
Department of Computer Sciences and Mathematics, Department of Molecular Biology,
Ariel University Center of Samaria.
Teaching: Bioinformatics, Structural Biology, and Programming courses. Research:
Designing protein-protein docking potentials. Developing protein
annotation algorithms.
2007 – 2009
Lecturer
Department of Computer Sciences and Mathematics, Department of Molecular Biology,
Ariel University Center of Samaria.
Teaching: Bioinformatics, Structural Biology, and Programming courses. Research:
Designing protein-protein docking potentials. Developing protein annotation
algorithms.
2002 - 2007
Research Associate
Department of Computational Biology, University of Pittsburgh, Pittsburgh, PA
Supervisor: Ivet Bahar
Investigating protein dynamics using coursed-grained elastic network models and
atomic scale simulation in order to understand structure and function. Calculated
dynamics of unbound complex monomers to infer the role of induced fit and
conformational selection as mechanisms for protein-protein binding. Studied
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Hemoglobin dynamics to understand the TR2 transition. Designed protein-protein
docking potentials using linear-programming technique. Developing a protein-protein
docking program. Analyzing sequences n-grams frequencies, and the correlation of
unique n-grams to proteins functionally important sites. Modeling and virtual
screening of small molecule inhibitors to human CDC25B, work in collaboration with
Dr. John Lazo.
2000 - 2002
Bioinformatics Researcher
KERYX Biopharmaceuticals, Jerusalem, Israel
Designed small molecule drugs using SYBYL (TRIPOS) modules. Calculated
proteins structure using the Homology Modeling technique. Performed sequence
analysis of protein kinase families. Performed molecular dynamic simulations.
Development of a novel algorithm for drug design.
1995 - 2000
Teaching Assistant
Department of Biological Chemistry, Hebrew University, Jerusalem, Israel
Taught recitations for Ph.D., graduate and undergraduate students in biochemistry
and computational biology. Developed quiz questions, directed laboratory
experiments, met with students upon requests, and graded written work.
1997 - 2000
Research Assistant
Department of Biological Chemistry, Hebrew University, Jerusalem, Israel
Supervisor: Ron Elber
Improved an algorithm for coupled folding of homologous proteins on lattice.
Designed coarse grained potentials for protein folding using a linear programming
technique,
which
became
part
of
the
LOOPP
program
(http://cbsu.tc.cornell.edu/software/loopp/index.htm). Performed molecular dynamic
simulations to understand the denaturing effect of urea on proteins.
1995 - 1996
Research Assistant
Department of Biological Chemistry, Hebrew University, Jerusalem, Israel
Supervisor: Daphne Atlas
Expressed proteins in E. coli; purified proteins on affinity columns. Preformed protein
binding experiments on columns and two-hybrid system experiments.
HONORS AND AWARDS
1995 - 2000 Teaching Assistant's Scholarship from the Institute of Life Sciences,
Hebrew University of Jerusalem
1996
M.SC in Biochemistry, magna cum laude
1994
B.SC in Biology, magna cum laude
1992
Cited in Dean’s register of outstanding students
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Research Grants
1.10.2009 – 30.9.2013 ISF grant "Developing potentials for protein docking and binding
sites recognition" 140,000NIS/year.
Publications
17. Cohavi O, Tobi D, Schreiber G. (2009) “Docking of antizyme to ornithine
decarboxylase and antizyme inhibitor using experimental mutant and doublemutant cycle data” J Mol Biol. 390:503-515.
16. Bahar I, Chennubhotla C, Tobi D. (2007) “Intrinsic Dynamics of Proteins:
Functionality and Biological Implications” Curr. Opin. Struct. Biol. 17:633-40.
15. Tobi D. and Bahar I. (2007) “Recruitment of rare 3-grams at functional sites: Is this
a mechanism for increasing enzyme specificity?”, BMC Bioinformatics 2007, 8:226.
14. Tobi D. and Bahar I. (2006) “Optimal Design of Protein Docking Potentials:
Efficiency and Limitations” Proteins: Structure, Function, and Bioinformatics, 62
970-981.
13. Esposito E.X, Tobi D, and Madura J.D. (2006) “The Methods and Implementation
of Comparative Protein Modelling”, in “Reviews in Computational Chemistry,
volume 22” Kenny B. Lipkowitz, Thomas R. Cundari, and Valerie J. Gillet, John
Wiley & Sons, Inc. 57-168.
12. Tobi D. and Bahar I. (2005) “Structural Changes Involved in Protein Binding
Correlate with intrinsic Motions of Proteins in the Unbound State”, Proc. Natl.
Acad. Sci. (U S A), 102 18908-18913.
11. John K. Vries, Rajan Munshi, Dror Tobi, Judith Klein-Seetharaman, Panayiotis V.
Benos, Ivet Bahar (2004) “A Sequence Alignment-Independent Method For
Protein Classification” Applied Bioinformatics 3(2-3) 137-148.
10. Brisson M, Nguyen T, Vogt A, Yalowich J, Giorgianni A, Tobi D, Bahar I,
Stephenson C.R, Wipf P, Lazo J.S. (2004) “Discovery and characterization of
novel small molecule inhibitors of human Cdc25B dual specificity phosphatase”
Mol. Pharmacol. 66(4) 824-833.
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9.
Niv MY, Rubin H, Cohen J, Tsirulnikov L, Licht T, Peretzman-Shemer A, Cna'an E,
Tartakovsky A, Stein I, Albeck S, Weinstein I, Goldenberg-Furmanov M, Tobi D,
Cohen E, Laster M, Ben-Sasson SA, Reuveni H. (2004) “Sequence-based design
of kinase inhibitors applicable for therapeutics and target identification.” J. Biol.
Chem. 279(2) 1242-1255.
8.
Xu C, Tobi D, Bahar I. (2003) “Allosteric changes in protein structure computed by
a simple mechanical model: hemoglobin T<-->R2 transition”, J. Mol. Biol. 333(1)
153-68. *
7.
Tobi D, Elber R, Thirumalai D. (2003) “The dominant interaction between peptide
and urea is electrostatic in nature: A molecular dynamics simulation study”,
Macromolecules, 68(3) 359-69.
6.
Tobi D, Elber R. (2000) “Distance-Dependent, Pair Potential for Protein Folding:
Results from Linear Optimization”, Proteins, 41,40-46. **
5.
Tobi D, Shafran G, Linial N, Elber R. (2000) “On the design and analysis of
protein folding potentials”, Proteins 40, 71-85. **
4.
Keasar C, Tobi D, Elber R, Skolnick J.
homologous proteins”, PNAS, 95, 5880-5883.
3.
Tobi D, Wiser O, Trus M, Atlas D. (1998) “N-type voltage-sensitive calcium
channel interact with syntaxin, synaptotagmin and SNAP-25 in a multiprotein
complex”, RECEPTORS & CHANNELS, 6, 89-98.
2.
Wiser O, Tobi D, Trus M, Atlas D. (1997) “Synaptotagmin restores kinetic
properties of a syntaxin–associated N-type voltage sensitive calcium channel”,
FEBS LETTERS, 404, 203-207 1997.
1.
Wiser O, Trus M, Tobi D, Halevi S, Giladi E, Atlas D. (1996) “The alpha 2/delta
subunit of voltage sensitive Ca2+ channels is a single transmembrane extracellular
protein which is involved in regular secretion”, FEBS LETTERS, 379, 15-20.
**
*
(1998) “Coupling the folding of
Cited more then 50 times
Cited more then 30 times
Invited Talks
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5.
4.
“Structural Changes Involved in Protein Binding Correlate with Intrinsic Motions of
Proteins in the Unbound State”, Biophysical theory club, University of Pittsburgh,
Pittsburgh PA, March 15 2006.
“Structural Changes Involved in Protein Binding Correlate with Intrinsic Motions of
Proteins in the Unbound State”, The 3rd Annual Biological Language Conference,
Carnegie Mellon University, Pittsburgh PA, November 28-29, 2005.
3.
“Structural Changes Involved in Protein Binding Correlate with Intrinsic Motions of
Proteins in the Unbound State”, Computational Studies of Proteins Workshop,
University of Cincinnati, Cincinnati, OH, September 8, 2005.
2.
“CDC25A / NSC663284 Docking Model”, Molecular-to-Cellular Modeling of
Complex Biological Processes workshop, University of Pittsburgh, Pittsburgh PA,
February 3, 2004.
1.
“The use of 4-grams for Protein Classification and Sequence Comparison”, 2nd
Biological Language Modeling Workshop, Carnegie Mellon University, Pittsburgh
PA, May 14 2003.
TECHNICAL COURSES



Protein Modeling Techniques (Tripos, Inc.)
Introduction to Structure-Based Design (Tripos, Inc.)
Virtual Screening (Tripos, Inc.)
TECHNICAL SKILLS
Programming languages: C/C++, FORTRAN, Perl, HTML.
Modeling:
SYBYL (Tripos Inc.), MEO (Chemical Computing Group Inc.), Gold
(Cambridge Crystallographic Data Centre), Silver (Cambridge Crystallographic Data
Centre).
Molecular dynamics: MOIL, GROMACS.
Protein visualization: PyMol, Swiss-PDB-Viewer, Rasmol.
AFFILIATIONS
International Society for Computational Biology
RESEARCH INTERESTS
My research has encompassed a broad range of interests including: primary sequence
analysis; molecules dynamics using both coarse-grain and atomic scale techniques;
protein folding studies using the Monte Carlo algorithm; designing potentials for protein
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folding and protein-protein docking; characterization of the mechanisms of protein
complexes formation; modeling drug candidates in a protein active site.
My current research efforts are directed towards understanding protein dynamics and
molecular recognition which are of fundamental importance to drug design and
biotechnology. My future research will include (i) Improving current computational
approaches for rational drug design. (II) Development novel computational tools to
assist in designing drugs capable of blocking protein-protein interaction sites. Such tools
do not currently exit and are of great need. (iii) Use of network models to understand
protein-protein interactions and protein folding. (iv) Combining coarse-grain and atomic
scale protein dynamics techniques.
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