Table of Contents

November 2004
Volume 44, Issue 6
Pages 1891-2226

About the Cover: Beginning in January 2005, the title of the journal will change to the Journal of Chemical Information and Modeling.

Beginning in January 2005, the title of the journal will change to the Journal of Chemical Information and Modeling.

For Selected Content:

ARTICLES
CHEMICAL INFORMATION

Molecules-in-Molecule Estimation of the Extent of Localization of Kekuléan Substructures in Polycyclic Aromatic Hydrocarbons

Tetsuo Morikawa, Susumu Narita, and Douglas J. Klein
pp 1891–1896
Publication Date (Web): September 25, 2004 ()
DOI: 10.1021/ci049894n

Combining Unsupervised and Supervised Artificial Neural Networks to PredictAquatic Toxicity

Giuseppina Gini, Marian Viorel Craciun, and Christoph KönigEmilio Benfenati
pp 1897–1902
Publication Date (Web): September 2, 2004 ()
DOI: 10.1021/ci0401219

Representation of the Molecular Topology of Cyclical Structures by Means of Cycle Graphs. 3. Hierarchical Model of Screening of Chemical Databases

Irene Luque Ruiz, Gonzalo Cerruela García, and Miguel Ángel Gómez-Nieto
pp 1903–1911
Publication Date (Web): August 31, 2004 ()
DOI: 10.1021/ci049889j

CHEMICAL COMPUTATION

Similarity to Molecules in the Training Set Is a Good Discriminator for Prediction Accuracy in QSAR

Robert P. Sheridan, Bradley P. Feuston, Vladimir N. Maiorov, and Simon K. Kearsley
pp 1912–1928
Publication Date (Web): October 7, 2004 ()
DOI: 10.1021/ci049782w

Accelerated K-Means Clustering in Metric Spaces

Andrew Smellie
pp 1929–1935
Publication Date (Web): September 30, 2004 ()
DOI: 10.1021/ci0499222

Active Learning with Support Vector Machine Applied to Gene Expression Data for Cancer Classification

Ying Liu
pp 1936–1941
Publication Date (Web): August 28, 2004 ()
DOI: 10.1021/ci049810a

Expanded Interaction Fingerprint Method for Analyzing Ligand Binding Modes in Docking and Structure-Based Drug Design

Matthew D. Kelly and Ricardo L. Mancera
pp 1942–1951
Publication Date (Web): October 1, 2004 (Article)
DOI: 10.1021/ci049870g

Computational Models for the Helix Tilt Angle

Yizong Cheng, Anping Liu, Yuping Guo, and Xiaoyang Qi
pp 1952–1960
Publication Date (Web): October 15, 2004 ()
DOI: 10.1021/ci049859g

Comparing Ligand Interactions with Multiple Receptors via Serial Docking

Miguel X. Fernandes, Visvaldas Kairys, and Michael K. Gilson
pp 1961–1970
Publication Date (Web): October 9, 2004 (Article)
DOI: 10.1021/ci049803m

Ensemble Methods for Classification in Cheminformatics

Christian Merkwirth, Harald Mauser, Tanja Schulz-Gasch, Olivier Roche, Martin Stahl, and Thomas Lengauer
pp 1971–1978
Publication Date (Web): October 13, 2004 ()
DOI: 10.1021/ci049850e

Quantitative Prediction of logk of Peptides in High-Performance Liquid Chromatography Based on Molecular Descriptors by Using the Heuristic Method and Support Vector Machine

H. X. Liu, C. X. Xue, R. S. Zhang, X. J. Yao, M. C. Liu, Z. D. Hu, and B. T. Fan
pp 1979–1986
Publication Date (Web): August 31, 2004 ()
DOI: 10.1021/ci049891a

Benzo[c]quinolizin-3-ones Theoretical Investigation:  SAR Analysis and Application to Nontested Compounds

S. F. Braga and D. S. Galvão
pp 1987–1997
Publication Date (Web): August 25, 2004 ()
DOI: 10.1021/ci049837u

A New Statistical Approach to Predicting Aromatic Hydroxylation Sites. Comparison with Model-Based Approaches

Yu. Borodina, A. Rudik, D. Filimonov, N. Kharchevnikova, A. Dmitriev, V. Blinova, and V. Poroikov
pp 1998–2009
Publication Date (Web): September 25, 2004 (Article)
DOI: 10.1021/ci049834h

Linear Indices of the “Molecular Pseudograph's Atom Adjacency Matrix”:  Definition, Significance-Interpretation, and Application to QSAR Analysis of Flavone Derivatives as HIV-1 Integrase Inhibitors

Yovani Marrero-Ponce
pp 2010–2026
Publication Date (Web): October 9, 2004 ()
DOI: 10.1021/ci049950k

Optimized Partition of Minimum Spanning Tree for Piecewise Modeling by Particle Swarm Algorithm. QSAR Studies of Antagonism of Angiotensin II Antagonists

Qi Shen, Jian-Hui Jiang, Chen-Xu Jiao, Shuang-Yan Huan, Guo-li Shen, and Ru-Qin Yu
pp 2027–2031
Publication Date (Web): August 25, 2004 (Article)
DOI: 10.1021/ci034292+

Similarity Search Profiling Reveals Effects of Fingerprint Scaling in Virtual Screening

Ling Xue, Florence L. Stahura, and Jürgen Bajorath
pp 2032–2039
Publication Date (Web): September 3, 2004 ()
DOI: 10.1021/ci0400819

Diagnosing Anorexia Based on Partial Least Squares, Back Propagation Neural Network, and Support Vector Machines

C. Y. Zhao, R. S. Zhang, H. X. Liu, C. X. Xue, S. G. Zhao, X. F. Zhou, M. C. Liu, and B. T. Fan
pp 2040–2046
Publication Date (Web): September 14, 2004 ()
DOI: 10.1021/ci049877y

Semiempirical Quantum Chemical Method and Artificial Neural Networks Applied for λmax Computation of Some Azo Dyes

Guo-Zheng Li, Jie Yang, Hai-Feng Song, Shang-Sheng Yang, Wen-Cong Lu, and Nian-Yi Chen
pp 2047–2050
Publication Date (Web): October 14, 2004 ()
DOI: 10.1021/ci049941b

EChem++An Object-Oriented Problem Solving Environment for Electrochemistry. 2. The Kinetic Facilities of EccoA Compiler for (Electro-)Chemistry

Kai Ludwig and Bernd Speiser
pp 2051–2060
Publication Date (Web): October 9, 2004 ()
DOI: 10.1021/ci0497814

Use of Classification Regression Tree in Predicting Oral Absorption in Humans

Jane P. F. Bai, Andrey Utis, Gordon Crippen, Han-Dan He, Volker Fischer, Robert Tullman, He-Qun Yin, Cheng-Pang Hsu, Lan Jiang, and Kin-Kai Hwang
pp 2061–2069
Publication Date (Web): October 22, 2004 ()
DOI: 10.1021/ci040023n

QSPR Using MOLGEN-QSPR:  The Example of Haloalkane Boiling Points

Christoph Rücker, Markus Meringer, and Adalbert Kerber
pp 2070–2076
Publication Date (Web): October 14, 2004 ()
DOI: 10.1021/ci049802u

How H-Bonding Affects Aromaticity of the Ring in Variously Substituted Phenol Complexes with Bases. 4. Molecular Geometry as a Source of Chemical Information

Tadeusz M. Krygowski, Halina Szatyłowicz, and Joanna E. Zachara
pp 2077–2082
Publication Date (Web): October 16, 2004 ()
DOI: 10.1021/ci049817s

Constructing Optimum Blood Brain Barrier QSAR Models Using a Combination of 4D-Molecular Similarity Measures and Cluster Analysis

Dahua Pan, Manisha Iyer, Jianzhong Liu, Yi Li, and Anton J. Hopfinger
pp 2083–2098
Publication Date (Web): October 7, 2004 ()
DOI: 10.1021/ci0498057

Quantitative Structure−Activity Relationship for Cyclic Imide Derivatives of Protoporphyrinogen Oxidase Inhibitors:  A Study of Quantum Chemical Descriptors from Density Functional Theory

Jian Wan, Li Zhang, Guangfu Yang, and Chang-Guo Zhan
pp 2099–2105
Publication Date (Web): October 13, 2004 (Article)
DOI: 10.1021/ci049793p

New Approach by Kriging Models to Problems in QSAR

Kai-Tai Fang, Hong Yin, and Yi-Zeng Liang
pp 2106–2113
Publication Date (Web): October 13, 2004 ()
DOI: 10.1021/ci049798m

An Extensive Test of 14 Scoring Functions Using the PDBbind Refined Set of 800 Protein−Ligand Complexes

Renxiao Wang, Yipin Lu, Xueliang Fang, and Shaomeng Wang
pp 2114–2125
Publication Date (Web): October 26, 2004 (Article)
DOI: 10.1021/ci049733j

MOLECULAR MODELING

Binding of Fatty Acids to β-Cryptogein:  Quantitative Structure−Activity Relationships and Design of Selective Protein Mutants

Petr Dobeš, Jan Kmuníek, Vladimír Mikeš, and Jiří Damborský
pp 2126–2132
Publication Date (Web): October 7, 2004 ()
DOI: 10.1021/ci049832x

Retrieval of Crystallographically-Derived Molecular Geometry Information

Ian J. Bruno, Jason C. Cole, Magnus Kessler, Jie Luo, W. D. Sam Motherwell, Lucy H. Purkis, Barry R. Smith, and Robin TaylorRichard I. CooperStephanie E. Harris and A. Guy Orpen
pp 2133–2144
Publication Date (Web): October 13, 2004 (Article)
DOI: 10.1021/ci049780b

BIOPHARMACEUTICAL CHEMISTRY

The Reduced Graph Descriptor in Virtual Screening and Data-Driven Clustering of High-Throughput Screening Data

G. Harper, G. S. Bravi, S. D. Pickett, J. Hussain, and D. V. S. Green
pp 2145–2156
Publication Date (Web): September 4, 2004 (Article)
DOI: 10.1021/ci049860f

Design and Characterization of Libraries of Molecular Fragments for Use in NMR Screening against Protein Targets

Nicolas Baurin, Fareed Aboul-Ela, Xavier Barril, Ben Davis, Martin Drysdale, Brian Dymock, Harry Finch, Christophe Fromont, Christine Richardson, Heather Simmonite, and Roderick E. Hubbard
pp 2157–2166
Publication Date (Web): October 9, 2004 (Article)
DOI: 10.1021/ci049806z

CoMFA 3D-QSAR Analysis of HIV-1 RT Nonnucleoside Inhibitors, TIBO Derivatives Based on Docking Conformation and Alignment

Zhigang Zhou and Jeffry D. Madura
pp 2167–2178
Publication Date (Web): September 17, 2004 (Article)
DOI: 10.1021/ci049893v

Development of Linear, Ensemble, and Nonlinear Models for the Prediction and Interpretation of the Biological Activity of a Set of PDGFR Inhibitors

Rajarshi Guha and Peter C. Jurs
pp 2179–2189
Publication Date (Web): September 14, 2004 ()
DOI: 10.1021/ci049849f

SitePrint:  Three-Dimensional Pharmacophore Descriptors Derived from Protein Binding Sites for Family Based Active Site Analysis, Classification, and Drug Design

James R. Arnold, Keith W. Burdick, Scott C.-H. Pegg, Samuel Toba, Michelle L. Lamb, and Irwin D. Kuntz
pp 2190–2198
Publication Date (Web): October 2, 2004 ()
DOI: 10.1021/ci049814f

REALISIS:  A Medicinal Chemistry-Oriented Reagent Selection, Library Design, and Profiling Platform

Aziz Yasri, Didier Berthelot, Harry Gijsen, Theo Thielemans, Patrick Marichal, Michael Engels, and Jan Hoflack
pp 2199–2206
Publication Date (Web): October 26, 2004 ()
DOI: 10.1021/ci049879i

Generalization of a Targeted Library Design Protocol:  Application to 5-HT7 Receptor Ligands

Erik Nordling and Evert Homan
pp 2207–2215
Publication Date (Web): October 7, 2004 ()
DOI: 10.1021/ci049822w

Application of Machine Learning To Improve the Results of High-Throughput Docking Against the HIV-1 Protease

Anthony E. Klon, Meir Glick, and John W. Davies
pp 2216–2224
Publication Date (Web): October 7, 2004 ()
DOI: 10.1021/ci0497861

COMPUTER SOFTWARE REVIEWS

ChemDraw 8 Ultra, Windows and Macintosh Versions

Loren D. Mendelsohn
pp 2225–2226
Publication Date (Web): September 28, 2004 ()
DOI: 10.1021/ci040123t
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