Journal of Chemical Information and Modeling, Volume 44

Volume 44, Number 1, January 2004

Perspective

• 
  Douglas M. Hawkins:
  The Problem of Overfitting. 1-12

Articles Chemical Information

• 
  Cheng-de Lin, Peng Tang:
  Kekulé Count in Capped Zigzag Boron-Nitride Nanotubes. 13-20
• 
  Jeffrey W. Godden, John R. Furr, Ling Xue, Florence L. Stahura, Jürgen Bajorath:
  Molecular Similarity Analysis and Virtual Screening by Mapping of Consensus Positions in Binary-Transformed Chemical Descriptor Spaces with Variable Dimensionality. 21-29
• 
  Gonzalo Cerruela García, Irene Luque Ruiz, Miguel Ángel Gómez-Nieto:
  Step-by-Step Calculation of All Maximum Common Substructures through a Constraint Satisfaction Based Algorithm. 30-41

Chemical Computation

• 
  Lionello Pogliani:
  Encoding the Core Electrons with Graph Concepts. 42-49
• 
  Alexandru T. Balaban, Milan Randic:
  Partitioning of pi-Electrons in Rings of Polycyclic Benzenoid Hydrocarbons. 2. Catacondensed Coronoids. 50-59
• 
  Francisco Torrens:
  Table of Periodic Properties of Fullerenes Based on Structural Parameters. 60-67
• 
  Guillermo Restrepo, Héber Mesa, Eugenio-José Llanos, José-Luis Villaveces:
  Topological Study of the Periodic System. 68-75
• 
  Thy-Hou Lin, Huang-Te Li, Keng-Chang Tsai:
  Implementing the Fisher's Discriminant Ratio in a k-Means Clustering Algorithm for Feature Selection and Data Set Trimming. 76-87
• 
  Sukjoon Yoon, William J. Welsh:
  Identification of a Minimal Subset of Receptor Conformations for Improved Multiple Conformation Docking and Two-Step Scoring. 88-96
• 
  Julius Sipilä, Jyrki Taskinen:
  CoMFA Modeling of Human Catechol O-Methyltransferase Enzyme Kinetics. 97-104
• 
  Paolo Mazzatorta, Emilio Benfenati, Paola Lorenzini, Marco Vighi:
  QSAR in Ecotoxicity: An Overview of Modern Classification Techniques. 105-112
• 
  Teuta Pilizota, Bono Lucic, Nenad Trinajstic:
  Use of Variable Selection in Modeling the Secondary Structural Content of Proteins from Their Composition of Amino Acid Residues. 113-121
• 
  Frederik E. Leys, Claudio Amovilli, Norman H. March:
  Topology, Connectivity, and Electronic Structure of C and B Cages and the Corresponding Nanotubes. 122-135
• 
  Alan R. Katritzky, Kaido Tämm, Minati Kuanar, Dan C. Fara, Alexander A. Oliferenko, Polina V. Oliferenko, Jonathan G. Huddleston, Robin D. Rogers:
  Aqueous Biphasic Systems. Partitioning of Organic Molecules: A QSPR Treatment. 136-142
• 
  James N. Cawse, Manfred Baerns, Martin Holena:
  Efficient Discovery of Nonlinear Dependencies in a Combinatorial Catalyst Data Set. 143-146
• 
  Ting-Lan Chiu, Sung-Sau So:
  Development of Neural Network QSPR Models for Hansch Substituent Constants. 1. Method and Validations. 147-153
• 
  Ting-Lan Chiu, Sung-Sau So:
  Development of Neural Network QSPR Models for Hansch Substituent Constants. 2. Applications in QSAR Studies of HIV-1 Reverse Transcriptase and Dihydrofolate Reductase Inhibitors. 154-160
• 
  Huanxiang Liu, Ruisheng Zhang, Xiaojun Yao, Mancang Liu, Zhide Hu, Bo Tao Fan:
  Prediction of the Isoelectric Point of an Amino Acid Based on GA-PLS and SVMs. 161-167
• 
  Daniel Faller, Thomas Reinheckel, Daniel Wenzler, Sascha Hagemann, Ke Xiao, Josef Honerkamp, Christoph Peters, Thomas Dandekar, Jens Timmer:
  An Open Source Protein Gel Documentation System for Proteome Analyses. 168-169
• 
  Andreas Bender, Hamse Y. Mussa, Robert C. Glen, Stephan Reiling:
  Molecular Similarity Searching Using Atom Environments, Information-Based Feature Selection, and a Naïve Bayesian Classifier. 170-178
• 
  Andrey A. Toropov, Kunal Roy:
  QSPR Modeling of Lipid-Water Partition Coefficient by Optimization of Correlation Weights of Local Graph Invariants. 179-186
• 
  Tomas Öberg:
  Boiling Points of Halogenated Aliphatic Compounds: A Quantitative Structure-Property Relationship for Prediction and Validation. 187-192

Molecular Modeling

• 
  Xueguang Shao, Haiyan Jiang, Wensheng Cai:
  Parallel Random Tunneling Algorithm for Structural Optimization of Lennard-Jones Clusters up to N = 330. 193-199
• 
  Christian Th. Klein, Dominik Kaiser, Gerhard F. Ecker:
  Topological Distance Based 3D Descriptors for Use in QSAR and Diversity Analysis. 200-209

Biopharmaceutical Chemistry

• 
  Prasanna A. Datar, Prashant V. Desai, Evans C. Coutinho:
  A 3D-QSAR of Angiotensin II (AT1) Receptor Antagonists Based on Receptor Surface Analysis. 210-220
• 
  David T. Stanton, Prakash J. Madhav, Larry J. Wilson, Timothy W. Morris, Paul M. Hershberger, Christian N. Parker:
  Development of a Quantitative Structure-Activity Relationship Model for Inhibition of Gram-positive Bacterial Cell Growth by Biarylamides. 221-229
• 
  Chenzhong Liao, Aihua Xie, Leming M. Shi, Jiaju Zhou, Xianping Lu:
  Eigenvalue Analysis of Peroxisome Proliferator-Activated Receptor gamma Agonists. 230-238
• 
  Marc Adenot, Roger Lahana:
  Blood-Brain Barrier Permeation Models: Discriminating between Potential CNS and Non-CNS Drugs Including P-Glycoprotein Substrates. 239-248
• 
  Xueliang Fang, Lei Shao, Hui Zhang, Shaomeng Wang:
  Web-Based Tools for Mining the NCI Databases for Anticancer Drug Discovery. 249-257
• 
  Tatiana I. Netzeva, John C. Dearden, Robert Edwards, Andrew D. P. Worgan, Mark T. D. Cronin:
  QSAR Analysis of the Toxicity of Aromatic Compounds to Chlorella vulgaris in a Novel Short-Term Assay. 258-265
• 
  Tingjun Hou, Ke Xia, Wei Zhang, Xiaojie Xu:
  ADME Evaluation in Drug Discovery. 4. Prediction of Aqueous Solubility Based on Atom Contribution Approach. 266-275
• 
  Nicolas Baurin, Jean-Christophe Mozziconacci, Eric Arnoult, Philippe Chavatte, Christophe Marot, Luc Morin-Allory:
  2D QSAR Consensus Prediction for High-Throughput Virtual Screening. An Application to COX-2 Inhibition Modeling and Screening of the NCI Database. 276-285
• 
  Marvin Carmack:
  Chirality of the Disulfide in the Prion Proteins. 286-288

Volume 44, Number 2, March 2004

Papers from the Eighteenth International Course & Conference on the Interfaces Among Mathematics, Chemistry & Computer Sciences, Dubrovnik, Croatia, June 23-28, 2003

• 
  Dusanka Janezic, Ante Graovac:
  The Eighteenth International Course & Conference on the Interfaces among Mathematics, Chemistry & Computer Sciences June 23-28, 2003 Dubrovnik, Croatia. 289
• 
  Pavo Dubcek, Aleksandra Turkovic, Zorica Crnjak Orel, Bozidar Etlinger, Sigrid Bernstorff:
  Synchrotron Light Scattering on Nanostructured V/Ce Oxide Films Intercalated with Li⁺ Ions. 290-295
• 
  Ivan Gutman, Damir Vukicevic, Ante Graovac, Milan Randic:
  Algebraic Kekulé Structures of Benzenoid Hydrocarbons. 296-299
• 
  Alessandra Roncaglioni, Marjana Novic, Marjan Vracko, Emilio Benfenati:
  Classification of Potential Endocrine Disrupters on the Basis of Molecular Structure Using a Nonlinear Modeling Method. 300-309
• 
  Philippe Huetz, Ezatul Ezleen Kamarulzaman, Habibah A. Wahab, Janez Mavri:
  Chemical Reactivity as a Tool To Study Carcinogenicity: Reaction between Estradiol and Estrone 3, 4-Quinones Ultimate Carcinogens and Guanine. 310-314
• 
  István László:
  The Electronic Structure of Nonpolyhex Carbon Nanotubes. 315-322
• 
  Franziska Berger, Christoph Flamm, Petra M. Gleiss, Josef Leydold, Peter F. Stadler:
  Counterexamples in Chemical Ring Perception. 323-331
• 
  Claudia Fried, Wim Hordijk, Sonja J. Prohaska, Claus R. Stadler, Peter F. Stadler:
  The Footprint Sorting Problem. 332-338
• 
  Neva Groselj, Jure Zupan, Silvia L. Reich, Laura Dawidowski, Darío Gomez, Jorge F. Magallanes:
  2D Mapping by Kohonen Networks of the Air Quality Data From a Large City. 339-346
• 
  Éva Tüdos, András Fiser, Ágnes Simon, Zsuzsanna Dosztányi, Mónika Fuxreiter, Csaba Magyar, István Simon:
  Noncovalent Cross-links in Context with Other Structural and Functional Elements of Proteins. 347-351
• 
  Marjan Vracko, Andrezej Szymoszek, Pierluigi Barbieri:
  Structure-Mutagenicity Study of 12 Trimethylimidazopyridine Isomers Using Orbital Energies and "Spectrum-like Representation" As Descriptors. 352-358
• 
  Urban Borstnik, Milan Hodoscek, Dusanka Janezic:
  Improving the Performance of Molecular Dynamics Simulations on Parallel Clusters. 359-364
• 
  Milan Randic:
  Algebraic Kekulé Formulas for Benzenoid Hydrocarbons. 365-372
• 
  Milan Randic:
  Wiener-Hosoya Index - A Novel Graph Theoretical Molecular Descriptor. 373-377
• 
  Christoph Rücker, Gerta Rücker, Steven H. Bertz:
  Organic Synthesis - Art or Science?. 378-386
• 
  Andrzej Sikorski, Piotr Romiszowski:
  Properties of Grafted Amphiphilic Chains. A Computer Simulation Study. 387-392
• 
  Piotr Romiszowski, Andrzej Sikorski:
  Properties of Star-Branched Polymer Brushes. 393-398
• 
  Matevz Pompe, Joe M. Davis, Clint D. Samuel:
  Prediction of Thermodynamic Parameters in Gas Chromatography from Molecular Structure: Hydrocarbons. 399-409
• 
  István Lukovits, Dusanka Janezic:
  Enumeration of Conjugated Circuits in Nanotubes. 410-414
• 
  Ante Milicevic, Sonja Nikolic, Nenad Trinajstic:
  Coding and Ordering Kekulé Structures. 415-421
• 
  Adolf Miklavc, Darko Kocjan:
  Entropic Trapping Binding Mechanism: Its Likely Role in Receptor-Ligand and Other Biochemical Systems. 422-426

Chemical Information

• 
  Jean-Loup Faulon, Michael J. Collins, Robert D. Carr:
  The Signature Molecular Descriptor. 4. Canonizing Molecules Using Extended Valence Sequences. 427-436
• 
  Qian-Nan Hu, Yi-Zeng Liang, Xiao-Ling Peng, Hong Yin, Kai-Tai Fang:
  Structural Interpretation of a Topological Index. 1. External Factor Variable Connectivity Index (EFVCI). 437-446
• 
  Gonzalo Cerruela García, Irene Luque Ruiz, Miguel Ángel Gómez-Nieto:
  Representation of the Molecular Topology of Cyclical Structures by Means of Cycle Graphs. 1. Extraction of Topological Properties. 447-461
• 
  Peter Murray-Rust, Henry S. Rzepa, Mark J. Williamson, Egon L. Willighagen:
  Chemical Markup, XML, and the World Wide Web. 5. Applications of Chemical Metadata in RSS Aggregators. 462-469

Chemical Computation

• 
  Suzanne K. Schreyer, Christian N. Parker, Gerald M. Maggiora:
  Data Shaving: A Focused Screening Approach. 470-479
• 
  Judith M. Rollinger, Sabine Haupt, Hermann Stuppner, Thierry Langer:
  Combining Ethnopharmacology and Virtual Screening for Lead Structure Discovery: COX-Inhibitors as Application Example. 480-488
• 
  Yongquan Han, Christoph Steinbeck:
  Evolutionary-Algorithm-Based Strategy for Computer-Assisted Structure Elucidation. 489-498
• 
  Omowunmi Sadik, Walker H. Land Jr., Adam K. Wanekaya, Michiko Uematsu, Mark J. Embrechts, Lut Wong, Dale Leibensperger, Alex Volykin:
  Detection and Classification of Organophosphate Nerve Agent Simulants Using Support Vector Machines with Multiarray Sensors. 499-507
• 
  Xinhua Li, Maolin Hu, Hongping Xiao:
  A Novel Definition of the Overall Hyper-Wiener Index for Unsaturated Hydrocarbons. 508-514
• 
  Enrique Molina Pérez, Humberto González Díaz, Maykel Pérez González, Elismary Rodríguez, Eugenio Uriarte:
  Designing Antibacterial Compounds through a Topological Substructural Approach. 515-521
• 
  Evgenii A. Smolenskii:
  The Wiener Distance Matrix for Acyclic Compounds and Polymers. 522-528
• 
  Alan R. Katritzky, Dan C. Fara, Hongfang Yang, Mati Karelson, Takahiro Suzuki, Vitaly P. Solov'ev, Alexandre Varnek:
  Quantitative Structure-Property Relationship Modeling of beta-Cyclodextrin Complexation Free Energies. 529-541
• 
  Joachim Braun, Ralf Gugisch, Adalbert Kerber, Reinhard Laue, Markus Meringer, Christoph Rücker:
  MOLGEN-CID - A Canonizer for Molecules and Graphs Accessible through the Internet. 542-548
• 
  Jonathan G. Huddleston, Heather D. Willauer, Marcel T. Burney, Lakeshia J. Tate, Ashley D. Carruth, Robin D. Rogers:
  Comparison of an Empirical and a Theoretical Linear Solvation Energy Relationship Applied to the Characterization of Solute Distribution in a Poly(ethylene) Glycol-Salt Aqueous Biphasic System. 549-558
• 
  Kunal Roy, Gopinath Ghosh:
  QSTR with Extended Topochemical Atom Indices. 2. Fish Toxicity of Substituted Benzenes. 559-567
• 
  Petr V. Nazarov, Vladimir V. Apanasovich, Vladimir M. Lutkovski, Mikalai M. Yatskou, Rob B. M. Koehorst, Marcus A. Hemminga:
  Artificial Neural Network Modification of Simulation-Based Fitting: Application to a Protein-Lipid System. 568-574
• 
  Francisco Torrens:
  A Chemical Index Inspired by Biological Plastic Evolution: Valence-Isoelectronic Series of Aromatics. 575-581
• 
  Assia Kovatcheva, Alexander Golbraikh, Scott Oloff, Yun-De Xiao, Weifan Zheng, Peter Wolschann, Gerhard Buchbauer, Alexander Tropsha:
  Combinatorial QSAR of Ambergris Fragrance Compounds. 582-595
• 
  Julian M. Ivanov:
  Molecular Symmetry Perception. 596-600
• 
  John W. Raymond, Mehran Jalaie, Mary P. Bradley:
  Conditional Probability: A New Fusion Method for Merging Disparate Virtual Screening Results. 601-609
• 
  Teodora Ivanciuc, Douglas J. Klein:
  Parameter-Free Structure-Property Correlation via Progressive Reaction Posets for Substituted Benzenes. 610-617
• 
  Rainer Brüggemann, Peter B. Sørensen, Dorte B. Lerche, Lars Carlsen:
  Estimation of Averaged Ranks by a Local Partial Order Model. 618-625
• 
  Andreas Teckentrup, Hans Briem, Johann Gasteiger:
  Mining High-Throughput Screening Data of Combinatorial Libraries: Development of a Filter to Distinguish Hits from Nonhits. 626-634
• 
  Jen-Shiang K. Yu, Jenn-Kang Hwang, Chuan Yi Tang, Chin-Hui Yu:
  Numerical Performance and Throughput Benchmark for Electronic Structure Calculations in PC-Linux Systems with New Architectures, Updated Compilers, and Libraries. 635-642
• 
  Nicolas Baurin, R. Baker, Christine M. Richardson, I-Jen Chen, Nicolas Foloppe, Andrew Potter, A. Jordan, Stephen D. Roughley, Martin J. Parratt, P. Greaney, D. Morley, Roderick E. Hubbard:
  Drug-like Annotation and Duplicate Analysis of a 23-Supplier Chemical Database Totalling 2.7 Million Compounds. 643-651
• 
  Lei Liu, Yao Fu, Rui Liu, Rui-Qiong Li, Qing-Xiang Guo:
  Hammett Equation and Generalized Pauling's Electronegativity Equation. 652-657
• 
  Bernd Ehresmann, Marcel J. de Groot, Alexander Alex, Timothy Clark:
  New Molecular Descriptors Based on Local Properties at the Molecular Surface and a Boiling-Point Model Derived from Them. 658-668
• 
  C. X. Xue, Ruisheng Zhang, Huanxiang Liu, Xiaojun Yao, Mancang Liu, Zhide Hu, Bo Tao Fan:
  An Accurate QSPR Study of O-H Bond Dissociation Energy in Substituted Phenols Based on Support Vector Machines. 669-677
• 
  Chenzhong Cao, Li Liu:
  Topological Steric Effect Index and Its Application. 678-687

Molecular Modeling

• 
  Ernesto Estrada, Grace Patlewicz, Yaquelin Gutierrez:
  From Knowledge Generation to Knowledge Archive. A General Strategy Using TOPS-MODE with DEREK To Formulate New Alerts for Skin Sensitization. 688-698

Biopharmaceutical Chemistry

• 
  Wei Deng, Curt M. Breneman, Mark J. Embrechts:
  Predicting Protein-Ligand Binding Affinities Using Novel Geometrical Descriptors and Machine-Learning Methods. 699-703
• 
  Gilles Klopman, Suman K. Chakravarti, Hao Zhu, Julian M. Ivanov, Roustem D. Saiakhov:
  ESP: A Method To Predict Toxicity and Pharmacological Properties of Chemicals Using Multiple MCASE Databases. 704-715
• 
  Michael Daszykowski, Beata Walczak, Qing-S. Xu, Frederik F. D. Daeyaert, Marc R. de Jonge, Jan Heeres, Lucien M. H. Koymans, Paul J. Lewi, H. Maarten Vinkers, Paul A. J. Janssen, Desire L. Massart:
  Classification and Regression Trees-Studies of HIV Reverse Transcriptase Inhibitors. 716-726
• 
  Robert P. Sheridan, Joseph Shpungin:
  Calculating Similarities between Biological Activities in the MDL Drug Data Report Database. 727-740
• 
  Jian-Ding Qiu, Ruping Liang, Xiaoyong Zou, Jinyuan Mo:
  Prediction of Transmembrane Proteins Based on the Continuous Wavelet Transform. 741-747
• 
  Hongmao Sun:
  A Universal Molecular Descriptor System for Prediction of LogP, LogS, LogBB, and Absorption. 748-757
• 
  Chris L. Waller:
  A Comparative QSAR Study Using CoMFA, HQSAR, and FRED/SKEYS Paradigms for Estrogen Receptor Binding Affinities of Structurally Diverse Compounds. 758-765

Errata

• 
  Tingjun Hou, Xiaojie Xu:
  ADME Evaluation in Drug Discovery. 3. Modeling Blood-Brain Barrier Partitioning Using Simple Molecular Descriptors [J. Chem. Inf. Comput. Sci. 43, 2137-2152 (2003)]. 766-770

Volume 44, Number 3, May 2004

Chemical Information

• 
  Mikhail E. Elyashberg, Kirill A. Blinov, Antony J. Williams, Sergey G. Molodtsov, Gary E. Martin, Eduard R. Martirosian:
  Structure Elucidator: A Versatile Expert System for Molecular Structure Elucidation from 1D and 2D NMR Data and Molecular Fragments. 771-792

Chemical Computation

• 
  Marcel L. Verdonk, Valerio Berdini, Michael J. Hartshorn, Wijnand T. M. Mooij, Christopher W. Murray, Richard D. Taylor, Paul Watson:
  Virtual Screening Using Protein-Ligand Docking: Avoiding Artificial Enrichment. 793-806
• 
  Anu J. Tervo, Tommi H. Nyrönen, Toni Rönkkö, Antti Poso:
  Comparing the Quality and Predictiveness between 3D QSAR Models Obtained from Manual and Automated Alignment. 807-816
• 
  Jan K. Rainey, M. Cynthia Goh:
  Statistically Based Reduced Representation of Amino Acid Side Chains. 817-830
• 
  João Aires-de-Sousa, Johann Gasteiger, Ivan Gutman, Dusica Vidovic:
  Chirality Codes and Molecular Structure. 831-836
• 
  Christian Hofbauer, Hans Lohninger, András Aszódi:
  SURFCOMP: A Novel Graph-Based Approach to Molecular Surface Comparison. 837-847
• 
  Olivier Lamarche, James A. Platts, Anne Hersey:
  Theoretical Prediction of Partition Coefficients via Molecular Electrostatic and Electronic Properties. 848-855
• 
  Robert P. Bywater, Thomas A. Poulsen, Peter Røgen, Poul G. Hjorth:
  De Novo Generation of Molecular Structures Using Optimization To Select Graphs on a Given Lattice. 856-861
• 
  Robert Kirk DeLisle, Steven L. Dixon:
  Induction of Decision Trees via Evolutionary Programming. 862-870
• 
  Romano T. Kroemer, Anna Vulpetti, Joseph J. McDonald, Douglas C. Rohrer, Jean-Yves Trosset, Fabrizio Giordanetto, Simona Cotesta, Colin McMartin, Mats Kihlén, Pieter F. W. Stouten:
  Assessment of Docking Poses: Interactions-Based Accuracy Classification (IBAC) versus Crystal Structure Deviations. 871-881
• 
  Fabrizio Giordanetto, Simona Cotesta, Cornel Catana, Jean-Yves Trosset, Anna Vulpetti, Pieter F. W. Stouten, Romano T. Kroemer:
  Novel Scoring Functions Comprising QXP, SASA, and Protein Side-Chain Entropy Terms. 882-893
• 
  John D. Holliday, Sarah L. Rodgers, Peter Willett, Min-You Chen, Mahdi Mahfouf, Kevin Lawson, Graham Mullier:
  Clustering Files of Chemical Structures Using the Fuzzy k-Means Clustering Method. 894-902
• 
  Igor Novak:
  Ab Initio vs Molecular Mechanics Thermochemistry: Homocubanes. 903-906
• 
  Chaoxiong Ma, Xueguang Shao:
  Continuous Wavelet Transform Applied to Removing the Fluctuating Background in Near-Infrared Spectra. 907-911
• 
  Jason A. Morrill, Robert E. Jensen, Phillip H. Madison, Cary F. Chabalowski:
  Prediction of the Formulation Dependence of the Glass Transition Temperatures of Amine-Epoxy Copolymers Using a QSPR Based on the AM1 Method. 912-920
• 
  Jörg K. Wegner, Holger Fröhlich, Andreas Zell:
  Feature Selection for Descriptor Based Classification Models. 1. Theory and GA-SEC Algorithm. 921-930
• 
  Jörg K. Wegner, Holger Fröhlich, Andreas Zell:
  Feature Selection for Descriptor Based Classification Models. 2. Human Intestinal Absorption (HIA). 931-939
• 
  Yuri Binev, João Aires-de-Sousa:
  Structure-Based Predictions of ¹H NMR Chemical Shifts Using Feed-Forward Neural Networks. 940-945
• 
  Yuri Binev, Marta Corvo, João Aires-de-Sousa:
  The Impact of Available Experimental Data on the Prediction of ¹H NMR Chemical Shifts by Neural Networks. 946-949
• 
  C. X. Xue, Ruisheng Zhang, Mancang Liu, Zhide Hu, Bo Tao Fan:
  Study of the Quantitative Structure-Mobility Relationship of Carboxylic Acids in Capillary Electrophoresis Based on Support Vector Machines. 950-957
• 
  Eduardo J. Delgado, Joel B. Alderete, Adelio R. Matamala, Gonzalo A. Jaña:
  On the Aggregation State and QSPR Models. The Solubility of Herbicides as a Case Study. 958-963
• 
  Alberto Gobbi, Sandra Funeriu, John Ioannou, Jinyi Wang, Man-Ling Lee, Chris Palmer, Bob Bamford, Robin Hewitt:
  Process-Driven Information Management System at a Biotech Company: Concept and Implementation. 964-975
• 
  Martin Smiesko, Emilio Benfenati:
  Predictive Models for Aquatic Toxicity of Aldehydes Designed for Various Model Chemistries. 976-984
• 
  Melek Türker Saçan, Safiye Sag Erdem, Gül Altinbas Özpinar, Isil Akmehmet Balcioglu:
  QSPR Study on the Bioconcentration Factors of Nonionic Organic Compounds in Fish by Characteristic Root Index and Semiempirical Molecular Descriptors. 985-992
• 
  Evgeny Byvatov, Gisbert Schneider:
  SVM-Based Feature Selection for Characterization of Focused Compound Collections. 993-999
• 
  John S. Delaney:
  ESOL: Estimating Aqueous Solubility Directly from Molecular Structure. 1000-1005
• 
  Satoshi Fujishima, Yoshimasa Takahashi:
  Classification of Dopamine Antagonists Using TFS-Based Artificial Neural Network. 1006-1009
• 
  David T. Stanton, Brian E. Mattioni, James J. Knittel, Peter C. Jurs:
  Development and Use of Hydrophobic Surface Area (HSA) Descriptors for Computer-Assisted Quantitative Structure-Activity and Structure-Property Relationship Studies. 1010-1023
• 
  Dario Duca, Giuseppe Bifulco, Giampaolo Barone, Agostino Casapullo, Alberta Fontana:
  SCSA Code: Applications on the Cyclopeptide Renieramide. 1024-1030
• 
  Miguel Murcia-Soler, Facundo Pérez-Giménez, Francisco J. García-March, M. Teresa Salabert-Salvador, Wladimiro Díaz Villanueva, María José Castro Bleda, Angel Villanueva-Pareja:
  Artificial Neural Networks and Linear Discriminant Analysis: A Valuable Combination in the Selection of New Antibacterial Compounds. 1031-1041
• 
  Alexander A. Oliferenko, Polina V. Oliferenko, Jonathan G. Huddleston, Robin D. Rogers, Vladimir A. Palyulin, Nikolai S. Zefirov, Alan R. Katritzky:
  Theoretical Scales of Hydrogen Bond Acidity and Basicity for Application in QSAR/QSPR Studies and Drug Design. Partitioning of Aliphatic Compounds. 1042-1055
• 
  Barry K. Lavine, Charles E. Davidson, David J. Westover:
  Spectral Pattern Recognition Using Self-Organizing MAPS. 1056-1064
• 
  Patrick C. Fricker, Marcus Gastreich, Matthias Rarey:
  Automated Drawing of Structural Molecular Formulas under Constraints. 1065-1078
• 
  Nathan Brown, Ben McKay, François Gilardoni, Johann Gasteiger:
  A Graph-Based Genetic Algorithm and Its Application to the Multiobjective Evolution of Median Molecules. 1079-1087

Molecular Modeling

• 
  Jack R. Smith, Doyle Knight, Joachim Kohn, Khaled Rasheed, Norbert Weber, Vladyslav V. Kholodovych, William J. Welsh:
  Using Surrogate Modeling in the Prediction of Fibrinogen Adsorption onto Polymer Surfaces. 1088-1097
• 
  Jesús Jover, Ramón Bosque, Joaquim Sales:
  Determination of Abraham Solute Parameters from Molecular Structure. 1098-1106

Biopharmaceutical Chemistry

• 
  Richard D. Beger, John F. Young, Hong Fang:
  Discriminant Function Analyses of Liver-Specific Carcinogens. 1107-1110
• 
  Suzanne W. Sirois, Dongqing Wei, Qishi Du, Kuo-Chen Chou:
  Virtual Screening for SARS-CoV Protease Based on KZ7088 Pharmacophore Points. 1111-1122
• 
  Eva M. Krovat, Thierry Langer:
  Impact of Scoring Functions on Enrichment in Docking-Based Virtual Screening: An Application Study on Renin Inhibitors. 1123-1129
• 
  Aijun Lu, Jiaju Zhou:
  Pseudoreceptor Models and 3D-QSAR for Imidazobenzodiazepines at GABA_A/BzR Subtypes alpha_xbeta₃gamma₂ [x = 1-3, 5, and 6] via Flexible Atom Receptor Model. 1130-1136
• 
  Modest von Korff, Matthias Steger:
  GPCR-Tailored Pharmacophore Pattern Recognition of Small Molecular Ligands. 1137-1147
• 
  Alban Lepailleur, Ronan Bureau, Stéphane Lemaître, François Dauphin, Jean-Charles Lancelot, Vincent Contesse, Sébastien Lenglet, Catherine Delarue, Hubert Vaudry, Sylvain Rault:
  Molecular Design Based on 3D Pharmacophores. Applications to 5-HT₇ Receptors. 1148-1152
• 
  Jaime Souza Jr., Fábio A. Molfetta, Káthia Maria Honório, Regina H. A. Santos, Albérico B. F. da Silva:
  A Study on the Antipicornavirus Activity of Flavonoid Compounds (Flavones) by Using Quantum Chemical and Chemometric Methods. 1153-1161
• 
  Caterina Bissantz, Antoine Logean, Didier Rognan:
  High-Throughput Modeling of Human G-Protein Coupled Receptors: Amino Acid Sequence Alignment, Three-Dimensional Model Building, and Receptor Library Screening. 1162-1176
• 
  Jérôme Hert, Peter Willett, David J. Wilton, Pierre Acklin, Kamal Azzaoui, Edgar Jacoby, Ansgar Schuffenhauer:
  Comparison of Fingerprint-Based Methods for Virtual Screening Using Multiple Bioactive Reference Structures. 1177-1185
• 
  Steven Trohalaki, Ruth Pachter, Kevin T. Geiss, John M. Frazier:
  Halogenated Aliphatic Toxicity QSARs Employing Metabolite Descriptors. 1186-1192

Volume 44, Number 4, July 2004

Articles Chemical Information

• 
  Qian-Nan Hu, Yi-Zeng Liang, Hong Yin, Xiao-Ling Peng, Kai-Tai Fang:
  Structural Interpretation of the Topological Index. 2. The Molecular Connectivity Index, the Kappa Index, and the Atom-type E-State Index. 1193-1201
• 
  Varvara A. Latysheva, Ray Hefferlin:
  Periodic Systems of Molecules as Elements of Shchukarev's "Supermatrix", i.e. the Chemical Element Periodic System. 1202-1209
• 
  Jerry Ray Dias:
  The Most Stable Class of Benzenoid Hydrocarbons-New Topological Correlations of Strain-Free Total Resonant Sextet Benzenoids. 1210-1220
• 
  Robert J. Jilek, Richard D. Cramer:
  Topomers: A Validated Protocol for Their Self-Consistent Generation. 1221-1227

Chemical Computation

• 
  Xiaoquan Lu, Hongde Liu, Zhonghua Xue, Zhang Qiang:
  Maximum Spectrum of Continuous Wavelet Transform and Its Application in Resolving an Overlapped Signal. 1228-1237
• 
  Ernesto Estrada:
  A Protein Folding Degree Measure and Its Dependence on Crystal Packing, Protein Size, Secondary Structure, and Domain Structural Class. 1238-1250
• 
  S. S. Sheik, Sumit K. Aggarwal, Anindya Poddar, N. Balakrishnan, Krishna Sekar:
  A FAST Pattern Matching Algorithm. 1251-1256
• 
  Xiaojun Yao, Annick Panaye, Jean-Pierre Doucet, Ruisheng Zhang, Haifeng Chen, Mancang Liu, Zhide Hu, Bo Tao Fan:
  Comparative Study of QSAR/QSPR Correlations Using Support Vector Machines, Radial Basis Function Neural Networks, and Multiple Linear Regression. 1257-1266
• 
  C. X. Xue, Ruisheng Zhang, Huanxiang Liu, Mancang Liu, Zhide Hu, Bo Tao Fan:
  Support Vector Machines-Based Quantitative Structure-Property Relationship for the Prediction of Heat Capacity. 1267-1274
• 
  Ling Xue, Jeffrey W. Godden, Florence L. Stahura, Jürgen Bajorath:
  Similarity Search Profiles as a Diagnostic Tool for the Analysis of Virtual Screening Calculations. 1275-1281
• 
  Michel Deza, Mathieu Dutour, Patrick W. Fowler:
  Zigzags, Railroads, and Knots in Fullerenes. 1282-1293
• 
  James L. Melville, Jonathan D. Hirst:
  On the Stability of CoMFA Models. 1294-1300
• 
  Wei Chen, Jing Huang, Michael K. Gilson:
  Identification of Symmetries in Molecules and Complexes. 1301-1313
• 
  Luca Bellarosa, Patrick W. Fowler, Erwin Lijnen, Michel Deza:
  Addition Patterns in Carbon Allotropes: Independence Numbers and d-Codes in the Klein and Related Graphs. 1314-1323
• 
  Jie Song, Huanwen Tang:
  Accurate Classification of Homodimeric vs Other Homooligomeric Proteins Using a New Measure of Information Discrepancy. 1324-1327
• 
  Mehdi Jalali-Heravi, Anahita Kyani:
  Use of Computer-Assisted Methods for the Modeling of the Retention Time of a Variety of Volatile Organic Compounds: A PCA-MLR-ANN Approach. 1328-1335
• 
  Edward S. Blurock:
  Detailed Mechanism Generation. 1. Generalized Reactive Properties as Reaction Class Substructures. 1336-1347
• 
  Edward S. Blurock:
  Detailed Mechanism Generation. 2. Aldehydes, Ketones, and Olefins. 1348-1357
• 
  Thomas Ott, Albert Kern, Ansgar Schuffenhauer, Maxim Popov, Pierre Acklin, Edgar Jacoby, Ruedi Stoop:
  Sequential Superparamagnetic Clustering for Unbiased Classification of High-Dimensional Chemical Data. 1358-1364
• 
  Alexandre Varnek, Denis Fourches, Vitaly P. Solov'ev, Vladimir E. Baulin, Alexander N. Turanov, Vasili K. Karandashev, Dan C. Fara, Alan R. Katritzky:
  "In Silico" Design of New Uranyl Extractants Based on Phosphoryl-Containing Podands: QSPR Studies, Generation and Screening of Virtual Combinatorial Library, and Experimental Tests. 1365-1382
• 
  Irene Luque Ruiz, Gonzalo Cerruela García, Miguel Ángel Gómez-Nieto:
  Representation of the Molecular Topology of Cyclical Structures by Means of Cycle Graphs. 2. Application to Clustering of Chemical Databases. 1383-1393
• 
  John Binamé, Nathalie Meurice, Laurence Leherte, Janice I. Glasgow, Suzanne Fortier, Daniel P. Vercauteren:
  Use of Electron Density Critical Points as Chemical Function-Based Reduced Representations of Pharmacological Ligands. 1394-1401
• 
  Christoph Helma, Tobias Cramer, Stefan Kramer, Luc De Raedt:
  Data Mining and Machine Learning Techniques for the Identification of Mutagenicity Inducing Substructures and Structure Activity Relationships of Noncongeneric Compounds. 1402-1411
• 
  W. Michael Brown, David L. Vander Jagt:
  Creating Artificial Binding Pocket Boundaries To Improve the Efficiency of Flexible Ligand Docking. 1412-1422
• 
  Jaroslaw Polanski, Rafal Gieleciak, Tomasz Magdziarz, Andrzej Bak:
  GRID Formalism for the Comparative Molecular Surface Analysis: Application to the CoMFA Benchmark Steroids, Azo Dyes, and HEPT Derivatives. 1423-1435

Molecular Modeling

• 
  Wei Wenying, Han Jinyu, Xu Wen:
  Group Vector Space Method for Estimating Enthalpy of Vaporization of Organic Compounds at the Normal Boiling Point. 1436-1439

Biopharmaceutical Chemistry

• 
  Rajarshi Guha, Peter C. Jurs:
  Development of QSAR Models To Predict and Interpret the Biological Activity of Artemisinin Analogues. 1440-1449
• 
  M. Letizia Barreca, Angela Rao, Laura De Luca, Maria Zappalà, Cristina Gurnari, Pietro Monforte, Erik De Clercq, Bénédicte Van Maele, Zeger Debyser, Myriam Witvrouw, James M. Briggs, Alba Chimirri:
  Efficient 3D Database Screening for Novel HIV-1 IN Inhibitors. 1450-1455
• 
  Huili Yao, Aurora D. Costache, Daniel S. Sem:
  Chemical Proteomic Tool for Ligand Mapping of CYP Antitargets: An NMR-Compatible 3D QSAR Descriptor in the Heme-Based Coordinate System. 1456-1465
• 
  Joong-Youn Shim, Allyn C. Howlett:
  Steric Trigger as a Mechanism for CB₁ Cannabinoid Receptor Activation. 1466-1476
• 
  Christel A. S. Bergström, Carola M. Wassvik, Ulf Norinder, Kristina Luthman, Per Artursson:
  Global and Local Computational Models for Aqueous Solubility Prediction of Drug-Like Molecules. 1477-1488
• 
  Richard D. Beger, Stephen Harris, Qian Xie:
  Models of Steroid Binding Based on the Minimum Deviation of Structurally Assigned ¹³C NMR Spectra Analysis (MiDSASA). 1489-1496
• 
  Ying Xue, Chun Wei Yap, Li Zhi Sun, Zhi Wei Cao, J. F. Wang, Yuzong Chen:
  Prediction of P-Glycoprotein Substrates by a Support Vector Machine Approach. 1497-1505
• 
  Hongmao Sun:
  Prediction of Chemical Carcinogenicity from Molecular Structure. 1506-1514

Book Reviews

• 
  Urban Borstnik, Dusanka Janezic:
  Reviews in Computational Chemistry. Volume 19 Edited by Kenny B. Lipkowitz, Raima Larter, and Thomas R. Cundari. Wiley-VCH 2003, ISBN 0-471-23585-7. 1515

Errata

• 
  Tingjun Hou, Xiaojie Xu:
  ADME Evaluation in Drug Discovery. 2. Prediction of Partition Coefficient by Atom-Additive Approach Based on Atom-Weighted Solvent Accessible Surface Areas [J. Chem. Inf. Comput. Sci. 1058-1067(2003)]. 1516

Volume 44, Number 5, September 2004

Articles Chemical Information

• 
  A. M. Livshits, Yurii E. Lozovik:
  Cut-and-Unfold Approach to Fullerene Enumeration. 1517-1520
• 
  Douglas J. Klein, José Luis Palacios, Milan Randic, Nenad Trinajstic:
  Random Walks and Chemical Graph Theory. 1521-1525
• 
  Craig L. Senese, José S. Duca, Dahua Pan, Anton J. Hopfinger, Yufeng J. Tseng:
  4D-Fingerprints, Universal QSAR and QSPR Descriptors. 1526-1539
• 
  Kristin Tøndel:
  Prediction of Homology Model Quality with Multivariate Regression. 1540-1551
• 
  Erwin Lijnen, Arnout Ceulemans:
  Oriented 2-Cell Embeddings of a Graph and Their Symmetry Classification: Generating Algorithms and Case Study of the Möbius-Kantor Graph. 1552-1564

Chemical Computation

• 
  István Lukovits:
  Resonance Energy in Graphite. 1565-1570
• 
  Wei Zhang, Tingjun Hou, Xuebin Qiao, Xiaojie Xu:
  Some Basic Data Structures and Algorithms for Chemical Generic Programming. 1571-1575
• 
  César Hervás-Martínez, Manuel Silva, Juan Manuel Serrano, Eva Orejuela:
  Heuristic Extraction of Rules in Pruned Artificial Neural Networks Models Used for Quantifying Highly Overlapping Chromatographic Peaks. 1576-1584
• 
  Tingjun Hou, Wei Zhang, Ke Xia, Xuebin Qiao, Xiaojie Xu:
  ADME Evaluation in Drug Discovery. 5. Correlation of Caco-2 Permeation with Simple Molecular Properties. 1585-1600
• 
  Daniel J. Graham, Christopher Malarkey, Matthew V. Schulmerich:
  Information Content in Organic Molecules: Quantification and Statistical Structure via Brownian Processing. 1601-1611
• 
  Daniel J. Graham, Matthew V. Schulmerich:
  Information Content in Organic Molecules: Reaction Pathway Analysis via Brownian Processing. 1612-1622
• 
  Raghuraman Venkatapathy, Chandrika J. Moudgal, Robert M. Bruce:
  Assessment of the Oral Rat Chronic Lowest Observed Adverse Effect Level Model in TOPKAT, a QSAR Software Package for Toxicity Prediction. 1623-1629
• 
  Ying Xue, Ze-Rong Li, Chun Wei Yap, Li Zhi Sun, Xin Chen, Yuzong Chen:
  Effect of Molecular Descriptor Feature Selection in Support Vector Machine Classification of Pharmacokinetic and Toxicological Properties of Chemical Agents. 1630-1638
• 
  Santiago Melchor, José A. Dobado Jimez:
  CoNTub: An Algorithm for Connecting Two Arbitrary Carbon Nanotubes. 1639-1646
• 
  Peter Tiño, Ian T. Nabney, Bruce S. Williams, Jens Lösel, Yi Sun:
  Nonlinear Prediction of Quantitative Structure-Activity Relationships. 1647-1653
• 
  Christoph Rücker, Ralf Gugisch, Adalbert Kerber:
  Manual Construction and Mathematics- and Computer-Aided Counting of Stereoisomers. The Example of Oligoinositols. 1654-1665
• 
  Bo Liao, Tian-Ming Wang:
  Analysis of Similarity/Dissimilarity of DNA Sequences Based on Nonoverlapping Triplets of Nucleotide Bases. 1666-1670
• 
  Oliver Trapp:
  Evaluation and Prediction of Stereoisomerizations in Comprehensive Two-Dimensional Chromatography. 1671-1679
• 
  Armando Navarro-Vázquez, Juan Carlos Cobas, Francisco Javier Sardina, Jorge Casanueva, Ernesto Díez:
  A Graphical Tool for the Prediction of Vicinal Proton-Proton ³J_HH Coupling Constants. 1680-1685
• 
  Vishwesh Venkatraman, Andrew R. Dalby, Zheng Rong Yang:
  Evaluation of Mutual Information and Genetic Programming for Feature Selection in QSAR. 1686-1692
• 
  C. X. Xue, Ruisheng Zhang, Huanxiang Liu, Xiaojun Yao, Mancang Liu, Zhide Hu, Bo Tao Fan:
  QSAR Models for the Prediction of Binding Affinities to Human Serum Albumin Using the Heuristic Method and a Support Vector Machine. 1693-1700
• 
  Alexandru T. Balaban, Milan Randic:
  Partitioning of pi-Electrons in Rings of Polycyclic Conjugated Hydrocarbons. 5. Nonalternant Compounds. 1701-1707
• 
  Andreas Bender, Hamse Y. Mussa, Robert C. Glen, Stephan Reiling:
  Similarity Searching of Chemical Databases Using Atom Environment Descriptors (MOLPRINT 2D): Evaluation of Performance. 1708-1718
• 
  Shinsaku Fujita:
  Group-Theoretical Discussion on the E/Z-Nomenclature for Ethylene Derivatives. Discrimination between RS-Stereoisomeric Groups and Stereoisomeric Groups. 1719-1726
• 
  Jesús Jover, Ramón Bosque, Joaquim Sales:
  Determination of Lithium Cation Basicity from Molecular Structure. 1727-1736
• 
  Sergey G. Molodtsov, Mikhail E. Elyashberg, Kirill A. Blinov, Antony J. Williams, Eduard R. Martirosian, Gary E. Martin, Brent Lefebvre:
  Structure Elucidation from 2D NMR Spectra Using the StrucEluc Expert System: Detection and Removal of Contradictions in the Data. 1737-1751
• 
  Guangyu Sun, Johannes H. Voigt, Igor V. Filippov, Victor E. Marquez, Marc C. Nicklaus:
  PROSIT: Pseudo-Rotational Online Service and Interactive Tool, Applied to a Conformational Survey of Nucleosides and Nucleotides. 1752-1762
• 
  Mulaisho Mwense, Xue Zhong Wang, Frances V. Buontempo, Nigel Horan, Anita Young, Daniel Osborn:
  Prediction of Noninteractive Mixture Toxicity of Organic Compounds Based on a Fuzzy Set Method. 1763-1773
• 
  Chong Hak Chae, Sung-Eun Yoo, Whanchul Shin:
  Novel Receptor Surface Approach for 3D-QSAR: The Weighted Probe Interaction Energy Method. 1774-1787

Molecular Modeling

• 
  Christian Neiss, Peter Saalfrank:
  Molecular Dynamics Simulation of the LOV2 Domain from Adiantum capillus-veneris. 1788-1793
• 
  Paola Gramatica, Pamela Pilutti, Ester Papa:
  Validated QSAR Prediction of OH Tropospheric Degradation of VOCs: Splitting into Training-Test Sets and Consensus Modeling. 1794-1802

Biopharmaceutical Chemistry

• 
  Felix Deanda, Eugene L. Stewart:
  Application of the PharmPrint Methodology to Two Protein Kinases. 1803-1809
• 
  Brett A. Tounge, Charles H. Reynolds:
  Defining Privileged Reagents Using Subsimilarity Comparison. 1810-1815
• 
  Martin Thimm, Andrean Goede, Stefan Hougardy, Robert Preissner:
  Comparison of 2D Similarity and 3D Superposition. Application to Searching a Conformational Drug Database. 1816-1822
• 
  Ying Liu:
  A Comparative Study on Feature Selection Methods for Drug Discovery. 1823-1828
• 
  Antonio Macchiarulo, Gabriele Costantino, Mirco Meniconi, Karin Pleban, Gerhard F. Ecker, Daniele Bellocchi, Roberto Pellicciari:
  Insights into Phenylalanine Derivatives Recognition of VLA-4 Integrin: From a Pharmacophoric Study to 3D-QSAR and Molecular Docking Analyses. 1829-1839
• 
  Martin Whittle, Valerie J. Gillet, Peter Willett, Alexander Alex, Jens Loesel:
  Enhancing the Effectiveness of Virtual Screening by Fusing Nearest Neighbor Lists: A Comparison of Similarity Coefficients. 1840-1848
• 
  Theodora M. Steindl, Thierry Langer:
  Influenza Virus Neuraminidase Inhibitors: Generation and Comparison of Structure-Based and Common Feature Pharmacophore Hypotheses and Their Application in Virtual Screening. 1849-1856
• 
  Keng-Chang Tsai, Thy-Hou Lin:
  A Ligand-Based Molecular Modeling Study on Some Matrix Metalloproteinase-1 Inhibitors Using Several 3D QSAR Techniques. 1857-1871
• 
  Gregor Mlinsek, Marjana Novic, Miha Kotnik, Tomaz Solmajer:
  Enzyme Binding Selectivity Prediction: alpha-Thrombin vs Trypsin Inhibition. 1872-1882

Computer Software Reviews

• 
  William G. Town:
  The Merck Index 13.2 CD-ROM Edition from CambridgeSoft. 1883-1885
• 
  Zhenjiang Li, Honggui Wan, Yuhu Shi, Pingkai Ouyang:
  Personal Experience with Four Kinds of Chemical Structure Drawing Software: Review on ChemDraw, ChemWindow, ISIS/Draw, and ChemSketch. 1886-1890

Volume 44, Number 6, November 2004

Articles Chemical Information

• 
  Tetsuo Morikawa, Susumu Narita, Douglas J. Klein:
  Molecules-in-Molecule Estimation of the Extent of Localization of Kekuléan Substructures in Polycyclic Aromatic Hydrocarbons. 1891-1896
• 
  Giuseppina C. Gini, Marian Viorel Craciun, Christoph König, Emilio Benfenati:
  Combining Unsupervised and Supervised Artificial Neural Networks to PredictAquatic Toxicity. 1897-1902
• 
  Irene Luque Ruiz, Gonzalo Cerruela García, Miguel Ángel Gómez-Nieto:
  Representation of the Molecular Topology of Cyclical Structures by Means of Cycle Graphs. 3. Hierarchical Model of Screening of Chemical Databases. 1903-1911

Chemical Computation

• 
  Robert P. Sheridan, Bradley P. Feuston, Vladimir N. Maiorov, Simon K. Kearsley:
  Similarity to Molecules in the Training Set Is a Good Discriminator for Prediction Accuracy in QSAR. 1912-1928
• 
  Andrew Smellie:
  Accelerated K-Means Clustering in Metric Spaces. 1929-1935
• 
  Ying Liu:
  Active Learning with Support Vector Machine Applied to Gene Expression Data for Cancer Classification. 1936-1941
• 
  Matthew D. Kelly, Ricardo L. Mancera:
  Expanded Interaction Fingerprint Method for Analyzing Ligand Binding Modes in Docking and Structure-Based Drug Design. 1942-1951
• 
  Yizong Cheng, Anping Liu, Yuping Guo, Xiaoyang Qi:
  Computational Models for the Helix Tilt Angle. 1952-1960
• 
  Miguel X. Fernandes, Visvaldas Kairys, Michael K. Gilson:
  Comparing Ligand Interactions with Multiple Receptors via Serial Docking. 1961-1970
• 
  Christian Merkwirth, Harald Mauser, Tanja Schulz-Gasch, Olivier Roche, Martin Stahl, Thomas Lengauer:
  Ensemble Methods for Classification in Cheminformatics. 1971-1978
• 
  Huanxiang Liu, C. X. Xue, Ruisheng Zhang, Xiaojun Yao, Mancang Liu, Zhide Hu, Bo Tao Fan:
  Quantitative Prediction of logk of Peptides in High-Performance Liquid Chromatography Based on Molecular Descriptors by Using the Heuristic Method and Support Vector Machine. 1979-1986
• 
  Scheila Furtado Braga, Douglas Soares Galvão:
  Benzo[c]quinolizin-3-ones Theoretical Investigation: SAR Analysis and Application to Nontested Compounds. 1987-1997
• 
  Yulia V. Borodina, Anastasia V. Rudik, Dmitrii Filimonov, N. Kharchevnikova, Alexander V. Dmitriev, V. Blinova, Vladimir Poroikov:
  A New Statistical Approach to Predicting Aromatic Hydroxylation Sites. Comparison with Model-Based Approaches. 1998-2009
• 
  Yovani Marrero-Ponce:
  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. 2010-2026
• 
  Qi Shen, Jian-Hui Jiang, Chen-Xu Jiao, Shuang-Yan Huan, Guo-Li Shen, Ru-Qin Yu:
  Optimized Partition of Minimum Spanning Tree for Piecewise Modeling by Particle Swarm Algorithm. QSAR Studies of Antagonism of Angiotensin II Antagonists. 2027-2031
• 
  Ling Xue, Florence L. Stahura, Jürgen Bajorath:
  Similarity Search Profiling Reveals Effects of Fingerprint Scaling in Virtual Screening. 2032-2039
• 
  C. Y. Zhao, Ruisheng Zhang, Huanxiang Liu, C. X. Xue, S. G. Zhao, X. F. Zhou, Mancang Liu, Bo Tao Fan:
  Diagnosing Anorexia Based on Partial Least Squares, Back Propagation Neural Network, and Support Vector Machines. 2040-2046
• 
  Guo-Zheng Li, Jie Yang, Haifeng Song, Shang-Sheng Yang, Wen-Cong Lu, Nian-yi Chen:
  Semiempirical Quantum Chemical Method and Artificial Neural Networks Applied for lambda_max Computation of Some Azo Dyes. 2047-2050
• 
  Kai Ludwig, Bernd Speiser:
  EChem++-An Object-Oriented Problem Solving Environment for Electrochemistry. 2. The Kinetic Facilities of Ecco-A Compiler for (Electro-)Chemistry. 2051-2060
• 
  Jane P. F. Bai, Andrey Utis, Gordon M. Crippen, Han-Dan He, Volker Fischer, Robert Tullman, He-Qun Yin, Cheng-Pang Hsu, Lan Jiang, Kin-Kai Hwang:
  Use of Classification Regression Tree in Predicting Oral Absorption in Humans. 2061-2069
• 
  Christoph Rücker, Markus Meringer, Adalbert Kerber:
  QSPR Using MOLGEN-QSPR: The Example of Haloalkane Boiling Points. 2070-2076
• 
  Tadeusz Marek Krygowski, Halina Szatylowicz, Joanna E. Zachara:
  How H-Bonding Affects Aromaticity of the Ring in Variously Substituted Phenol Complexes with Bases. 4. Molecular Geometry as a Source of Chemical Information. 2077-2082
• 
  Dahua Pan, Manisha Iyer, Jianzhong Liu, Yi Li, Anton J. Hopfinger:
  Constructing Optimum Blood Brain Barrier QSAR Models Using a Combination of 4D-Molecular Similarity Measures and Cluster Analysis. 2083-2098
• 
  Jian Wan, Li Zhang, Guangfu Yang, Chang-Guo Zhan:
  Quantitative Structure-Activity Relationship for Cyclic Imide Derivatives of Protoporphyrinogen Oxidase Inhibitors: A Study of Quantum Chemical Descriptors from Density Functional Theory. 2099-2105
• 
  Kai-Tai Fang, Hong Yin, Yi-Zeng Liang:
  New Approach by Kriging Models to Problems in QSAR. 2106-2113
• 
  Renxiao Wang, Yipin Lu, Xueliang Fang, Shaomeng Wang:
  An Extensive Test of 14 Scoring Functions Using the PDBbind Refined Set of 800 Protein-Ligand Complexes. 2114-2125

Molecular Modeling

• 
  Petr Dobes, Jan Kmunícek, Vladimír Mikes, Jirí Damborský:
  Binding of Fatty Acids to beta-Cryptogein: Quantitative Structure-Activity Relationships and Design of Selective Protein Mutants. 2126-2132
• 
  Ian J. Bruno, Jason C. Cole, Magnus Kessler, Jie Luo, W. D. Sam Motherwell, Lucy H. Purkis, Barry R. Smith, Robin Taylor, Richard I. Cooper, Stephanie E. Harris, A. Guy Orpen:
  Retrieval of Crystallographically-Derived Molecular Geometry Information. 2133-2144

Biopharmaceutical Chemistry

• 
  Gavin Harper, Gianpaolo Bravi, Stephen D. Pickett, Jameed Hussain, Darren V. S. Green:
  The Reduced Graph Descriptor in Virtual Screening and Data-Driven Clustering of High-Throughput Screening Data. 2145-2156
• 
  Nicolas Baurin, Fareed Aboul-Ela, Xavier Barril, Ben Davis, Martin Drysdale, Brian Dymock, Harry Finch, Christophe Fromont, Christine M. Richardson, Heather Simmonite, Roderick E. Hubbard:
  Design and Characterization of Libraries of Molecular Fragments for Use in NMR Screening against Protein Targets. 2157-2166
• 
  Zhigang Zhou, Jeffry D. Madura:
  CoMFA 3D-QSAR Analysis of HIV-1 RT Nonnucleoside Inhibitors, TIBO Derivatives Based on Docking Conformation and Alignment. 2167-2178
• 
  Rajarshi Guha, Peter C. Jurs:
  Development of Linear, Ensemble, and Nonlinear Models for the Prediction and Interpretation of the Biological Activity of a Set of PDGFR Inhibitors. 2179-2189
• 
  James R. Arnold, Keith W. Burdick, Scott C.-H. Pegg, Samuel Toba, Michelle L. Lamb, Irwin D. Kuntz:
  SitePrint: Three-Dimensional Pharmacophore Descriptors Derived from Protein Binding Sites for Family Based Active Site Analysis, Classification, and Drug Design. 2190-2198
• 
  Aziz Yasri, Didier Berthelot, Harry Gijsen, Theo Thielemans, Patrick Marichal, Michael F. M. Engels, Jan Hoflack:
  REALISIS: A Medicinal Chemistry-Oriented Reagent Selection, Library Design, and Profiling Platform. 2199-2206
• 
  Erik Nordling, Evert J. Homan:
  Generalization of a Targeted Library Design Protocol: Application to 5-HT₇ Receptor Ligands. 2207-2215
• 
  Anthony E. Klon, Meir Glick, John W. Davies:
  Application of Machine Learning To Improve the Results of High-Throughput Docking Against the HIV-1 Protease. 2216-2224

Computer Software Reviews

• 
  Loren D. Mendelsohn:
  ChemDraw 8 Ultra, Windows and Macintosh Versions. 2225-2226