Journal of Chemical Information and Modeling, Volume 45

Volume 45, Number 1, January 2005

• William L. Jorgensen:
  Journal of Chemical Information and Modeling. 1
  

• Atipat Rojnuckarin, Daniel A. Gschwend, Sergio H. Rotstein, David S. Hartsough:
  ArQiologist: An Integrated Decision Support Tool for Lead Optimization. 2-9
  

• Zhenming Liu, Changkang Huang, Keqiang Fan, Ping Wei, Hao Chen, Shiyong Liu, Jianfeng Pei, Lei Shi, Bo Li, Kun Yang, Ying Liu, Luhua Lai:
  Virtual Screening of Novel Noncovalent Inhibitors for SARS-CoV 3C-like Proteinase. 10-17
  
• Tomasz Spalek, Piotr Pietrzyk, Zbigniew Sojka:
  Application of the Genetic Algorithm Joint with the Powell Method to Nonlinear Least-Squares Fitting of Powder EPR Spectra. 18-29
  
• Matthew Clark:
  Generalized Fragment-Substructure Based Property Prediction Method. 30-38
  
• Jaroslaw J. Panek, Aneta Jezierska, Krzysztof Mierzwicki, Zdzislaw Latajka, Aleksander Koll:
  Molecular Modeling Study of Leflunomide and Its Active Metabolite Analogues. 39-48
  
• Karthigeyan Nagarajan, Randy J. Zauhar, William J. Welsh:
  Enrichment of Ligands for the Serotonin Receptor Using the Shape Signatures Approach. 49-57
  
• Sasa Kovacic, Antonija Lesar, Milan Hodoscek:
  Quantum Mechanical Study of the Potential Energy Surface of the ClO + NO₂ Reaction. 58-64
  
• Rajarshi Guha, Peter C. Jurs:
  Determining the Validity of a QSAR Model - A Classification Approach. 65-73
  
• Christoph Rücker, Markus Meringer, Adalbert Kerber:
  QSPR Using MOLGEN-QSPR: The Challenge of Fluoroalkane Boiling Points. 74-80
  
• K. M. Nalin de Silva, Jonathan M. Goodman:
  What Is the Smallest Saturated Acyclic Alkane that Cannot Be Made?. 81-87
  
• Wei Zhang, Tingjun Hou, Xiaojie Xu:
  New Born Radii Deriving Method for Generalized Born Model. 88-93
  
• Iiris Kahn, Dan C. Fara, Mati Karelson, Uko Maran, Patrik L. Andersson:
  QSPR Treatment of the Soil Sorption Coefficients of Organic Pollutants. 94-105
  

• Tatiana I. Netzeva, Aynur O. Aptula, Emilio Benfenati, Mark T. D. Cronin, Giuseppina C. Gini, Iglika Lessigiarska, Uko Maran, Marjan Vracko, Gerrit Schüürmann:
  Description of the Electronic Structure of Organic Chemicals Using Semiempirical and Ab Initio Methods for Development of Toxicological QSARs. 106-114
  
• Chun Li, Jun Wang:
  New Invariant of DNA Sequences. 115-120
  
• Huabei Zhang:
  A New Approach for the Tissue-Blood Partition Coefficients of Neutral and Ionized Compounds. 121-127
  
• Edward J. Bertaccini, Jessica Shapiro, Douglas L. Brutlag, James R. Trudell:
  Homology Modeling of a Human Glycine Alpha 1 Receptor Reveals a Plausible Anesthetic Binding Site. 128-135
  
• Philip Prathipati, Gyanendra Pandey, Anil K. Saxena:
  CoMFA and Docking Studies on Glycogen Phosphorylase a Inhibitors as Antidiabetic Agents. 136-145
  
• Eva M. Krovat, Karin H. Frühwirth, Thierry Langer:
  Pharmacophore Identification, in Silico Screening, and Virtual Library Design for Inhibitors of the Human Factor Xa. 146-159
  

• Gerhard Wolber, Thierry Langer:
  LigandScout: 3-D Pharmacophores Derived from Protein-Bound Ligands and Their Use as Virtual Screening Filters. 160-169
  
• Cornel Catana, Hua Gao, Christian Orrenius, Pieter F. W. Stouten:
  Linear and Nonlinear Methods in Modeling the Aqueous Solubility of Organic Compounds. 170-176
  
• John J. Irwin, Brian K. Shoichet:
  ZINC - A Free Database of Commercially Available Compounds for Virtual Screening. 177-182
  

• Mauro Colafranceschi, Alfredo Colosimo, Joseph P. Zbilut, Vladimir N. Uversky, Alessandro Giuliani:
  Structure-Related Statistical Singularities along Protein Sequences: A Correlation Study. 183-189
  
• Bahram Hemmateenejad, Mohammad A. Safarpour, Ramin Miri, Nasim Nesari:
  Toward an Optimal Procedure for PC-ANN Model Building: Prediction of the Carcinogenic Activity of a Large Set of Drugs. 190-199
  
• Simon Spycher, Eric Pellegrini, Johann Gasteiger:
  Use of Structure Descriptors To Discriminate between Modes of Toxic Action of Phenols. 200-208
  

• Beth Thomsett-Scott:
  Origin 7.5. 209-210
  
• Stephen R. Heller:
  ACT! 2005. 211
  
• David J. Wild:
  MINITAB Release 14. 212
  

Volume 45, Number 2, March 2005

• Paul Labute:
  On the Perception of Molecules from 3D Atomic Coordinates. 215-221
  
• Ivan Gutman, Pierre Hansen, Hadrien Mélot:
  Variable Neighborhood Search for Extremal Graphs. 10. Comparison of Irregularity Indices for Chemical Trees. 222-230
  
• Gonzalo Cerruela García, Irene Luque Ruiz, Miguel Ángel Gómez-Nieto, Juan Antonio Cabrero Doncel, Antonio Guevara Plaza:
  From Wiener Index to Molecules. 231-238
  
• Stephan C. Schürer, Prashant Tyagi, Steven M. Muskal:
  Prospective Exploration of Synthetically Feasible, Medicinally Relevant Chemical Space. 239-248
  
• Klaus-Robert Müller, Gunnar Rätsch, Sören Sonnenburg, Sebastian Mika, Michael Grimm, Nikolaus Heinrich:
  Classifying 'Drug-likeness' with Kernel-Based Learning Methods. 249-253
  

• Youngyong In, Han Ha Chai, Kyoung Tai No:
  A Partition Coefficient Calculation Method with the SFED Model. 254-263
  
• Jaroslaw J. Panek, Aneta Jezierska, Marjan Vracko:
  Kohonen Network Study of Aromatic Compounds Based on Electronic and Nonelectronic Structure Descriptors. 264-272
  
• Michael E. Beck:
  Do Fukui Function Maxima Relate to Sites of Metabolism? A Critical Case Study. 273-282
  
• Ovanes Mekenyan, Todor Pavlov, Vanjo Grancharov, Milen Todorov, Patricia Schmieder, Gilman Veith:
  2D-3D Migration of Large Chemical Inventories with Conformational Multiplication. Application of the Genetic Algorithm. 283-292
  
• Mircea V. Diudea, Csaba L. Nagy, Ioan Silaghi-Dumitrescu, Ante Graovac, Dusanka Janezic, Drazen Vikic-Topic:
  Periodic Cages. 293-299
  
• Kitiyaporn Wittayanarakul, Ornjira Aruksakunwong, Pornthep Sompornpisut, Vannajan Sanghiran-Lee, Vudhichai Parasuk, Surapong Pinitglang, Supot Hannongbua:
  Structure, Dynamics and Solvation of HIV-1 Protease/Saquinavir Complex in Aqueous Solution and Their Contributions to Drug Resistance: Molecular Dynamic Simulations. 300-308
  
• Jure Zupan, Milan Randic:
  Algorithm for Coding DNA Sequences into "Spectrum-like" and "Zigzag" Representations. 309-313
  
• Nikolay P. Todorov, Christoph L. Buenemann, Ian L. Alberts:
  Combinatorial Ligand Design Targeted at Protein Families. 314-320
  
• Anna Gallegos, Xavier Gironés:
  Topological Quantum Similarity Indices Based on Fitted Densities: Theoretical Background and QSPR Application. 321-326
  
• Ivo Cacelli, Silvio Campanile, Alessandro Giolitti, Dafne Molin:
  Theoretical Prediction of the Abraham Hydrogen Bond Acidity and Basicity Factors from a Reaction Field Method. 327-333
  
• Igor Novak:
  Molecular Modeling of Anti-Bredt Compounds. 334-338
  
• Orsolya Farkas, Károly Héberger:
  Comparison of Ridge Regression, Partial Least-Squares, Pairwise Correlation, Forward- and Best Subset Selection Methods for Prediction of Retention Indices for Aliphatic Alcohols. 339-346
  
• Qishi Du, Peng-Jun Liu, Paul G. Mezey:
  Theoretical Derivation of Heuristic Molecular Lipophilicity Potential: A Quantum Chemical Description for Molecular Solvation. 347-353
  
• Norberto Castillo, Chérif F. Matta, Russell J. Boyd:
  Fluorine-Fluorine Spin-Spin Coupling Constants in Aromatic Compounds: Correlations with the Delocalization Index and with the Internuclear Separation. 354-359
  
• Laura K. Schnackenberg, Richard D. Beger:
  Whole-Molecule Calculation of Log P Based on Molar Volume, Hydrogen Bonds, and Simulated ¹³C NMR Spectra. 360-365
  
• Marjan A. Rafiee, Nasser L. Hadipour, Hossein Naderi-manesh:
  The Role of Charge Distribution on the Antimalarial Activity of Artemisinin Analogues. 366-370
  
• Fei Cai, Heqing Shao, Chungen Liu, Yuansheng Jiang:
  An Alternative Strategy for Count and Storage of Kekulé and Longer Range Resonance Valence Bond Structures. 371-378
  

• Martin Smiesko, Emilio Benfenati:
  Thermodynamic Descriptors Derived from Density Functional Theory Calculations in Prediction of Aquatic Toxicity. 379-385
  
• David Vidal, Michael Thormann, Miquel Pons:
  LINGO, an Efficient Holographic Text Based Method To Calculate Biophysical Properties and Intermolecular Similarities. 386-393
  
• Janez Strancar, Tilen Koklic, Zoran Arsov, Bogdan Filipic, David Stopar, Marcus A. Hemminga:
  Spin Label EPR-Based Characterization of Biosystem Complexity. 394-406
  
• Kuo-Chen Chou, Yu-Dong Cai:
  Prediction of Membrane Protein Types by Incorporating Amphipathic Effects. 407-413
  
• Christian Hofbauer, András Aszódi:
  SH2 Binding Site Comparison: A New Application of the SURFCOMP Method. 414-421
  

• Johannes Kirchmair, Christian Laggner, Gerhard Wolber, Thierry Langer:
  Comparative Analysis of Protein-Bound Ligand Conformations with Respect to Catalyst's Conformational Space Subsampling Algorithms. 422-430
  
• Daniela Schuster, Thierry Langer:
  The Identification of Ligand Features Essential for PXR Activation by Pharmacophore Modeling. 431-439
  
• Huabei Zhang, Hua Li, Chunping Liu:
  CoMFA, CoMSIA, and Molecular Hologram QSAR Studies of Novel Neuronal nAChRs Ligands-Open Ring Analogues of 3-Pyridyl Ether. 440-448
  
• Markus H. J. Seifert:
  ProPose: Steered Virtual Screening by Simultaneous Protein-Ligand Docking and Ligand-Ligand Alignment. 449-460
  
• Rajendra Kristam, Valerie J. Gillet, Richard A. Lewis, David A. Thorner:
  Comparison of Conformational Analysis Techniques To Generate Pharmacophore Hypotheses Using Catalyst. 461-476
  
• Bernard Pirard, Joachim Brendel, Stefan Peukert:
  The Discovery of Kv1.5 Blockers as a Case Study for the Application of Virtual Screening Approaches. 477-485
  

• Wei-Qi Lin, Jian-Hui Jiang, Qi Shen, Guo-Li Shen, Ru-Qin Yu:
  Optimized Block-wise Variable Combination by Particle Swarm Optimization for Partial Least Squares Modeling in Quantitative Structure-Activity Relationship Studies. 486-493
  
• M. Michael Gromiha:
  A Statistical Model for Predicting Protein Folding Rates from Amino Acid Sequence with Structural Class Information. 494-501
  
• Santiago Vilar, Ernesto Estrada, Eugenio Uriarte, Lourdes Santana, Yaquelin Gutierrez:
  In Silico Studies toward the Discovery of New Anti-HIV Nucleoside Compounds through the Use of TOPS-MODE and 2D/3D Connectivity Indices. 2. Purine Derivatives. 502-514
  

• Kejun Liu, Jun Feng, S. Stanley Young:
  PowerMV: A Software Environment for Molecular Viewing, Descriptor Generation, Data Analysis and Hit Evaluation. 515-522
  
• Christopher Kibbey, Alain Calvet:
  Molecular Property eXplorer: A Novel Approach to Visualizing SAR Using Tree-Maps and Heatmaps. 523-532
  

• Alan R. Katritzky, Ritu Jain, Andre Lomaka, Ruslan Petrukhin, Mati Karelson, Ann E. Visser, Robin D. Rogers:
  Correlation of the Melting Points of Potential Ionic Liquids (Imidazolium Bromides and Benzimidazolium Bromides) Using the CODESSA Program [J. Chem. Inf. Comput. Sci. 42, 225-231 (2002)]. 533-534
  
• Tomas Öberg:
  Boiling Points of Halogenated Aliphatic Compounds: A Quantitative Structure-Property Relationship for Prediction and Validation [J. Chem. Inf. Comput. Sci. 44, 187-192 (2004)]. 534
  

Volume 45, Number 3, May 2005

• Wei-Qi Lin, Jian-Hui Jiang, Qi Shen, Hai-Long Wu, Guo-Li Shen, Ru-Qin Yu:
  Piecewise Hypersphere Modeling by Particle Swarm Optimization in QSAR Studies of Bioactivities of Chemical Compounds. 535-541
  
• Martin Stahl, Harald Mauser:
  Database Clustering with a Combination of Fingerprint and Maximum Common Substructure Methods. 542-548
  
• Robert N. Jorissen, Michael K. Gilson:
  Virtual Screening of Molecular Databases Using a Support Vector Machine. 549-561
  
• Jerry Ray Dias:
  Perimeter Topology of Benzenoid Polycyclic Hydrocarbons. 562-571
  
• Muthukumarasamy Karthikeyan, Andreas Bender:
  Encoding and Decoding Graphical Chemical Structures as Two-Dimensional (PDF417) Barcodes. 572-580
  

• Muthukumarasamy Karthikeyan, Robert C. Glen, Andreas Bender:
  General Melting Point Prediction Based on a Diverse Compound Data Set and Artificial Neural Networks. 581-590
  
• Tulay Ercanli, Donald B. Boyd:
  Evaluation of Computational Chemistry Methods: Crystallographic and Cheminformatics Analysis of Aminothiazole Methoximes. 591-601
  
• Stefano Alcaro, Francesco Ortuso, Robert S. Coleman:
  Molecular Modeling of DNA Cross-linking Analogues Based on the Azinomycin Scaffold. 602-609
  
• Milind Misra, Amit Banerjee, Rajesh N. Davé, Carol A. Venanzi:
  Novel Feature Extraction Technique for Fuzzy Relational Clustering of a Flexible Dopamine Reuptake Inhibitor. 610-623
  
• Alfonso T. García-Sosa, Stuart Firth-Clark, Ricardo L. Mancera:
  Including Tightly-Bound Water Molecules in de Novo Drug Design. Exemplification through the in Silico Generation of Poly(ADP-ribose)polymerase Ligands. 624-633
  
• Filip Fratev, Emilio Benfenati:
  3D-QSAR and Molecular Mechanics Study for the Differences in the Azole Activity against Yeastlike and Filamentous Fungi and Their Relation to P450DM Inhibition. 1. 3-Substituted-4(3H)-quinazolinones. 634-644
  
• Alessandra R. Rufino, Antônio J. C. Brant, João B. O. Santos, Marcelo J. P. Ferreira, Vicente de Paulo Emerenciano:
  Simple Method for Identification of Skeletons of Aporphine Alkaloids from ¹³C NMR Data Using Artificial Neural Networks. 645-651
  
• Tadeusz Marek Krygowski, Halina Szatylowicz, Joanna E. Zachara:
  Molecular Geometry as a Source of Chemical Information. 5. Substituent Effect on Proton Transfer in Para-Substituted Phenol Complexes with Fluoride-a B3LYP/6-311+G** Study. 652-656
  
• Yegor Zyrianov:
  Distribution-Based Descriptors of the Molecular Shape. 657-672
  
• James A. Haigh, Barry T. Pickup, J. Andrew Grant, Anthony Nicholls:
  Small Molecule Shape-Fingerprints. 673-684
  
• Philippe Vismara, Yannic S. Tognetti, Claude Laurenço:
  Maximum Symmetrical Split of Molecular Graphs. Application to Organic Synthesis Design. 685-695
  

• Martin J. Bayley, Eleanor J. Gardiner, Peter Willett, Peter J. Artymiuk:
  A Fourier Fingerprint-Based Method for Protein Surface Representation. 696-707
  

• Elodie Lescot, Ronan Bureau, Jana Sopkova-de Oliveira Santos, Christophe Rochais, Vincent Lisowski, Jean-Charles Lancelot, Sylvain Rault:
  3D-QSAR and Docking Studies of Selective GSK-3beta Inhibitors. Comparison with a Thieno[2, 3-b]pyrrolizinone Derivative, a New Potential Lead for GSK-3beta Ligands. 708-715
  
• Theodora M. Steindl, Christian Laggner, Thierry Langer:
  Human Rhinovirus 3C Protease: Generation of Pharmacophore Models for Peptidic and Nonpeptidic Inhibitors and Their Application in Virtual Screening. 716-724
  
• Vema Aparna, G. Rambabu, Sunil K. Panigrahi, J. A. R. P. Sarma, Gautam R. Desiraju:
  Virtual Screening of 4-Anilinoquinazoline Analogues as EGFR Kinase Inhibitors: Importance of Hydrogen Bonds in the Evaluation of Poses and Scoring Functions. 725-738
  
• Nikolaus Stiefl, Knut Baumann:
  Structure-Based Validation of the 3D-QSAR Technique MaP. 739-749
  
• Yong-Hua Wang, Yan Li, Sheng-Li Yang, Ling Yang:
  Classification of Substrates and Inhibitors of P-Glycoprotein Using Unsupervised Machine Learning Approach. 750-757
  
• Céline Le Bailly de Tilleghem, Benoît Beck, Bruno Boulanger, Bernadette Govaerts:
  A Fast Exchange Algorithm for Designing Focused Libraries in Lead Optimization. 758-767
  
• T. John McNeany, Jonathan D. Hirst:
  Inhibition of the Tyrosine Kinase, Syk, Analyzed by Stepwise Nonparametric Regression. 768-776
  
• Peter Itskowitz, Alexander Tropsha:
  k Nearest Neighbors QSAR Modeling as a Variational Problem: Theory and Applications. 777-785
  
• Vladimir Svetnik, Ting Wang, Christopher Tong, Andy Liaw, Robert P. Sheridan, Qinghua Song:
  Boosting: An Ensemble Learning Tool for Compound Classification and QSAR Modeling. 786-799
  

• Rajarshi Guha, Peter C. Jurs:
  Interpreting Computational Neural Network QSAR Models: A Measure of Descriptor Importance. 800-806
  

Volume 45, Number 4, July 2005

• Alexander Böcker, Swetlana Derksen, Elena Schmidt, Andreas Teckentrup, Gisbert Schneider:
  A Hierarchical Clustering Approach for Large Compound Libraries. 807-815
  
• Michael Frenkel, Robert D. Chirico, Vladimir V. Diky, Xinjian Yan, Qian Dong, Chris Muzny:
  ThermoData Engine (TDE): Software Implementation of the Dynamic Data Evaluation Concept. 816-838
  
• Sabcho Dimitrov, Gergana Dimitrova, Todor Pavlov, Nadezhda Dimitrova, Grace Patlewicz, Jay Niemela, Ovanes Mekenyan:
  A Stepwise Approach for Defining the Applicability Domain of SAR and QSAR Models. 839-849
  
• Lijie Wang, Peter Warburton, Zsolt Szekeres, Peter Surjan, Paul G. Mezey:
  Stability and Properties of Polyhelicenes and Annelated Fused-Ring Carbon Helices: Models Toward Helical Graphites. 850-855
  
• Suxin Zheng, Xiaomin Luo, Gang Chen, Weiliang Zhu, Jianhua Shen, Kaixian Chen, Hualiang Jiang:
  A New Rapid and Effective Chemistry Space Filter in Recognizing a Druglike Database. 856-862
  
• Robin Hewitt, Alberto Gobbi, Man-Ling Lee:
  A Searching and Reporting System for Relational Databases Using a Graph-Based Metadata Representation. 863-869
  
• Teodora Ivanciuc, Ovidiu Ivanciuc, Douglas J. Klein:
  Posetic Quantitative Superstructure/Activity Relationships (QSSARs) for Chlorobenzenes. 870-879
  

• Peter Zinn:
  Adaptive Multicomponent Analysis by Genetic Algorithms. 880-887
  
• Sorel Muresan, Jens Sadowski:
  "In-House Likeness": Comparison of Large Compound Collections Using Artificial Neural Networks. 888-893
  
• César Hervás-Martínez, Alfonso Carlos Martínez, Manuel Silva, Juan Manuel Serrano:
  Improving the Quantification of Highly Overlapping Chromatographic Peaks by Using Product Unit Neural Networks Modeled by an Evolutionary Algorithm. 894-903
  
• Frances V. Buontempo, Xue Zhong Wang, Mulaisho Mwense, Nigel Horan, Anita Young, Daniel Osborn:
  Genetic Programming for the Induction of Decision Trees to Model Ecotoxicity Data. 904-912
  
• Alan R. Katritzky, Indrek Tulp, Dan C. Fara, Antonino Lauria, Uko Maran, William E. Acree Jr.:
  A General Treatment of Solubility. 3. Principal Component Analysis (PCA) of the Solubilities of Diverse Solutes in Diverse Solvents. 913-923
  
• Matthew D. Miller, David M. Yourtee, Alan G. Glaros, Cecil C. Chappelow, J. David Eick, Andrew J. Holder:
  Quantum Mechanical Structure-Activity Relationship Analyses for Skin Sensitization. 924-929
  
• Milan Soskic, Dejan Plavsic:
  Modeling the Octanol-Water Partition Coefficients by an Optimized Molecular Connectivity Index. 930-938
  
• Pierre Mahé, Nobuhisa Ueda, Tatsuya Akutsu, Jean-Luc Perret, Jean-Philippe Vert:
  Graph Kernels for Molecular Structure-Activity Relationship Analysis with Support Vector Machines. 939-951
  
• Shengqiao Li, Adam Fedorowicz, Harshinder Singh, Sidney C. Soderholm:
  Application of the Random Forest Method in Studies of Local Lymph Node Assay Based Skin Sensitization Data. 952-964
  
• Corneliu Buda, Abul B. Kazi, Adriana Dinescu, Thomas R. Cundari:
  Stability Studies of Transition-Metal Linkage Isomers Using Quantum Mechanical Methods. Groups 11 and 12 Transition Metals. 965-970
  
• James L. Melville, Kevin R. J. Lovelock, Claire Wilson, Bryan Allbutt, Edmund K. Burke, Barry Lygo, Jonathan D. Hirst:
  Exploring Phase-Transfer Catalysis with Molecular Dynamics and 3D/4D Quantitative Structure-Selectivity Relationships. 971-981
  
• Chun Wei Yap, Yu Zong Chen:
  Prediction of Cytochrome P450 3A4, 2D6, and 2C9 Inhibitors and Substrates by Using Support Vector Machines. 982-992
  
• Simon S. J. Cross:
  Improved FlexX Docking Using FlexS-Determined Base Fragment Placement. 993-1001
  
• Mircea V. Diudea:
  Nanoporous Carbon Allotropes by Septupling Map Operations. 1002-1009
  
• Jr-Hung Lin, Timothy Clark:
  Nanoporous Carbon Allotropes by Septupling Map Operations. 1010-1016
  
• Vladimir N. Maiorov, Robert P. Sheridan:
  Enhanced Virtual Screening by Combined Use of Two Docking Methods: Getting the Most on a Limited Budget. 1017-1023
  

• Qi Shen, Jian-Hui Jiang, Jing-chao Tao, Guo-Li Shen, Ru-Qin Yu:
  Modified Ant Colony Optimization Algorithm for Variable Selection in QSAR Modeling: QSAR Studies of Cyclooxygenase Inhibitors. 1024-1029
  
• Jan Cz. Dobrowolski, Aleksander P. Mazurek:
  Model Carbyne vs Ideal and DNA Catenanes. 1030-1038
  

• Harald Mauser, Olivier Roche, Martin Stahl, Stephan Müller:
  Prediction of UV and ESI-MS Signal Intensities. 1039-1046
  
• Brian S. Henriksen, Todd J. Zahn, Jeffrey D. Evanseck, Steven M. Firestine, Richard A. Gibbs:
  Computational and Conformational Evaluation of FTase Alternative Substrates: Insight into a Novel Enzyme Binding Pocket. 1047-1052
  
• Bernd Ehresmann, Marcel J. de Groot, Timothy Clark:
  Surface-Integral QSPR Models: Local Energy Properties. 1053-1060
  
• Chidochangu P. Mpamhanga, Beining Chen, Iain M. McLay, Daniel L. Ormsby, Mika K. Lindvall:
  Retrospective Docking Study of PDE4B Ligands and an Analysis of the Behavior of Selected Scoring Functions. 1061-1074
  
• Alban Lepailleur, Ronan Bureau, Magalie Paillet-Loilier, Frédéric Fabis, Nicolas Saettel, Stéphane Lemaître, François Dauphin, Aurélien Lesnard, Jean-Charles Lancelot, Sylvain Rault:
  Molecular Modeling Studies Focused on 5-HT₇ versus 5-HT_1A Selectivity. Discovery of Novel Phenylpyrrole Derivatives with High Affinity for 5-HT₇ Receptors. 1075-1081
  
• Yovani Marrero-Ponce, Maité Iyarreta-Veitía, Alina Montero-Torres, Carlos Romero-Zaldivar, Carlos A. Brandt, Priscilla E. Ávila, Karin Kirchgatter, Yanetsy Machado:
  Ligand-Based Virtual Screening and in Silico Design of New Antimalarial Compounds Using Nonstochastic and Stochastic Total and Atom-Type Quadratic Maps. 1082-1100
  
• B. Gopalakrishnan, V. Aparna, J. Jeevan, M. Ravi, G. R. Desiraju:
  A Virtual Screening Approach for Thymidine Monophosphate Kinase Inhibitors as Antitubercular Agents Based on Docking and Pharmacophore Models. 1101-1108
  
• Rajarshi Guha, David T. Stanton, Peter C. Jurs:
  Interpreting Computational Neural Network Quantitative Structure-Activity Relationship Models: A Detailed Interpretation of the Weights and Biases. 1109-1121
  
• Jamal C. Saeh, Paul D. Lyne, Bryan K. Takasaki, David A. Cosgrove:
  Lead Hopping Using SVM and 3D Pharmacophore Fingerprints. 1122-1133
  

• Jinn-Moon Yang, Yen-Fu Chen, Tsai-Wei Shen, Bruce S. Kristal, D. Frank Hsu:
  Consensus Scoring Criteria for Improving Enrichment in Virtual Screening. 1134-1146
  
• Pasak Senawongse, Andrew R. Dalby, Zheng Rong Yang:
  Predicting the Phosphorylation Sites Using Hidden Markov Models and Machine Learning Methods. 1147-1152
  

Volume 45, Number 5, September 2005

• Boris L. Milman:
  Literature-Based Generation of Hypotheses on Chemical Composition Using Database Co-occurrence of Chemical Compounds. 1153-1158
  
• Christian Merkwirth, Thomas Lengauer:
  Automatic Generation of Complementary Descriptors with Molecular Graph Networks. 1159-1168
  
• Martin Hornig, Andreas Klamt:
  COSMOfrag: A Novel Tool for High-Throughput ADME Property Prediction and Similarity Screening Based on Quantum Chemistry. 1169-1177
  
• Irene Luque Ruiz, Gonzalo Cerruela García, Miguel Ángel Gómez-Nieto:
  Clustering Chemical Databases Using Adaptable Projection Cells and MCS Similarity Values. 1178-1194
  
• John W. Raymond, Christopher E. Kibbey:
  An Automated Method for Exploring Targeted Substructural Diversity within Sets of Chemical Structures. 1195-1204
  
• Milan Randic, Marjana Novic, Marjan Vracko:
  Novel Characterization of Proteomics Maps by Sequential Neighborhoods of Protein Spots. 1205-1213
  
• Qian Zhu, Jianhua Yao, Shengang Yuan, Feng Li, Haifeng Chen, Wei Cai, Quan Liao:
  Superstructure Searching Algorithm for Generic Reaction Retrieval. 1214-1222
  
• Daniel J. Graham:
  Information Content in Organic Molecules: Aggregation States and Solvent Effects. 1223-1236
  
• Tharun Kumar Allu, Tudor I. Oprea:
  Rapid Evaluation of Synthetic and Molecular Complexity for in Silico Chemistry. 1237-1243
  
• Mats G. Gustafsson:
  Independent Component Analysis Yields Chemically Interpretable Latent Variables in Multivariate Regression. 1244-1255
  
• Ester Papa, Fulvio Villa, Paola Gramatica:
  Statistically Validated QSARs, Based on Theoretical Descriptors, for Modeling Aquatic Toxicity of Organic Chemicals in Pimephales promelas (Fathead Minnow). 1256-1266
  

• Matheus Froeyen, Piet Herdewijn:
  Correct Bond Order Assignment in a Molecular Framework Using Integer Linear Programming with Application to Molecules Where Only Non-Hydrogen Atom Coordinates Are Available. 1267-1274
  
• Ludovic Kurunczi, Edward Seclaman, Tudor I. Oprea, Luminita Crisan, Zeno Simon:
  MTD-PLS: A PLS Variant of the Minimal Topologic Difference Method. III. Mapping Interactions between Estradiol Derivatives and the Alpha Estrogenic Receptor. 1275-1281
  
• Anna Vulpetti, Patrizia Crivori, Alexander Cameron, Jay Bertrand, Maria Gabriella Brasca, Roberto D'Alessio, Paolo Pevarello:
  Structure-Based Approaches to Improve Selectivity: CDK2-GSK3beta Binding Site Analysis. 1282-1290
  
• Iris Antes, Christian Merkwirth, Thomas Lengauer:
  POEM: Parameter Optimization Using Ensemble Methods: Application to Target Specific Scoring Functions. 1291-1302
  
• Duangkamol Tantanak, Jumras Limtrakul, Matthew Paul Gleeson:
  Probing the Structural and Electronic Factors Affecting the Adsorption and Reactivity of Alkenes in Acidic Zeolites Using DFT Calculations and Multivariate Statistical Methods. 1303-1312
  
• Marie M. Ahlström, Marianne Ridderström, Kristina Luthman, Ismael Zamora:
  Virtual Screening and Scaffold Hopping Based on GRID Molecular Interaction Fields. 1313-1323
  

• Nicole A. Kratochwil, Pari Malherbe, Lothar Lindemann, Martin Ebeling, Marius C. Hoener, Andreas Mühlemann, Richard H. P. Porter, Martin Stahl, Paul R. Gerber:
  An Automated System for the Analysis of G Protein-Coupled Receptor Transmembrane Binding Pockets: Alignment, Receptor-Based Pharmacophores, and Their Application. 1324-1336
  

• Ron Jones, Paul C. Connolly, Andreas Klamt, Michael Diedenhofen:
  Use of Surface Charges from DFT Calculations To Predict Intestinal Absorption. 1337-1342
  
• Hsin-Yuan Wei, Keng-Chang Tsai, Thy-Hou Lin:
  Modeling Ligand-Receptor Interaction for Some MHC Class II HLA-DR4 Peptide Mimetic Inhibitors Using Several Molecular Docking and 3D QSAR Techniques. 1343-1351
  
• Kunal Roy, J. Thomas Leonard:
  QSAR Analyses of 3-(4-Benzylpiperidin-1-yl)-N-phenylpropylamine Derivatives as Potent CCR5 Antagonists. 1352-1368
  
• Andreas Bender, Robert C. Glen:
  A Discussion of Measures of Enrichment in Virtual Screening: Comparing the Information Content of Descriptors with Increasing Levels of Sophistication. 1369-1375
  
• Hu Li, Chun Wei Yap, Choong Yong Ung, Ying Xue, Zhi Wei Cao, Yu Zong Chen:
  Effect of Selection of Molecular Descriptors on the Prediction of Blood-Brain Barrier Penetrating and Nonpenetrating Agents by Statistical Learning Methods. 1376-1384
  
• Brian W. Clare, Claudiu T. Supuran:
  Predictive Flip Regression: A Technique for QSAR of Derivatives of Symmetric Molecules. 1385-1391
  

• Yun Xu, Richard G. Brereton:
  Diagnostic Pattern Recognition on Gene-Expression Profile Data by Using One-Class Classification. 1392-1401
  
• Joel R. Bock, David A. Gough:
  Virtual Screen for Ligands of Orphan G Protein-Coupled Receptors. 1402-1414
  
• Channa K. Hattotuwagama, Irini A. Doytchinova, Darren R. Flower:
  In Silico Prediction of Peptide Binding Affinity to Class I Mouse Major Histocompatibility Complexes: A Comparative Molecular Similarity Index Analysis (CoMSIA) Study. 1415-1423
  
• Zheng Rong Yang, Felicia Charles Johnson:
  Prediction of T-Cell Epitopes Using Biosupport Vector Machines. 1424-1428
  
• Daniele Dell'Orco, Michele Seeber, Pier Giuseppe De Benedetti, Francesca Fanelli:
  Probing Fragment Complementation by Rigid-Body Docking: in Silico Reconstitution of Calbindin D9k. 1429-1438
  

• Ralph T. Mosley, J. Christopher Culberson, Bryan Kraker, Bradley P. Feuston, Robert P. Sheridan, John F. Conway, Joseph K. Forbes, Subhas J. Chakravorty, Simon K. Kearsley:
  Reagent Selector: Using Synthon Analysis to Visualize Reagent Properties and Assist in Combinatorial Library Design. 1439-1446
  
• Rafal Gieleciak, Tomasz Magdziarz, Andrzej Bak, Jaroslaw Polanski:
  Modeling Robust QSAR. 1. Coding Molecules in 3D-QSAR - from a Point to Surface Sectors and Molecular Volumes. 1447-1455
  
• Frank Oellien, Wolf-Dietrich Ihlenfeldt, Johann Gasteiger:
  InfVis - Platform-Independent Visual Data Mining of Multidimensional Chemical Data Sets. 1456-1467
  

• John J. Irwin:
  Software Review: ChemOffice 2005 Pro by CambridgeSoft. 1468-1469
  
• Dana L. Roth:
  SPRESIweb 2.1, a Selective Chemical Synthesis and Reaction Database. 1470-1473
  
• Achim Zielesny:
  Chemistry Software Package ChemOffice Ultra 2005. 1474-1477
  

Volume 45, Number 6, November 2005

• Dusanka Janezic:
  The Regional Biophysics Meeting March 16-20, 2005, Zrece, Slovenia. 1481
  
• Volkmar Heinrich, Andrew Leung, Evan Evans:
  Nano-to-Microscale Mechanical Switches and Fuses Mediate Adhesive Contacts between Leukocytes and the Endothelium. 1482-1490
  
• Vlado Malacic, Patricija Mozetic:
  Modeling of the Spread of an Effluent and the Overturning Length Scale near an Underwater Source in the Northern Adriatic. 1491-1501
  
• Joachim Scholz-Starke, Alessia Naso, Armando Carpaneto:
  A Perspective on the Slow Vacuolar Channel in Vacuoles from Higher Plant Cells. 1502-1506
  

• Federico Marini, Alessandra Roncaglioni, Marjana Novic:
  Variable Selection and Interpretation in Structure-Affinity Correlation Modeling of Estrogen Receptor Binders. 1507-1519
  
• Katalin Tenger, Petro Khoroshyy, Balázs Leitgeb, Gábor Rákhely, Natalia Borovok, Alexander Kotlyar, Dmitry A. Dolgikh, László Zimányi:
  Complex Kinetics of the Electron Transfer between the Photoactive Redox Label TUPS and the Heme of Cytochrome c. 1520-1526
  
• Klavdija Kutnar, Aleksander Malnic, Dragan Marusic:
  Chirality of Toroidal Molecular Graphs. 1527-1535
  
• Pavle R. Andjus, Aleksandar Bajic, Lan Zhu, Piergiorgio Strata:
  Metabotropic Glutamate Receptor-Mediated Currents at the Climbing Fiber to Purkinje Cell Synapse. 1536-1538
  
• Mauro Dalla Serra, Manuela Coraiola, Gabriella Viero, Massimiliano Comai, Cristina Potrich, Mercedes Ferreras, Lamine Baba-Moussa, Didier A. Colin, Gianfranco Menestrina, Sucharit Bhakdi, Gilles Prévost:
  Staphylococcus aureus Bicomponent gamma-Hemolysins, HlgA, HlgB, and HlgC, Can Form Mixed Pores Containing All Components. 1539-1545
  
• Urban Bren, Milan Hodoscek, Joze Koller:
  Development and Validation of Empirical Force Field Parameters for Netropsin. 1546-1552
  
• Magdy Lucic Lavcevic, Pavo Dubcek, Zorica Crnjak Orel, Aleksandra Turkovic:
  GISAXS View of Vanadium/Cerium Oxide Thin Films and Influence of Lithium Intercalation. 1553-1557
  
• Marjan Sterk, Roman Trobec:
  Biomedical Simulation of Heat Transfer in a Human Heart. 1558-1563
  
• Philippe Huetz, Nasim Mavaddat, Janez Mavri:
  Reaction between Ellagic Acid and an Ultimate Carcinogen. 1564-1570
  
• Matej Praprotnik, Dusanka Janezic:
  Molecular Dynamics Integration Meets Standard Theory of Molecular Vibrations. 1571-1579
  
• Marilena Di Valentin, Arianna Bisol, Giancarlo Agostini, Donatella Carbonera:
  Electronic Coupling Effects on Photoinduced Electron Transfer in Carotene-Porphyrin-Fullerene Triads Detected by Time-Resolved EPR. 1580-1588
  
• David Halozan, Christophe Déjugnat, Milan Brumen, Gleb B. Sukhorukov:
  Entrapment of a Weak Polyanion and H⁺/Na⁺ Exchange in Confined Polyelectrolyte Microcapsules. 1589-1592
  
• Franci Merzel, Jeremy C. Smith:
  High-Density Hydration Layer of Lysozymes: Molecular Dynamics Decomposition of Solution Scattering Data. 1593-1599
  
• Urban Borstnik, Dusanka Janezic:
  Symplectic Molecular Dynamics Simulations on Specially Designed Parallel Computers. 1600-1604
  
• Ales Fajmut, Marko Jagodic, Milan Brumen:
  Mathematical Modeling of the Myosin Light Chain Kinase Activation. 1605-1609
  
• Ales Fajmut, Andrej Dobovisek, Milan Brumen:
  Mathematical Modeling of the Relation between Myosin Phosphorylation and Stress Development in Smooth Muscles. 1610-1615
  
• Dubravka Krilov, Janko N. Herak:
  Probabilistic Kinetic Model of Slow Oxidation of Low-Density Lipoprotein. 3. Hydroperoxide-Free Initiation. 1616-1620
  
• David Stopar, Janez Strancar, Ruud B. Spruijt, Marcus A. Hemminga:
  Exploring the Local Conformational Space of a Membrane Protein by Site-Directed Spin Labeling. 1621-1627
  
• Aleh A. Kavalenka, Bogdan Filipic, Marcus A. Hemminga, Janez Strancar:
  Speeding Up a Genetic Algorithm for EPR-Based Spin Label Characterization of Biosystem Complexity. 1628-1635
  
• Marija Raguz, Jasminka Brnjas-Kraljevic:
  Resolved Fluorescence Emission Spectra of PRODAN in Ethanol/Buffer Solvents. 1636-1640
  
• Árpád Karsai, Attila Nagy, András Kengyel, Zsolt Mártonfalvi, László Grama, Botondtól Penke, Miklós S. Z. Kellermayer:
  Effect of Lysine-28 Side-Chain Acetylation on the Nanomechanical Behavior of Alzheimer Amyloid beta25-35 Fibrils. 1641-1646
  
• Igor Weber:
  Receptor Occupancy on an Ellipsoidal Cell in the Presence of a Point Source of a Chemoattractant. 1647-1651
  
• Miha Fosnaric, Klemen Bohinc, Dorit R. Gauger, Ales Iglic, Veronika Kralj-Iglic, Sylvio May:
  The Influence of Anisotropic Membrane Inclusions on Curvature Elastic Properties of Lipid Membranes. 1652-1661
  
• Zoran Arsov, Janez Strancar:
  Determination of Partition Coefficient of Spin Probe between Different Lipid Membrane Phases. 1662-1671
  
• Andrej Vilfan:
  Influence of Fluctuations in Actin Structure on Myosin V Step Size. 1672-1675
  
• Nejc Tomsiè, Blaz Babnik, Darko Lombardo, Blaz Mavcic, Masa Kanduser, Ales Iglic, Veronika Kralj-Iglic:
  Shape and Size of Giant Unilamellar Phospholipid Vesicles Containing Cardiolipin. 1676-1679
  
• Ivan Spasojevic, Vuk Maksimovic, Joanna Zakrzewska, Goran Bacic:
  Effects of 5-Fluorouracil on Erythrocytes in Relation to Its Cardiotoxicity: Membrane Structure and Functioning. 1680-1685
  
• Igor Sersa, Gregor Tratar, Ales Blinc:
  Blood Clot Dissolution Dynamics Simulation during Thrombolytic Therapy. 1686-1690
  
• Anna Segalla, Ildikó Szabó, Paola Costantini, Giorgio Mario Giacometti:
  Study of the Effect of Ion Channel Modulators on Photosynthetic Oxygen Evolution. 1691-1700
  
• Tilen Koklic, Mateja Pirs, Reiner Zeisig, Zrinka Abramovic, Marjeta Sentjurc:
  Membrane Switch Hypothesis. 1. Cell Density Influences Lateral Domain Structure of Tumor Cell Membranes. 1701-1707
  
• Petra Kramaric, Zlatko Pavlica, Tilen Koklic, Alenka Nemec, Nevenka Kozuh Erzen, Marjeta Sentjurc:
  Membrane Switch Hypothesis. 2. Domain Structure of Phagocytes in Horses with Recurrent Airway Obstruction. 1708-1715
  
• Milos Mojovic, Ivan Spasojevic, Goran Bacic:
  Detection of Hydrogen Atom Adduct of Spin-Trap DEPMPO. The Relevance for Studies of Biological Systems. 1716-1718
  

• Erwin Lijnen, Arnout Ceulemans:
  Topology-Aided Molecular Design: The Platonic Molecules of Genera 0 to 3. 1719-1726
  

• Stephanie E. Harris, A. Guy Orpen, Ian J. Bruno, Robin Taylor:
  Factors Affecting d-Block Metal-Ligand Bond Lengths: Toward an Automated Library of Molecular Geometry for Metal Complexes. 1727-1748
  
• Yun-De Xiao, Aaron Clauset, Rebecca Harris, Ersin Bayram, Peter Santago II, Jeffrey D. Schmitt:
  Supervised Self-Organizing Maps in Drug Discovery. 1. Robust Behavior with Overdetermined Data Sets. 1749-1758
  
• Alba T. Macias, Md. Younus Mia, Guanjun Xia, Jun Hayashi, Alexander D. MacKerell Jr.:
  Lead Validation and SAR Development via Chemical Similarity Searching; Application to Compounds Targeting the pY+3 Site of the SH2 Domain of p56^lck. 1759-1766
  
• Paolo Mazzatorta, Martin Smiesko, Elena Lo Piparo, Emilio Benfenati:
  QSAR Model for Predicting Pesticide Aquatic Toxicity. 1767-1774
  
• Qing-You Zhang, João Aires-de-Sousa:
  Structure-Based Classification of Chemical Reactions without Assignment of Reaction Centers. 1775-1783
  
• S. Frank Yan, Hayk Asatryan, Jing Li, Yingyao Zhou:
  Novel Statistical Approach for Primary High-Throughput Screening Hit Selection. 1784-1790
  
• Ralph A. Mansson, Jeremy G. Frey, Jonathan W. Essex, Alan H. Welsh:
  Prediction of Properties from Simulations: A Re-examination with Modern Statistical Methods. 1791-1803
  
• Lei Yang, Peng Wang, Yilin Jiang, Jian Chen:
  Studying the Explanatory Capacity of Artificial Neural Networks for Understanding Environmental Chemical Quantitative Structure-Activity Relationship Models. 1804-1811
  
• Jeffrey W. Godden, Florence L. Stahura, Jürgen Bajorath:
  Anatomy of Fingerprint Search Calculations on Structurally Diverse Sets of Active Compounds. 1812-1819
  
• Yongliang Yang, Dmitri V. Nesterenko, Ryan P. Trump, Ken Yamaguchi, Paul A. Bartlett, Dale G. Drueckhammer:
  Virtual Hydrocarbon and Combinatorial Databases for Use with CAVEAT. 1820-1823
  
• Justin Klekota, Erik Brauner, Stuart L. Schreiber:
  Identifying Biologically Active Compound Classes Using Phenotypic Screening Data and Sampling Statistics. 1824-1836
  

• Tadeusz Marek Krygowski, Joanna E. Zachara, Robert Moszynski:
  Theoretical Study of Changes in pi-Electron Delocalization in the Analogues of an ortho-Hydroxy Schiff Base When the Proton Is Replaced with Li⁺ or BeH⁺. 1837-1841
  
• Artem Cherkasov, Zheng Shi, Yvonne Y. Li, Steven J. M. Jones, Magid Fallahi, Geoffrey L. Hammond:
  'Inductive' Charges on Atoms in Proteins: Comparative Docking with the Extended Steroid Benchmark Set and Discovery of a Novel SHBG Ligand. 1842-1853
  
• Kaushal Rege, Asif Ladiwala, Shanghui Hu, Curt M. Breneman, Jonathan S. Dordick, Steven M. Cramer:
  Investigation of DNA-Binding Properties of an Aminoglycoside-Polyamine Library Using Quantitative Structure-Activity Relationship (QSAR) Models. 1854-1863
  

• Pierre Crettaz, Romualdo Benigni:
  Prediction of the Rodent Carcinogenicity of 60 Pesticides by the DEREKfW Expert System. 1864-1873
  

• Samuli-Petrus Korhonen, Kari Tuppurainen, Reino Laatikainen, Mikael Peräkylä:
  Comparing the Performance of FLUFF-BALL to SEAL-CoMFA with a Large Diverse Estrogen Data Set: From Relevant Superpositions to Solid Predictions. 1874-1883
  
• Michael Fernández, Alain Tundidor-Camba, Julio Caballero:
  Modeling of Cyclin-Dependent Kinase Inhibition by 1H-Pyrazolo[3, 4-d]Pyrimidine Derivatives Using Artificial Neural Network Ensembles. 1884-1895
  
• Nahoum G. Anthony, Guillaume Huchet, Blair F. Johnston, John A. Parkinson, Colin J. Suckling, Roger D. Waigh, Simon P. Mackay:
  In Silico Footprinting of Ligands Binding to the Minor Groove of DNA. 1896-1907
  
• Andrew J. S. Knox, Mary J. Meegan, Giorgio Carta, David G. Lloyd:
  Considerations in Compound Database Preparation-"Hidden" Impact on Virtual Screening Results. 1908-1919
  
• Jianfeng Pei, Hao Chen, Zhenming Liu, Xiaofeng Han, Qi Wang, Bin Shen, Jiaju Zhou, Luhua Lai:
  Improving the Quality of 3D-QSAR by Using Flexible-Ligand Receptor Models. 1920-1933
  
• Madhu Chopra, Anil K. Mishra:
  Ligand-Based Molecular Modeling Study on a Chemically Diverse Series of Cholecystokinin-B/Gastrin Receptor Antagonists: Generation of Predictive Model. 1934-1942
  

• Konstantin B. Tarmyshov, Florian Müller-Plathe:
  Parallelizing a Molecular Dynamics Algorithm on a Multiprocessor Workstation Using OpenMP. 1943-1952
  
• Mikko J. Vainio, Mark S. Johnson:
  McQSAR: A Multiconformational Quantitative Structure-Activity Relationship Engine Driven by Genetic Algorithms. 1953-1961
  

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