Volume 43, Number 1, January 2003
Chemical Information
- Pierre Hansen, Hadrien Mélot:
Variable Neighborhood Search for Extremal Graphs, 6. Analyzing Bounds for the Connectivity Index.
1-14
- Vladimir V. Diky, Robert D. Chirico, Randolph C. Wilhoit, Qian Dong, Michael Frenkel:
Windows-Based Guided Data Capture Software for Mass-Scale Thermophysical and Thermochemical Property Data Collection.
15-24
- Zina Ben-Miled, Yang Liu, David Powers, Omran A. Bukhres, Michael Bem, Robert Jones, Robert J. Oppelt:
An Efficient Implementation of a Drug Candidate Database.
25-35
- Artur Ratkiewicz, Thanh N. Truong:
Application of Chemical Graph Theory for Automated Mechanism Generation.
36-44
- Tibor Braun:
The Reliability of Total Citation Rankings.
45-46
- Jennifer L. Miller, Erin K. Bradley, Steven L. Teig:
Luddite: An Information-Theoretic Library Design Tool.
47-54
Chemical Computation
- Swati Puri, James S. Chickos, William J. Welsh:
Three-Dimensional Quantitative Structure-Property Relationship (3D-QSPR) Models for Prediction of Thermodynamic Properties of Polychlorinated Biphenyls (PCBs): Enthalpies of Fusion and Their Application to Estimates of Enthalpies of Sublimation and Aqueous Solubilities.
55-62
- Gustavo A. Arteca:
A Measure of Folding Complexity for D-Dimensional Polymers.
63-67
- Ned C. Haubein, Scott A. McMillan, Linda J. Broadbelt:
Many-Body Optimization Using an Ab Initio Monte Carlo Method.
68-74
- Ernesto Estrada, Humberto González:
What Are the Limits of Applicability for Graph Theoretic Descriptors in QSPR/QSAR? Modeling Dipole Moments of Aromatic Compounds with TOPS-MODE Descriptors.
75-84
- Denise Yaffe, Yoram Cohen, Gabriela Espinosa, Alex Arenas, Francesc Giralt:
A Fuzzy ARTMAP-Based Quantitative Structure-Property Relationship (QSPR) for the Henry's Law Constant of Organic Compounds.
85-112
- Tomoko Niwa:
Using General Regression and Probabilistic Neural Networks To Predict Human Intestinal Absorption with Topological Descriptors Derived from Two-Dimensional Chemical Structures.
113-119
- Corwin Hansch, Wayne E. Steinmetz, Albert J. Leo, Suresh Babu Mekapati, Alka Kurup, David Hoekman:
On the Role of Polarizability in Chemical-Biological Interactions.
120-125
- Tomas Edvinsson, Gustavo A. Arteca, Christer Elvingson:
Path-Space Ratio as a Molecular Shape Descriptor of Polymer Conformation.
126-133
- Benjamin C. P. Allen, Guy H. Grant, W. Graham Richards:
Calculation of Protein Domain Structural Similarity Using Two-Dimensional Representations.
134-143
- Alexander Golbraikh, Alexander Tropsha:
QSAR Modeling Using Chirality Descriptors Derived from Molecular Topology.
144-154
- Ola Engkvist, Paul Wrede, Ulrich Rester:
Prediction of CNS Activity of Compound Libraries Using Substructure Analysis.
155-160
- Biye Ren:
Atomic-Level-Based AI Topological Descriptors for Structure-Property Correlations.
161-169
- Patrick Bultinck, Ramon Carbó-Dorca:
Molecular Quantum Similarity Matrix Based Clustering of Molecules Using Dendrograms.
170-177
- M. Lawrence Ellzey Jr.:
Finite Group Theory for Large Systems. 1. Symmetry-Adaptation.
178-181
- Jeffrey W. Godden, John R. Furr, Jürgen Bajorath:
Recursive Median Partitioning for Virtual Screening of Large Databases.
182-188
- Les M. Sztandera, Mendel Trachtman, Charles Bock, Janardhan Velga, Ashish Garg:
Soft Computing in the Design of Nontoxic Chemicals.
189-198
- Rosalia Pascual, Marta Mateu, Johann Gasteiger, José I. Borrell, Jordi Teixidó:
Design and Analysis of a Combinatorial Library of HEPT Analogues: Comparison of Selection Methodologies and Inspection of the Actually Covered Chemical Space.
199-207
- Doron Chema, Amiram Goldblum:
The "Nearest Single Neighbor" Method-Finding Families of Conformations within a Sample.
208-217
- Miklos Feher, Jonathan M. Schmidt:
Property Distributions: Differences between Drugs, Natural Products, and Molecules from Combinatorial Chemistry.
218-227
- Vladimir Poroikov, Dmitrii Filimonov, Wolf-Dietrich Ihlenfeldt, Tatyana Gloriozova, Alexey Lagunin, Yulia V. Borodina, Alla Stepanchikova, Marc C. Nicklaus:
PASS Biological Activity Spectrum Predictions in the Enhanced Open NCI Database Browser.
228-236
- Robert Jäger, Stefan M. Kast, Jürgen Brickmann:
Parametrization Strategy for the MolFESD Concept: Quantitative Surface Representation of Local Hydrophobicity.
237-247
Molecular Modeling
Biopharmaceutical Chemistry
- Yongping Pan, Niu Huang, Sam Cho, Alexander D. MacKerell Jr.:
Consideration of Molecular Weight during Compound Selection in Virtual Target-Based Database Screening.
267-272
- Tingjun Hou, Lili Zhu, Lirong Chen, Xiaojie Xu:
Mapping the Binding Site of a Large Set of Quinazoline Type EGF-R Inhibitors Using Molecular Field Analyses and Molecular Docking Studies.
273-287
- Nathan Brown, Peter Willett, David J. Wilton, Richard A. Lewis:
Generation and Display of Activity-Weighted Chemical Hyperstructures.
288-297
- Tao Peng, Jianfeng Pei, Jiaju Zhou:
3D-QSAR and Receptor Modeling of Tyrosine Kinase Inhibitors with Flexible Atom Receptor Model (FLARM).
298-303
- Gerhard Bringmann, Christian Rummey:
3D QSAR Investigations on Antimalarial Naphthylisoquinoline Alkaloids by Comparative Molecular Similarity Indices Analysis (CoMSIA), Based on Different Alignment Approaches.
304-316
- Alberto Gobbi, Man-Ling Lee:
DISE: Directed Sphere Exclusion.
317-323
- Xuan Hong, Anton J. Hopfinger:
3D-Pharmacophores of Flavonoid Binding at the Benzodiazepine GABAA Receptor Site Using 4D-QSAR Analysis.
324-336
Volume 43, Number 2, March 2003
- Wendy A. Warr:
Sixth International Conference on Chemical Structures.
337
Chemical Information
Chemical Computation
- Peter Ertl:
Cheminformatics Analysis of Organic Substituents: Identification of the Most Common Substituents, Calculation of Substituent Properties, and Automatic Identification of Drug-like Bioisosteric Groups.
374-380
- Trudi Wright, Valerie J. Gillet, Darren V. S. Green, Stephen D. Pickett:
Optimizing the Size and Configuration of Combinatorial Libraries.
381-390
- Ansgar Schuffenhauer, Philipp Floersheim, Pierre Acklin, Edgar Jacoby:
Similarity Metrics for Ligands Reflecting the Similarity of the Target Proteins.
391-405
- John D. Holliday, Stephen P. Jelfs, Peter Willett, Peter Gedeck:
Calculation of Intersubstituent Similarity Using R-Group Descriptors.
406-411
- Ruth V. Spriggs, Peter J. Artymiuk, Peter Willett:
Searching for Patterns of Amino Acids in 3D Protein Structures.
412-421
- Patrick Bultinck, Wilfried Langenaeker, Ramon Carbó-Dorca, Jan P. Tollenaere:
Fast Calculation of Quantum Chemical Molecular Descriptors from the Electronegativity Equalization Method.
422-428
- Aixia Yan, Johann Gasteiger:
Prediction of Aqueous Solubility of Organic Compounds Based on a 3D Structure Representation.
429-434
- Naomie Salim, John D. Holliday, Peter Willett:
Combination of Fingerprint-Based Similarity Coefficients Using Data Fusion.
435-442
Biopharmaceutical Chemistry
- Nicholas Rhodes, Peter Willett, Alain Calvet, James B. Dunbar Jr., Christine Humblet:
CLIP: Similarity Searching of 3D Databases Using Clique Detection.
443-448
- Martin Whittle, Peter Willett, Werner Klaffke, Paula van Noort:
Evaluation of Similarity Measures for Searching the Dictionary of Natural Products Database.
449-457
- Edmond J. Abrahamian, Peter C. Fox, Lars Nærum, Inge Thøger Christensen, Henning Thøgersen, Robert D. Clark:
Efficient Generation, Storage, and Manipulation of Fully Flexible Pharmacophore Multiplets and Their Use in 3-D Similarity Searching.
458-468
- David J. Wilton, Peter Willett, Kevin Lawson, Graham Mullier:
Comparison of Ranking Methods for Virtual Screening in Lead-Discovery Programs.
469-474
Chemical Information
- Dimitris K. Agrafiotis, Huafeng Xu:
A Geodesic Framework for Analyzing Molecular Similarities.
475-484
- Paolo Mazzatorta, Marjan Vracko, Aneta Jezierska, Emilio Benfenati:
Modeling Toxicity by Using Supervised Kohonen Neural Networks.
485-492
- Christoph Steinbeck, Yongquan Han, Stefan Kuhn, Oliver Horlacher, Edgar Luttmann, Egon L. Willighagen:
The Chemistry Development Kit (CDK): An Open-Source Java Library for Chemo- and Bioinformatics.
493-500
- Hua Yuan, Chenzhong Cao:
Topological Indices Based on Vertex, Edge, Ring, and Distance: Application to Various Physicochemical Properties of Diverse Hydrocarbons.
501-512
Chemical Computation
- Paolo Mazzatorta, Emilio Benfenati, Ciprian-Daniel Neagu, Giuseppina C. Gini:
Tuning Neural and Fuzzy-Neural Networks for Toxicity Modeling.
513-518
- István László, André Rassat:
The Geometric Structure of Deformed Nanotubes and the Topological Coordinates.
519-524
- Weida Tong, Huixiao Hong, Hong Fang, Qian Xie, Roger Perkins:
Decision Forest: Combining the Predictions of Multiple Independent Decision Tree Models.
525-531
- Milan Randic, Alexandru T. Balaban:
On A Four-Dimensional Representation of DNA Primary Sequences.
532-539
- Yuji Takahata, Maria Cristina Andreazza Costa, Anderson Coser Gaudio:
Comparison between Neural Networks (NN) and Principal Component Analysis (PCA): Structure Activity Relationships of 1, 4-Dihydropyridine Calcium Channel Antagonists (Nifedipine Analogues).
540-544
- Errol F. McCoy, Matthew J. Sykes:
Quantum-Mechanical QSAR/QSPR Descriptors from Momentum-Space Wave Functions.
545-553
- Nolan E. Dean, Jeffrey E. Miller, Christopher J. Halkides, Michael Messina:
On the Possibility of Detecting Low Barrier Hydrogen Bonds with Kinetic Measurements.
554-559
- Andrey A. Toropov, T. Wayne Schultz:
Prediction of Aquatic Toxicity: Use of Optimization of Correlation Weights of Local Graph Invariants.
560-567
- David W. Miller:
A Chemical Class-Based Approach to Predictive Model Generation.
568-578
- Douglas M. Hawkins, Subhash C. Basak, Denise R. Mills:
Assessing Model Fit by Cross-Validation.
579-586
- Münevver Köküer, Fionn Murtagh, Norman D. McMillan, Sven Riedel, Brian O'Rourke, Katie Beverly, Andy T. Augousti, Julian Mason:
A Wavelet, Fourier, and PCA Data Analysis Pipeline: Application to Distinguishing Mixtures of Liquids.
587-594
- Michel Deza, Patrick W. Fowler, Mikhail Shtogrin:
Version of Zones and Zigzag Structure in Icosahedral Fullerenes and Icosadeltahedra.
595-599
- Chenzhong Cao, Hua Yuan:
A New Approach of Evaluating Bond Dissociation Energy from Eigenvalue of Bonding Orbital-Connection Matrix for C-C and C-H Bonds in Alkane.
600-608
- István Lukovits, Ante Graovac, Erika Kálmán, György Kaptay, Peter I. Nagy, Sonja Nikolic, Jaroslav Sytchev, Nenad Trinajstic:
Nanotubes: Number of Kekulé Structures and Aromaticity.
609-614
- Zhigang Zhou, Qianhuan Dai, Tong Gu:
A QSAR Model of PAHs Carcinogenesis Based on Thermodynamic Stabilities of Biactive Sites.
615-621
Molecular Modeling
Biopharmaceutical Chemistry
- M. Letizia Barreca, Rosaria Gitto, Silvana Quartarone, Laura De Luca, Giovambattista De Sarro, Alba Chimirri:
Pharmacophore Modeling as an Efficient Tool in the Discovery of Novel Noncompetitive AMPA Receptor Antagonists.
651-655
- Jaroslaw Polanski, Rafal Gieleciak:
The Comparative Molecular Surface Analysis (CoMSA) with Modified Uniformative Variable Elimination-PLS (UVE-PLS) Method: Application to the Steroids Binding the Aromatase Enzyme.
656-666
- Manfred K. Warmuth, Jun Liao, Gunnar Rätsch, Michael Mathieson, Santosh Putta, Christian Lemmen:
Active Learning with Support Vector Machines in the Drug Discovery Process.
667-673
- David T. Manallack, Benjamin G. Tehan, Emanuela Gancia, Brian D. Hudson, Martyn G. Ford, David J. Livingstone, David C. Whitley, Will R. Pitt:
A Consensus Neural Network-Based Technique for Discriminating Soluble and Poorly Soluble Compounds.
674-679
- Dragos Horvath, Catherine Jeandenans:
Neighborhood Behavior of in Silico Structural Spaces with Respect to in Vitro Activity Spaces-A Novel Understanding of the Molecular Similarity Principle in the Context of Multiple Receptor Binding Profiles.
680-690
- Dragos Horvath, Catherine Jeandenans:
Neighborhood Behavior of in Silico Structural Spaces with Respect to In Vitro Activity Spaces-A Benchmark for Neighborhood Behavior Assessment of Different in Silico Similarity Metrics.
691-698
- Scheila Furtado Braga, Douglas Soares Galvão:
A Structure-Activity Study of Taxol, Taxotere, and Derivatives Using the Electronic Indices Methodology (EIM).
699-706
Volume 43, Number 3, May 2003
Chemical Information
- Jean-Loup Faulon, Donald P. Visco Jr., Ramdas S. Pophale:
The Signature Molecular Descriptor. 1. Using Extended Valence Sequences in QSAR and QSPR Studies.
707-720
- Jean-Loup Faulon, Carla J. Churchwell, Donald P. Visco Jr.:
The Signature Molecular Descriptor. 2. Enumerating Molecules from Their Extended Valence Sequences.
721-734
- Hsi-Wu Wong, Xuegeng Li, Mark T. Swihart, Linda J. Broadbelt:
Encoding of Polycyclic Si-Containing Molecules for Determining Species Uniqueness in Automated Mechanism Generation.
735-742
- Suresh B. Singh, Richard D. Hull, Eugene M. Fluder:
Text Influenced Molecular Indexing (TIMI): A Literature Database Mining Approach that Handles Text and Chemistry.
743-752
- Feng Yang, Zhen-Dong Wang, Yun-Ping Huang, Xiu-Rong Ding, Pei-jiang Zhou:
Modification of Wiener Index and Its Application.
753-756
- Peter Murray-Rust, Henry S. Rzepa:
Chemical Markup, XML, and the World Wide Web. 4. CML Schema.
757-772
- Qian-Nan Hu, Yi-Zeng Liang, Ya-Li Wang, Cheng-Jian Xu, Zhong-Da Zeng, Kai-Tai Fang, Xiao-Ling Peng, Hong Yin:
External Factor Variable Connectivity Index.
773-778
- Christian J. A. Heidorn, Kirsten Rasmussen, Bjørn G. Hansen, Ole Nørager, Remi Allanou, René Seynaeve, Stefan Scheer, Dag Kappes, Roberta Bernasconi:
IUCLID: An Information Management Tool for Existing Chemicals and Biocides.
779-786
Chemical Computation
- Rudolf Kiralj, Márcia M. C. Ferreira:
On Heteroaromaticity of Nucleobases. Bond Lengths as Multidimensional Phenomena.
787-809
- Miklos Feher, Jonathan M. Schmidt:
Fuzzy Clustering as a Means of Selecting Representative Conformers and Molecular Alignments.
810-818
- John D. Holliday, Naomie Salim, Martin Whittle, Peter Willett:
Analysis and Display of the Size Dependence of Chemical Similarity Coefficients.
819-828
- Robert D. Clark, Julia Kar, Lakshmi B. Akella, Farhad Soltanshahi:
OptDesign: Extending Optimizable k-Dissimilarity Selection to Combinatorial Library Design.
829-836
- Darko Butina, Joelle M. R. Gola:
Modeling Aqueous Solubility.
837-841
- Gunnar Brinkmann, Gilles Caporossi, Pierre Hansen:
A Survey and New Results on Computer Enumeration of Polyhex and Fusene Hydrocarbons.
842-851
- Sergey V. Trepalin, Andrey V. Skorenko, Konstantin V. Balakin, Anatoly F. Nasonov, Stanley A. Lang, Andrey A. Ivashchenko, Nikolay P. Savchuk:
Advanced Exact Structure Searching in Large Databases of Chemical Compounds.
852-860
- Jan Cz. Dobrowolski, Aleksander P. Mazurek:
Model Carbyne Knots vs Ideal Knots.
861-869
- Li Xing, Robert C. Glen, Robert D. Clark:
Predicting pKa by Molecular Tree Structured Fingerprints and PLS.
870-879
- Grozdana Bogdani, Lajos Jakab:
Pearson-type I Distribution Function for Polydisperse Polymer Systems. Molar Mass Distribution.
880-884
- Su J. Patankar, Peter C. Jurs:
Classification of Inhibitors of Protein Tyrosine Phosphatase 1B Using Molecular Structure Based Descriptors.
885-899
- H. X. Liu, Ruisheng Zhang, F. Luan, X. J. Yao, Mancang Liu, Z. D. Hu, Bo Tao Fan:
Diagnosing Breast Cancer Based on Support Vector Machines.
900-907
- John W. Raymond, Peter Willett:
Similarity Searching in Databases of Flexible 3D Structures Using Smoothed Bounded Distance Matrices.
908-916
- Gunnar Brinkmann, Patrick W. Fowler, C. Justus:
A Catalogue of Isomerization Transformations of Fullerene Polyhedra.
917-927
- Clarimar José Coelho, Roberto Kawakami Harrop Galvão, Mário César Ugulino de Araújo, Maria Fernanda Pimentel, Edvan Cirino da Silva:
A Linear Semi-infinite Programming Strategy for Constructing Optimal Wavelet Transforms in Multivariate Calibration Problems.
928-933
- Simona Funar-Timofei, Takahiro Suzuki, Joachim A. Paier, Andreas Steinreiber, Kurt Faber, Walter M. F. Fabian:
Quantitative Structure-Activity Relationships for the Enantioselectivity of Oxirane Ring-Opening Catalyzed by Epoxide Hydrolases.
934-940
- A. Michiel van Rhee:
Use of Recursion Forests in the Sequential Screening Process: Consensus Selection by Multiple Recursion Trees.
941-948
- Brian E. Mattioni, Gregory W. Kauffman, Peter C. Jurs, Laura L. Custer, Stephen K. Durham, Greg M. Pearl:
Predicting the Genotoxicity of Secondary and Aromatic Amines Using Data Subsetting To Generate a Model Ensemble.
949-963
Molecular Modeling
Biopharmaceutical Chemistry
- Wolfgang H. B. Sauer, Matthias K. Schwarz:
Molecular Shape Diversity of Combinatorial Libraries: A Prerequisite for Broad Bioactivity.
987-1003
- Eugene Myshkin, Bingcheng Wang:
Chemometrical Classification of Ephrin Ligands and Eph Kinases Using GRID/CPCA Approach.
1004-1010
- Xiao-Qin Xia, Michael J. Wise:
DiMSim: A Discrete-Event Simulator of Metabolic Networks.
1011-1019
- Jonas Boström, Markus Böhm, Klaus Gundertofte, Gerhard Klebe:
A 3D QSAR Study on a Set of Dopamine D4 Receptor Antagonists.
1020-1027
- Jeffrey J. Sutherland, Donald F. Weaver:
Development of Quantitative Structure-Activity Relationships and Classification Models for Anticonvulsant Activity of Hydantoin Analogues.
1028-1036
- Robert P. Sheridan:
Finding Multiactivity Substructures by Mining Databases of Drug-Like Compounds.
1037-1050
- Bo Kyeng Hou, Lawrence P. Wackett, Lynda B. M. Ellis:
Microbial Pathway Prediction: A Functional Group Approach.
1051-1057
- T. J. Hou, X. J. Xu:
ADME Evaluation in Drug Discovery. 2. Prediction of Partition Coefficient by Atom-Additive Approach Based on Atom-Weighted Solvent Accessible Surface Areas.
1058-1067
- Yiyu Cheng, Minjun Chen, Weida Tong:
An Approach to Comparative Analysis of Chromatographic Fingerprints for Assuring the Quality of Botanical Drugs.
1068-1076
- Jörg K. Wegner, Andreas Zell:
Prediction of Aqueous Solubility and Partition Coefficient Optimized by a Genetic Algorithm Based Descriptor Selection Method.
1077-1084
Volume 43, Number 4, July 2003
Chemical Computation
- Gil Benkö, Christoph Flamm, Peter F. Stadler:
A Graph-Based Toy Model of Chemistry.
1085-1093
- Bono Lucic, Damir Nadramija, Ivan Basic, Nenad Trinajstic:
Toward Generating Simpler QSAR Models: Nonlinear Multivariate Regression versus Several Neural Network Ensembles and Some Related Methods.
1094-1102
- Subhash C. Basak, Krishnan Balasubramanian, Brian D. Gute, Denise R. Mills, Anna Gorczynska, Szczepan Roszak:
Prediction of Cellular Toxicity of Halocarbons from Computed Chemodescriptors: A Hierarchical QSAR Approach.
1103-1109
- István Lukovits, Nenad Trinajstic:
Atomic Walk Counts of Negative Order.
1110-1114
- Gerta Rücker, Christoph Rücker:
Walking Backward: Walk Counts of Negative Order.
1115-1120
- Biye Ren:
Atom-Type-Based AI Topological Descriptors: Application in Structure-Boiling Point Correlations of Oxo Organic Compounds.
1121-1131
- Qing-zhang Lü, Jian-Hui Jiang, Ru-Qin Yu, Guo-Li Shen:
A Genetic Algorithm Based on Prepotency Evolution Using Chaotic Initiation Used for Network Training.
1132-1137
- Bo Liao, Tian-Ming Wang:
General Combinatorics of RNA Hairpins and Cloverleaves.
1138-1142
- Patrick Bultinck, Tom Kuppens, Xavier Gironés, Ramon Carbó-Dorca:
Quantum Similarity Superposition Algorithm (QSSA): A Consistent Scheme for Molecular Alignment and Molecular Similarity Based on Quantum Chemistry.
1143-1150
- Ling Xue, Jeffrey W. Godden, Florence L. Stahura, Jürgen Bajorath:
Design and Evaluation of a Molecular Fingerprint Involving the Transformation of Property Descriptor Values into a Binary Classification Scheme.
1151-1157
- Michael P. Barnett:
Transformation of Harmonics for Molecular Calculations.
1158-1165
- Ana Gallegos Saliner, Lluís Amat, Ramon Carbó-Dorca, T. Wayne Schultz, Mark T. D. Cronin:
Molecular Quantum Similarity Analysis of Estrogenic Activity.
1166-1176
- Christel A. S. Bergström, Ulf Norinder, Kristina Luthman, Per Artursson:
Molecular Descriptors Influencing Melting Point and Their Role in Classification of Solid Drugs.
1177-1185
- Huafeng Xu, Sergei Izrailev, Dimitris K. Agrafiotis:
Conformational Sampling by Self-Organization.
1186-1191
- Maykel Pérez González, Humberto González Díaz, Reinaldo Molina Ruiz, Miguel A. Cabrera, Ronal Ramos de Armas:
TOPS-MODE Based QSARs Derived from Heterogeneous Series of Compounds. Applications to the Design of New Herbicides.
1192-1199
- Latifa Douali, Didier Villemin, Driss Cherqaoui:
Neural Networks: Accurate Nonlinear QSAR Model for HEPT Derivatives.
1200-1207
- Patrick Bultinck, Ramon Carbó-Dorca, Christian Van Alsenoy:
Quality of Approximate Electron Densities and Internal Consistency of Molecular Alignment Algorithms in Molecular Quantum Similarity.
1208-1217
- Ling Xue, Jeffrey W. Godden, Florence L. Stahura, Jürgen Bajorath:
Profile Scaling Increases the Similarity Search Performance of Molecular Fingerprints Containing Numerical Descriptors and Structural Keys.
1218-1225
- Eduardo J. Delgado, Joel B. Alderete:
Prediction of Henry's Law Constants of Triazine Derived Herbicides from Quantum Chemical Continuum Solvation Models.
1226-1230
- Jorge Gálvez:
Prediction of Molecular Volume and Surface of Alkanes by Molecular Topology.
1231-1239
Molecular Modeling
Biopharmaceutical Chemistry
- Martin G. Grigorov, Hedwig Schlichtherle-Cerny, Michael Affolter, Sunil Kochhar:
Design of Virtual Libraries of Umami-Tasting Molecules.
1248-1258
- Ilie Fishtik, Ravindra Datta:
A Stoichiometric Approach to Quantitative Structure-Property Relationships (QSPR).
1259-1268
- Yuji Takaoka, Yutaka Endo, Susumu Yamanobe, Hiroyuki Kakinuma, Taketoshi Okubo, Youichi Shimazaki, Tomomi Ota, Shigeyuki Sumiya, Kensei Yoshikawa:
Development of a Method for Evaluating Drug-Likeness and Ease of Synthesis Using a Data Set in Which Compounds Are Assigned Scores Based on Chemists' Intuition.
1269-1275
- Helen M. McSparron, Martin J. Blythe, Christianna Zygouri, Irini A. Doytchinova, Darren R. Flower:
JenPep: A Novel Computational Information Resource for Immunobiology and Vaccinology.
1276-1287
- H. X. Liu, Ruisheng Zhang, X. J. Yao, Mancang Liu, Z. D. Hu, Bo Tao Fan:
QSAR Study of Ethyl 2-[(3-Methyl-2, 5-dioxo(3-pyrrolinyl))amino]-4-(trifluoromethyl) pyrimidine-5-carboxylate: An Inhibitor of AP-1 and NF-B Mediated Gene Expression Based on Support Vector Machines.
1288-1296
- Craig L. Senese, Anton J. Hopfinger:
Receptor-Independent 4D-QSAR Analysis of a Set of Norstatine Derived Inhibitors of HIV-1 Protease.
1297-1307
- Roberta Susnow, Steven L. Dixon:
Use of Robust Classification Techniques for the Prediction of Human Cytochrome P450 2D6 Inhibition.
1308-1315
- Miklos Feher, Eugen Deretey, Samir Roy:
BHB: A Simple Knowledge-Based Scoring Function to Improve the Efficiency of Database Screening.
1316-1327
- Bahram Hemmateenejad, Morteza Akhond, Ramin Miri, Mojtaba Shamsipur:
Genetic Algorithm Applied to the Selection of Factors in Principal Component-Artificial Neural Networks: Application to QSAR Study of Calcium Channel Antagonist Activity of 1, 4-Dihydropyridines (Nifedipine Analogous).
1328-1334
Errata
- Xavier Gironés, Ramon Carbó-Dorca:
Molecular Quantum Similarity-Based QSARs for Binding Affinities of Several Steroid Sets J. Chem. Inf. Comput. Sci. 42, 1185-1193 (2002).
1335-1336
Volume 43, Number 5, September 2003
Chemical Information
Chemical Computation
- Philip N. Judson, Jonathan D. Vessey:
A Comprehensive Approach to Argumentation.
1356-1363
- Philip N. Judson, Carol A. Marchant, Jonathan D. Vessey:
Using Argumentation for Absolute Reasoning about the Potential Toxicity of Chemicals.
1364-1370
- William G. Button, Philip N. Judson, Anthony Long, Jonathan D. Vessey:
Using Absolute and Relative Reasoning in the Prediction of the Potential Metabolism of Xenobiotics.
1371-1377
- Irene Luque Ruiz, Gonzalo Cerruela García, Miguel Ángel Gómez-Nieto:
Computer-Assisted Learning Using a Dialogue System for Virtual Teacher-Student Communication.
1378-1389
- Masamoto Arakawa, Kiyoshi Hasegawa, Kimito Funatsu:
Novel Alignment Method of Small Molecules Using the Hopfield Neural Network.
1390-1395
- Masamoto Arakawa, Kiyoshi Hasegawa, Kimito Funatsu:
Application of the Novel Molecular Alignment Method Using the Hopfield Neural Network to 3D-QSAR.
1396-1402
- Jorge F. Magallanes, Jure Zupan, Darío Gomez, Silvia Reich, Laura Dawidowski, Neva Groselj:
The Mean Angular Distance Among Objects and Its Relationships with Kohonen Artificial Neural Networks.
1403-1411
- Suwipa Saen-oon, Supa Hannongbua, Peter Wolschann:
Structural Flexibility of Non-Nucleoside HIV-1 Reverse Transcriptase Inhibitor: 9-Cl TIBO as Explained by Potential Energy Surface and 13C and 1H NMR Calculations, Based on ab initio and Density Functional Study.
1412-1422
- David T. Stanton:
On the Physical Interpretation of QSAR Models.
1423-1433
- Andrey A. Korytko, Klaus-Peter Schulz, Mark S. Madison, Morton E. Munk:
HOUDINI: A New Approach to Computer-Based Structure Generation.
1434-1446
- Klaus-Peter Schulz, Andrey A. Korytko, Morton E. Munk:
Applications of a HOUDINI-Based Structure Elucidation System.
1447-1456
- Jarmo Huuskonen:
Prediction of Soil Sorption Coefficient of a Diverse Set of Organic Chemicals From Molecular Structure.
1457-1462
- Jun Feng, Laura Lurati, Haojun Ouyang, Tracy Robinson, Yuanyuan Wang, Shenglan Yuan, S. Stanley Young:
Predictive Toxicology: Benchmarking Molecular Descriptors and Statistical Methods.
1463-1470
- Dorte B. Lerche, Peter B. Sørensen, Rainer Brüggemann:
Improved Estimation of the Ranking Probabilities in Partial Orders Using Random Linear Extensions by Approximation of the Mutual Ranking Probability.
1471-1480
- M. Michael Gromiha:
Importance of Native-State Topology for Determining the Folding Rate of Two-State Proteins.
1481-1485
- Marko Golicnik, Jure Stojan:
Generalized Theoretical and Practical Treatment of the Kinetics of an Enzyme-Catalyzed Reaction in the Presence of an Enzyme Equimolar Irreversible Inhibitor.
1486-1493
- Jerry Ray Dias:
Disjoint Molecular Orbitals in Nonalternant Conjugated Diradical Hydrocarbons.
1494-1501
Molecular Modeling
Biopharmaceutical Chemistry
- Branimir Bertosa, Biserka Kojic-Prodic, Rebecca C. Wade, Michael Ramek, Stavroula Piperaki, Anna Tsantili-Kakoulidou, Sanja Tomic:
A New Approach To Predict the Biological Activity of Molecules Based on Similarity of Their Interaction Fields and the logP and logD Values: Application to Auxins.
1532-1541
- Fabio Zuccotto:
Pharmacophore Features Distributions in Different Classes of Compounds.
1542-1552
- Konstantin V. Balakin, Stanley A. Lang, Andrey V. Skorenko, Sergey E. Tkachenko, Andrey A. Ivashchenko, Nikolay P. Savchuk:
Structure-Based versus Property-Based Approaches in the Design of G-Protein-Coupled Receptor-Targeted Libraries.
1553-1562
- Julius Sipilä, Alan M. Hood, Michael W. H. Coughtrie, Jyrki Taskinen:
CoMFA Modeling of Enzyme Kinetics: Km Values for Sulfation of Diverse Phenolic Substrates by Human Catecholamine Sulfotransferase SULT1A3.
1563-1569
- Taesung Moon, Jin-Soo Song, Jin Kak Lee, Chang No Yoon:
QSAR Analysis of SH2-Binding Phosphopeptides: Using Interaction Energies and Cross-Correlation Coefficients.
1570-1575
- Csaba Hetényi, Uko Maran, Mati Karelson:
A Comprehensive Docking Study on the Selectivity of Binding of Aromatic Compounds to Proteins.
1576-1583
- Mayuso Kuno, Rungtiva Palangsuntikul, Supa Hannongbua:
Investigation on an Orientation and Interaction Energy of the Water Molecule in the HIV-1 Reverse Transcriptase Active Site by Quantum Chemical Calculations.
1584-1590
- Dahua Pan, Yufeng J. Tseng, Anton J. Hopfinger:
Quantitative Structure-Based Design: Formalism and Application of Receptor-Dependent RD-4D-QSAR Analysis to a Set of Glucose Analogue Inhibitors of Glycogen Phosphorylase.
1591-1607
- Thomas P. Stockfisch:
Partially Unified Multiple Property Recursive Partitioning (PUMP-RP): A New Method for Predicting and Understanding Drug Selectivity.
1608-1613
- Shashidhar N. Rao, Thomas P. Stockfisch:
Partially Unified Multiple Property Recursive Partitioning (PUMP-RP) Analyses of Cyclooxygenase (COX) Inhibitors.
1614-1622
- Santosh Putta, John Eksterowicz, Christian Lemmen, Robert Stanton:
A Novel Subshape Molecular Descriptor.
1623-1635
- Yulia V. Borodina, A. Sadym, Dmitrii Filimonov, V. Blinova, A. Dmitriev, Vladimir Poroikov:
Predicting Biotransformation Potential from Molecular Structure.
1636-1646
- Corwin Hansch, Alka Kurup:
QSAR of Chemical Polarizability and Nerve Toxicity. 2.
1647-1651
- Kenneth A. Marx, Philip O'Neil, Patrick Hoffman, M. L. Ujwal:
Data Mining the NCI Cancer Cell Line Compound GI50 Values: Identifying Quinone Subtypes Effective Against Melanoma and Leukemia Cell Classes.
1652-1667
- Jian Shen:
HAD: An Automated Database Tool for Analyzing Screening Hits in Drug Discovery.
1668-1672
- Steven M. Muskal, Sanjiv Kumar Jha, M. Phani Kishore, Prashant Tyagi:
A Simple and Readily Integratable Approach to Toxicity Prediction.
1673-1678
- Shijin Ren:
Modeling the Toxicity of Aromatic Compounds to Tetrahymena pyriformis: The Response Surface Methodology with Nonlinear Methods.
1679-1687
- Miguel Murcia-Soler, Facundo Pérez-Giménez, Francisco J. García-March, M. Teresa Salabert-Salvador, Wladimiro Díaz Villanueva, María José Castro Bleda:
Drugs and Nondrugs: An Effective Discrimination with Topological Methods and Artificial Neural Networks.
1688-1702
- Vitaly P. Solov'ev, Alexandre Varnek:
Anti-HIV Activity of HEPT, TIBO, and Cyclic Urea Derivatives: Structure-Property Studies, Focused Combinatorial Library Generation, and Hits Selection Using Substructural Molecular Fragments Method.
1703-1719
Book Reviews
- Anselm H. C. Horn:
Essentials of Computational Chemistry, Theories and Models By Christopher J. Cramer. Wiley 2002, ISBN 0-471-48551-9.
1720-1720
- Ivan Gutman:
QSPR/QSAR Studies by Molecular Descriptors By Mircea V. Diudea. Nova Science Publishers 2001, ISBN 1-5672-859-0.
1720-1721
- Robert E. Buntrock:
Library Handbook for Organic Chemists By Andrew Poss. Chemical Publishing 2000, ISBN 0-8206-0361-9.
1721-1722
- D. J. Klein:
Applied Finite Group Actions By Adalbert Kerber. Springer-Verlag 1999, ISBN 35-4065-9412.
1722-1723
Errata
- Milan Randic, Alexandru T. Balaban:
On a Four-Dimensional Representation of DNA Primary Sequences [Journal of Chemical Information and Computer Sciences 43, 532-539 (2003)].
1724-1724
Volume 43, Number 6, November 2003
Chemical Information
Chemical Computation
- Jaroslaw Polanski, Rafal Gieleciak, Miroslaw Wyszomirski:
Comparative Molecular Surface Analysis (CoMSA) for Modeling Dye-Fiber Affinities of the Azo and Anthraquinone Dyes.
1754-1762
- M. Lawrence Ellzey Jr., Dino Villagran:
Finite Group Theory for Large Systems. 2. Generating Relations and Irreducible Representations for the Icosahedral Point Group, h.
1763-1770
- Rainer Brüggemann, Gerhard Welzl, Kristina Voigt:
Order Theoretical Tools for the Evaluation of Complex Regional Pollution Patterns.
1771-1779
- Samuli-Petrus Korhonen, Kari Tuppurainen, Reino Laatikainen, Mikael Peräkylä:
FLUFF-BALL, A Template-Based Grid-Independent Superposition and QSAR Technique: Validation Using a Benchmark Steroid Data Set.
1780-1793
- Alan R. Katritzky, Alexander A. Oliferenko, Polina V. Oliferenko, Ruslan Petrukhin, Douglas B. Tatham, Uko Maran, Andre Lomaka, William E. Acree Jr.:
A General Treatment of Solubility. 1. The QSPR Correlation of Solvation Free Energies of Single Solutes in Series of Solvents.
1794-1805
- Alan R. Katritzky, Alexander A. Oliferenko, Polina V. Oliferenko, Ruslan Petrukhin, Douglas B. Tatham, Uko Maran, Andre Lomaka, William E. Acree Jr.:
A General Treatment of Solubility. 2. QSPR Prediction of Free Energies of Solvation of Specified Solutes in Ranges of Solvents.
1806-1814
- V. Kozic, L. C. Lipus:
Magnetic Water Treatment for a Less Tenacious Scale.
1815-1819
- Scott A. McMillan, Ned C. Haubein, Randall Q. Snurr, Linda J. Broadbelt:
Ab Initio Stochastic Optimization of Conformational and Many-Body Degrees of Freedom.
1820-1828
- Rozália Vanyúr, Károly Héberger, Judit Jakus:
Prediction of Anti-HIV-1 Activity of a Series of Tetrapyrrole Molecules.
1829-1836
- Gunnar Brinkmann, Patrick W. Fowler:
A Catalogue of Growth Transformations of Fullerene Polyhedra.
1837-1843
- Danko Milosevic, Danica Batinic, Pasko Konjevoda, Nenad Blau, Nikola Stambuk, Ljiljana Nizic, Kristina Vrljicak, Danko Batinic:
Analysis of Calcium, Oxalate, and Citrate Interaction in Idiopathic Calcium Urolithiasis in Children.
1844-1847
- Yuan H. Zhao, Michael H. Abraham, Andreas M. Zissimos:
Determination of McGowan Volumes for Ions and Correlation with van der Waals Volumes.
1848-1854
- Peter Lind, Tatiana Maltseva:
Support Vector Machines for the Estimation of Aqueous Solubility.
1855-1859
- Elena V. Konstantinova, Maxim V. Vidyuk:
Discriminating Tests of Information and Topological Indices. Animals and Trees.
1860-1871
- Wenbin Liu, Lin Gao, Xiangrong Liu, Shudong Wang, Jin Xu:
Solving the 3-SAT Problem Based on DNA Computing.
1872-1875
- Chen Jiang, Yougui Li, Qingshan Tian, Tianpa You:
QSAR Study of Catalytic Asymmetric Reactions with Topological Indices.
1876-1881
- Evgeny Byvatov, Uli Fechner, Jens Sadowski, Gisbert Schneider:
Comparison of Support Vector Machine and Artificial Neural Network Systems for Drug/Nondrug Classification.
1882-1889
- Barry K. Lavine, Charles E. Davidson, Curt M. Breneman, William P. Katt:
Electronic van der Waals Surface Property Descriptors and Genetic Algorithms for Developing Structure-Activity Correlations in Olfactory Databases.
1890-1905
- Jeffrey J. Sutherland, Lee A. O'Brien, Donald F. Weaver:
Spline-Fitting with a Genetic Algorithm: A Method for Developing Classification Structure-Activity Relationships.
1906-1915
- S. Stanley Young, Marcia Wang, Fei Gu:
Design of Diverse and Focused Combinatorial Libraries Using an Alternating Algorithm.
1916-1921
- Dusanka Janezic, Matej Praprotnik:
Molecular Dynamics Integration Time Step Dependence of the Split Integration Symplectic Method on System Density.
1922-1927
- Eduardo J. Delgado, Joel B. Alderete, Gonzalo A. Jaña:
A Simple QSPR Model for Predicting Soil Sorption Coefficients of Polar and Nonpolar Organic Compounds from Molecular Formula.
1928-1932
- Huafeng Xu, Dimitris K. Agrafiotis:
Nearest Neighbor Search in General Metric Spaces Using a Tree Data Structure with a Simple Heuristic.
1933-1941
- Gordon G. Cash:
Immanants and Immanantal Polynomials of Chemical Graphs.
1942-1946
- Vladimir Svetnik, Andy Liaw, Christopher Tong, J. Christopher Culberson, Robert P. Sheridan, Bradley P. Feuston:
Random Forest: A Classification and Regression Tool for Compound Classification and QSAR Modeling.
1947-1958
- Yiyu Cheng, Minjun Chen, William J. Welsh:
Fractal Fingerprinting of Chromatographic Profiles Based on Wavelet Analysis and Its Application To Characterize the Quality Grade of Medicinal Herbs.
1959-1965
- Cyril Ruckebusch, Ludovic Duponchel, Bernard Sombret, Jean-Pierre Huvenne, Javier Saurina:
Time-Resolved Step-Scan FT-IR Spectroscopy: Focus on Multivariate Curve Resolution.
1966-1973
- Arja Asikainen, Juhani Ruuskanen, Kari Tuppurainen:
Spectroscopic QSAR Methods and Self-Organizing Molecular Field Analysis for Relating Molecular Structure and Estrogenic Activity.
1974-1981
- Michael K. Gilson, Hillary S. R. Gilson, Michael J. Potter:
Fast Assignment of Accurate Partial Atomic Charges: An Electronegativity Equalization Method that Accounts for Alternate Resonance Forms.
1982-1997
- Chunsheng Yang, Chongli Zhong:
Modified Connectivity Indices and Their Application to QSPR Study.
1998-2004
- Yong Feng, Lei Liu, Jin-Ti Wang, Hao Huang, Qing-Xiang Guo:
Assessment of Experimental Bond Dissociation Energies Using Composite ab Initio Methods and Evaluation of the Performances of Density Functional Methods in the Calculation of Bond Dissociation Energies.
2005-2013
- Wenbin Liu, Shudong Wang, Lin Gao, Fengyue Zhang, Jin Xu:
DNA Sequence Design Based on Template Strategy.
2014-2018
- Michael J. Sorich, John O. Miners, Ross A. McKinnon, David A. Winkler, Frank R. Burden, Paul A. Smith:
Comparison of Linear and Nonlinear Classification Algorithms for the Prediction of Drug and Chemical Metabolism by Human UDP-Glucuronosyltransferase Isoforms.
2019-2024
- P. M. Kroonenberg, William J. Dunn, J. J. F. Commandeur:
Consensus Molecular Alignment Based on Generalized Procrustes Analysis.
2025-2032
- Xavier Gironés, Ramon Carbó-Dorca, Robert Ponec:
Molecular Basis of LFER. Modeling of the Electronic Substituent Effect Using Fragment Quantum Self-Similarity Measures.
2033-2038
- Artem Cherkasov:
Inductive Electronegativity Scale. Iterative Calculation of Inductive Partial Charges.
2039-2047
- Vladimir V. Zernov, Konstantin V. Balakin, Andrey A. Ivaschenko, Nikolay P. Savchuk, Igor V. Pletnev:
Drug Discovery Using Support Vector Machines. The Case Studies of Drug-likeness, Agrochemical-likeness, and Enzyme Inhibition Predictions.
2048-2056
- Ludovic Duponchel, Waiss Elmi-Rayaleh, Cyril Ruckebusch, Jean-Pierre Huvenne:
Multivariate Curve Resolution Methods in Imaging Spectroscopy: Influence of Extraction Methods and Instrumental Perturbations.
2057-2067
- Kerby Shedden, Julie Brumer, Young Tae Chang, Gustavo R. Rosania:
Chemoinformatic Analysis of a Supertargeted Combinatorial Library of Styryl Molecules.
2068-2080
Molecular Modeling
- Jaroslaw Polanski, Andrzej Bak:
Modeling Steric and Electronic Effects in 3D- and 4D-QSAR Schemes: Predicting Benzoic pKa Values and Steroid CBG Binding Affinities.
2081-2092
Biopharmaceutical Chemistry
- Viera Lukacova, Stefan Balaz:
Multimode Ligand Binding in Receptor Site Modeling: Implementation in CoMFA.
2093-2105
- Shijin Ren, Hyunjoong Kim:
Comparative Assessment of Multiresponse Regression Methods for Predicting the Mechanisms of Toxic Action of Phenols.
2106-2110
- Nathan R. McElroy, E. D. Thompson, Peter C. Jurs:
Classification of Diverse Organic Compounds That Induce Chromosomal Aberrations in Chinese Hamster Cells.
2111-2119
- L. Mark Hall, Lowell H. Hall, Lemont B. Kier:
Modeling Drug Albumin Binding Affinity with E-State Topological Structure Representation.
2120-2128
- Juan M. Luco, Adriana P. Salinas, Angel A. J. Torriero, Rodolfo Nieto Vázquez, Julio Raba, Eduardo Marchevsky:
Immobilized Artificial Membrane Chromatography: Quantitative Structure-Retention Relationships of Structurally Diverse Drugs.
2129-2136
- Tingjun Hou, Xiaojie Xu:
ADME Evaluation in Drug Discovery. 3. Modeling Blood-Brain Barrier Partitioning Using Simple Molecular Descriptors.
2137-2152
- Karsten H. Siegmund, Ulrich E. Steiner, Clemens Richert:
ChipCheck-A Program Predicting Total Hybridization Equilibria for DNA Binding to Small Oligonucleotide Microarrays.
2153-2162
- J. Kevin Lanctot, Santosh Putta, Christian Lemmen, Jonathan Greene:
Using Ensembles to Classify Compounds for Drug Discovery.
2163-2169
- Jianzhong Liu, Dahua Pan, Yufeng J. Tseng, Anton J. Hopfinger:
4D-QSAR Analysis of a Series of Antifungal P450 Inhibitors and 3D-Pharmacophore Comparisons as a Function of Alignment.
2170-2179
- Craig L. Senese, Anton J. Hopfinger:
A Simple Clustering Technique To Improve QSAR Model Selection and Predictivity: Application to a Receptor Independent 4D-QSAR Analysis of Cyclic Urea Derived Inhibitors of HIV-1 Protease.
2180-2193
Computer Software Reviews
Last update Fri May 24 20:33:00 2013
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