BioChem Press
Internet Electronic Journal of Molecular Design 2005, 4, 000–000
ISSN 1538–6414
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The Title of the Manuscript Should be Written in Bold, Size 18
pt, Centered, with the First Letter of Each Main Word
Capitalized
First Author,1,* Second Author,2 Third Author,3 and Fourth Author2
1
2
Address for First Author
Address for Second Author and Fourth Author
3
Address for Third Author
Internet Electron. J. Mol. Des. 2005, 4, 000–000
Abstract
Motivation. Write the abstract of the manuscript using the font Times New Roman size 10. The abstract should
present briefly and clearly, in less than 20 lines, the main goal and results of the investigation. The abstract
should be independent of the main text, without equations, figures and references. Include all relevant phrases
and key words that describe your research, because the title and abstract are the main source of bibliographical
information; a missing key word from the abstract can make a paper hard to find from bibliographical databases.
In the Motivation section explain the importance of the problem investigated in the paper.
Method. Give a short account of the most important methods used in your investigation.
Results. Present the main results reported in the paper.
Conclusions. Briefly present the conclusions and importance of the results.
Availability. If the original software used in the investigation is available for distribution, give here the Internet
address.
Keywords. Write here up to six keywords relevant for the research presented in the manuscript. Cyclodextrin;
molecular mechanics; PM3.
Abbreviations and notations
Collect here in alphabetical order all abbreviations and
ANN, artificial neural network
CC, combinatorial chemistry
notations used in the paper
PLS, partial least squares
QSAR, quantitative structure-activity relationships
* Correspondence author; phone: 00-000-000-000; fax: 00-000-000-000; E-mail: author@uni.edu
Copyright © 2005 BioChem Press
Authors
Internet Electronic Journal of Molecular Design 2005, 4, 000–000
CL, combinatorial library
GA, genetic algorithm
QSPR, quantitative structure-property relationships
1 INTRODUCTION
Use this Word template to prepare the manuscript by closely following the instructions for
authors included here. The entire manuscript, including mathematical equations, chemical
structures, tables, and figures must be prepared in electronic form and submitted as Word for
Windows files. Use only fonts that come with Windows software. For the text use Times New
Roman size 12. For all special characters (e.g., Greek characters) use the font Symbol. Use carriage
returns only to end headings and paragraphs, not to break lines of text. Automatic hyphenation
should be turned off. Do not insert spaces before punctuation. Verify the correct spelling for the
final version with the Spelling and Grammar function of Word.
Primary headings are numbered, font size 14, centered, bold, and with all letters capitalized. The
headings from this template are
In the Introduction section present clearly and briefly the problem investigated, with relevant
references. The main results should be enunciated.
2 MATERIALS AND METHODS
Descriptions of chemical compounds, chemical databases, software, and algorithms should be
given in detail to enable qualified scientists to reproduce the results.
Simple mathematical notations and equations must be inserted as Word text, using Times New
Roman and Symbol fonts, and the appropriate style (italics or bold). For example: Uij, y2.
All complex mathematical equations must be prepared with the equation editor from Word and
placed in the proper place. Example:
N
N
W (G) =  Dij (G)
(1)
1 / [Dp ]ij if i  j
[RDp ]ij  
if i  j
 0
(2)
i 1 j i
HyWi(M, w, G) =

1 N N
[M( w)]ij 2  [M( w)]ij


2 i 1 j i

(3)
1
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Running title
Internet Electronic Journal of Molecular Design 2005, 4, 000–000
d ( w) ijp val( w) iq val( w) rj if i  j
[Dval( p, q, r , w)]ij  
q r
if i  j
Vw( w) i val( w) i
(4)
The equations are labeled in the order in which they appear in the text with Arabic numbers in
parentheses aligned to the left margin. In writing the equations use the following rules: vectors and
matrices with bold, functions such as log, sin, cos normal, and all other mathematical symbols with
italic.
2.1 Chemical Data
Secondary headings are numbered, font size 14, centered, bold, and with the first letter of each
main word capitalized.
Papers presenting QSPR or QSAR models must present in tables all compounds studied,
structural descriptors and the experimental, calculated and residual values for the physical,
chemical, or biological property. Complete information regarding the sources of experimental data
should be provided. Compounds that are not included in the final structure-property model must be
identified and explanations must be provided for their removal. Clustering and intercorrelation of
structural descriptors should be investigated. Comprehensive statistical data must be presented. All
QSPR and QSAR models must be tested with a cross-validation method. The molecular files for all
compounds must be deposited as an archive in the supplementary material. This can help other
researchers to verify the QSPR and QSAR models.
All chemical structures should be prepared with a suitable graphics program, such as:




ISIS/Draw from MDL Information Systems, http://www.mdli.com/
ACD/ChemSketch from Advanced Chemistry Development, http://www.acdlabs.com/
ChemWindow from SoftShell, http://www.softshell.com/
ChemDraw from CambridgeSoft, http://www.camsoft.com/
Use the following settings for chemical drawings:
text font
text size
standard bond/grid length
line width
stereo bond width
double/triple bond spacing
down bond hashes
Times New Roman
10 pt
16 pt
0.7 pt
2.0 pt
20% of width
2.5 pt
All compounds must be labeled with Arabic numbers, with font Times New Roman, size 10,
bold.
2
BioChem Press
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Authors
Internet Electronic Journal of Molecular Design 2005, 4, 000–000
2.2 Computer Software
Secondary headings are numbered, font size 14, centered, bold, and with the first letter of each
main word capitalized.
2.2.1 Quantum chemistry software
Tertiary headings are numbered, font size 12, centered, bold, and with the first letter of the
heading capitalized.
2.2.2 Neural network software
Tertiary headings are numbered, font size 12, centered, bold, and with the first letter of the
heading capitalized.
2.3 Clustering Algorithms
Secondary headings are numbered, font size 14, centered, bold, and with the first letter of each
main word capitalized.
3 RESULTS AND DISCUSSION
A clear presentation of all new results should be given, followed by a discussion of their
significance and relationships with previous knowledge in the field.
No
1
2
3
4
5
6
7
8
9
10
a0
-1.894
-1.995
-1.934
-2.161
-2.039
-2.022
-2.277
-2.765
-2.149
-2.051
a1
4.313
4.151
4.323
4.502
4.159
4.540
5.026
4.147
4.356
4.437
a2
0.014
0.014
0.015
0.012
0.016
0.013
0.014
0.009
0.013
0.014
Table 1. Example
a3
a4
a5
0.510
0.178 -10.045
0.489
-1.473 -10.621
8.037 -11.639
0.161
7.231 -12.742
0.124
8.010 -12.131
-1.405
0.636
0.261
5.380
0.619
0.172
-2.108
0.366 -13.808
0.731
0.580
0.188
-2.091
0.567
0.151 -12.007
r
0.919
0.917
0.916
0.916
0.916
0.916
0.915
0.915
0.915
0.915
s
0.516
0.522
0.523
0.525
0.526
0.526
0.526
0.526
0.526
0.527
F
394
383
382
378
377
376
376
376
376
374
Table 1. An empty table. To add a column, select a column and then select from the top menu line:
Table/Insert/Columns to the Left or Table/Insert/Columns to the Right. To add a row, select a row and then select from
the top menu line: Table/Insert/Rows above or Table/Insert/Rows below.
Column 1 Column 2 Column 3 Column 4 Column 5 Column 6 Column 7 Column 8
3
BioChem Press
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Running title
Internet Electronic Journal of Molecular Design 2005, 4, 000–000
1
2
3
Figure 1. Example. All figures and pictures must be IN LINE WITH TEXT: mouse right click on the picture, Format
picture/Layout/In line with text.
4 PRESENTATION OF QSAR MODELS
The biological data must be presented in detail, with special attention for the following aspects:
description of the biological data; how the experimental data were obtained; units for experimental
data from the original publication; references.
Previous QSAR studies developed for the same datasets must be referenced, described (including
statistical indices), and compared with the results from the paper.
The experimental data must be presented in a table in exactly the same format as published in the
original paper.
Consider the following situation: in the original paper the biological activity was IC50 expressed
in units of µg/ml; these values must be reported in a table. In the same table one must report also
IC50 expressed in units of mol/l, as well as pIC50 = log1/IC50 = -logIC50.
The computation of pIC50 = log1/IC50 = -logIC50 is presented below:
Step 1. transform IC50 from µg/ml to mol/l
Step 2. consider a value of 3.1 µmol/l = 3.1×10-6 mol/l
Step 3. compute pIC50 = -log IC50 = - (log 3.1×10-6) = - ( -5.51) = 5.51
Chemical compounds must be denoted by numbers in bold:
No
1
2
3
4
5
6
R
H
H
H
6–F
6–CF3
6–OCH3
R'
H
4–Cl
4–OCH3
H
H
H
R'
0
0.23
–0.27
0
0
0
MRR8
0.103
0.103
0.103
0.103
0.103
0.103
LR'4'
2.06
3.52
3.98
2.06
2.06
2.06
I
0
0
0
0
0
0
B5R
1
1
1
1.35
3.07
1
log 1/IC50
9.35
9.00
9.17
8.16
5.73
5.66
4
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Authors
Internet Electronic Journal of Molecular Design 2005, 4, 000–000
8–F
8–F
8–F
8–F
7
8
9
10
H
3–NH2
4–OCH3
4–OH
0
–0.16
–0.27
–0.37
0.092
0.092
0.092
0.092
2.06
2.06
3.98
2.74
0
0
0
0
1
1
1
1
9.54
9.26
9.48
9.34
Typically, classical QSAR models must be reported as in the following example:
n = 18
pIC50 =  2.528 (0.509) + 2.791 (0.426) Sav1  0.441 (0.235) pA
R = 0.864 %EV = 74.582 R2A = 0.712 F(2,15) = 22.007 p<0.001 SEE = 0.259
PRESS = 1.328 SSY = 2.980 R2CV = 0.554 SPRESS = 0.298 PSE = 0.272
(5)
All QSAR models must be cross-validated, using a k-fold cross-validation technique (usual
values for k are between 10 and 4, but lower values can be used).
5 CONCLUSIONS
The main results should be presented clearly and briefly, insisting on their significance and
degree of novelty.
Acknowledgment
The authors acknowledge the financial of this research by the XYZ Foundation. Use font Times New Roman size
10.
Supplementary Material
The molecular files for all compounds used in QSPR and QSAR models, must be deposited as an archive in the
supplementary material.
Extensive numerical results from molecular mechanics, quantum mechanics, or molecular dynamics computations
can be deposited as supplementary material.
Molecular files containing the geometry of important chemical species must be deposited as an archive in the
supplementary material.
Use font Times New Roman size 10.
Appendix 1
Write here the text for Appendix; delete this section if it does not apply. Use font Times New Roman size 10.
6 REFERENCES
[1]
[2]
[3]
[4]
Do not delete this template. Replace the examples presented here with your references. For the
REFERENCES section use the Bibliography style. References are presented as a numbered list. Use font Times
New Roman size 10. Substitute the references presented here as examples with your own references. To create a
new numbered reference press ENTER at the end of an existing reference. You can delete a reference, or
insert a new one. Follow the examples presented below for journal papers with one, two, or more authors, books,
edited books, chapters in a book.
H. Kubinyi, Variable Selection in QSAR Studies. I. An Evolutionary Algorithm, Quant. Struct.-Act. Relat. 1994,
13, 285-294.
M. V. Diudea, Cluj Matrix Invariants, J. Chem. Inf. Comput. Sci. 1997, 37, 300-305.
J. G. Topliss and R. P. Edwards, Chance Factors in Studies of Quantitative Structure-Activity Relationships, J.
5
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Running title
Internet Electronic Journal of Molecular Design 2005, 4, 000–000
[5]
[6]
[7]
[8]
[9]
[10]
[11]
[12]
[13]
[14]
[15]
Med. Chem. 1979, 22, 1238-1244.
R. P. Sheridan and S. K. Kearsley, Using a Genetic Algorithm to Suggest Combinatorial Libraries, J. Chem. Inf.
Comput. Sci. 1995, 35, 310-320
J. Sadowski and H. Kubinyi, A Scoring Scheme for Discriminating between Drugs and Nondrugs, J. Med. Chem.
1998, 41, 3325-3329.
W. Zheng, S. J. Cho, and A. Tropsha, Rational Design of a Targeted Combinatorial Chemical Library with
Opiatelike Activity, Int. J. Quantum Chem. 1998, 69, 65-75.
S. H. Yalkowsky, J. F. Krzyzaniak and P. B. Myrdal, Relationships between Melting Point and Boiling Point of
Organic Compounds, Ind. Eng. Chem. Res. 1994, 33, 1872-1877.
M. J. S. Dewar, E. G. Zoebisch, E. F. Healy and J. J. P. Stewart, AM1: A New General Purpose Quantum
Mechanical Molecular Model, J. Am. Chem. Soc. 1985, 107, 3902-3909.
M. A. Gallop, R. W. Barrett, W. J. Dower, S. P. A. Fodor, and E. M. Gordon, Application of Combinatorial
Technologies to Drug Discovery. 1. Background and Peptide Combinatorial Libraries, J. Med. Chem. 1994, 37,
1233-1251.
L. B. Kier and L. H. Hall, Molecular Connectivity in Structure-Activity Analysis, Research Studies Press,
Letchworth, 1986, pp. 20-25.
A. T. Balaban (Ed.), From Chemical Topology to Three-Dimensional Geometry, Plenum, New York, 1997.
M. V. Diudea (Ed.), QSPR/QSAR Studies by Molecular Descriptors, Nova Science, Huntington, N.Y., 2001.
H. Kubinyi, Comparative molecular field analysis (CoMFA); in: The Encyclopedia of Computational Chemistry,
Eds. P. v. R. Schleyer, N. L. Allinger, T. Clark, J. Gasteiger, P. A. Kollman, H. F. Schaefer III, and P. R.
Schreiner, John Wiley & Sons, Chichester, 1998, pp. 448-460.
S. C. Basak, Information Theoretic Indices of Neighborhood Complexity and Their Applications; in: Topological
Indices and Related Descriptors in QSAR and QSPR, Eds. J. Devillers and A. T. Balaban, Gordon and Breach
Science Publishers, Amsterdam, 1999, pp 563-593.
Biographies
First Author is assistant professor of medicinal chemistry at the University of XXXX. After obtaining a Ph.D.
degree in inorganic chemistry and mathematical modeling of ZZZ from the University of XXXX, Dr. YYY undertook
postdoctoral research with Professor ZZZ at the University of ZZZZ. More recently, Dr. YYY has collaborated on
projects with Professor XXX. You can include also: major research projects, scientific accomplishments,
extracurricular activities.
Second Author is computational chemist at …
Each author can insert here a short biography. Use font Times New Roman size 10.
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