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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 - Ana 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 Rodrigues 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-Estudillo
, 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