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ORCIDJournal of Chemical Information and Modeling, Volume 47
Volume 47, Number 1, January 2007
- Qing-You Zhang, João Aires-de-Sousa
:
Random Forest Prediction of Mutagenicity from Empirical Physicochemical Descriptors. 1-8 - Dimitar Hristozov, Fernando B. Da Costa, Johann Gasteiger:
Sesquiterpene Lactones-Based Classification of the Family Asteraceae Using Neural Networks and k-Nearest Neighbors. 9-19 - Jerry Ray Dias:
Strain-Free Total Resonant Sextet Benzenoids and Their Antisextet Dualists and Retro-Leapfrogs. 20-24 - James L. Melville, Jenna F. Riley, Jonathan D. Hirst:
Similarity by Compression. 25-33 - Paolo Mazzatorta, Liên-Anh Tran, Benoît Schilter, Martin G. Grigorov:
Integration of Structure-Activity Relationship and Artificial Intelligence Systems To Improve in Silico Prediction of Ames Test Mutagenicity. 34-38 - Martin Vogt, Jeffrey W. Godden, Jürgen Bajorath:
Bayesian Interpretation of a Distance Function for Navigating High-Dimensional Descriptor Spaces. 39-46 - Ansgar Schuffenhauer, Peter Ertl, Silvio Roggo, Stefan Wetzel, Marcus A. Koch, Herbert Waldmann:
The Scaffold Tree - Visualization of the Scaffold Universe by Hierarchical Scaffold Classification. 47-58 - José Batista, Jürgen Bajorath:
Chemical Database Mining through Entropy-Based Molecular Similarity Assessment of Randomly Generated Structural Fragment Populations. 59-68 - Dimitris K. Agrafiotis, Deepak Bandyopadhyay, Michael Farnum:
Radial Clustergrams: Visualizing the Aggregate Properties of Hierarchical Clusters. 69-75
- Simone Sciabola, Iñaki Morao, Marcel J. de Groot:
Pharmacophoric Fingerprint Method (TOPP) for 3D-QSAR Modeling: Application to CYP2D6 Metabolic Stability. 76-84 - Cornel Catana, Pieter F. W. Stouten:
Novel, Customizable Scoring Functions, Parameterized Using N-PLS, for Structure-Based Drug Discovery. 85-91 - Tatjana Eitrich, Achim Kless, Claudia Druska, Wolfgang Meyer, Johannes Grotendorst:
Classification of Highly Unbalanced CYP450 Data of Drugs Using Cost Sensitive Machine Learning Techniques. 92-103 - Hiroshi Takeuchi:
Novel Method for Geometry Optimization of Molecular Clusters: Application to Benzene Clusters. 104-109 - Andrew C. Good, Mark A. Hermsmeier:
Measuring CAMD Technique Performance, 2. How "Druglike" Are Drugs? Implications of Random Test Set Selection Exemplified Using Druglikeness Classification Models. 110-114 - Christina Mintz, Michael Clark, William E. Acree Jr., Michael H. Abraham:
Enthalpy of Solvation Correlations for Gaseous Solutes Dissolved in Water and in 1-Octanol Based on the Abraham Model. 115-121
- Marwen Naïm, Sathesh Bhat, Kathryn N. Rankin, Sheldon Dennis, Shafinaz F. Chowdhury, Imran Siddiqi, Piotr Drabik, Traian Sulea, Christopher I. Bayly, Araz Jakalian, Enrico O. Purisima:
Solvated Interaction Energy (SIE) for Scoring Protein-Ligand Binding Affinities, 1. Exploring the Parameter Space. 122-133 - Cristian Obiol-Pardo, Jaime Rubio-Martinez:
Comparative Evaluation of MMPBSA and XSCORE To Compute Binding Free Energy in XIAP-Peptide Complexes. 134-142
- David W. Salt, Subhash Ajmani, Ray Crichton, David J. Livingstone:
An Improved Approximation to the Estimation of the Critical F Values in Best Subset Regression. 143-149 - David S. Palmer, Noel M. O'Boyle, Robert C. Glen, John B. O. Mitchell:
Random Forest Models To Predict Aqueous Solubility. 150-158 - Hua Yuan, Yongyan Wang, Yiyu Cheng:
Local and Global Quantitative Structure-Activity Relationship Modeling and Prediction for the Baseline Toxicity. 159-169 - Yuan H. Zhao, Michael H. Abraham, Adam Ibrahim, Paul V. Fish, Susan Cole, Mark L. Lewis, Marcel J. de Groot, Derek P. Reynolds:
Predicting Penetration Across the Blood-Brain Barrier from Simple Descriptors and Fragmentation Schemes. 170-175 - Barna Bordás, Iván Bélai, Antal Lopata, Z. Szántó:
Interpretation of Scoring Functions Using 3D Molecular Fields. Mapping the Diacyl-Hydrazine-Binding Pocket of an Insect Ecdysone Receptor. 176-185 - Michael C. Hutter:
Separating Drugs from Nondrugs: A Statistical Approach Using Atom Pair Distributions. 186-194 - Gilles Marcou, Didier Rognan:
Optimizing Fragment and Scaffold Docking by Use of Molecular Interaction Fingerprints. 195-207 - Tingjun Hou, Junmei Wang, Wei Zhang, Xiaojie Xu:
ADME Evaluation in Drug Discovery, 7. Prediction of Oral Absorption by Correlation and Classification. 208-218 - Craig L. Bruce, James L. Melville, Stephen D. Pickett, Jonathan D. Hirst:
Contemporary QSAR Classifiers Compared. 219-227 - Karin Wichmann, Michael Diedenhofen, Andreas Klamt:
Prediction of Blood-Βrain Partitioning and Human Serum Albumin Binding Based on COSMO-RS σ-Moments. 228-233
- Irini A. Doytchinova, Darren R. Flower:
Predicting Class I Major Histocompatibility Complex (MHC) Binders Using Multivariate Statistics: Comparison of Discriminant Analysis and Multiple Linear Regression. 234-238 - Claes R. Andersson, Mårten Fryknäs, Linda Rickardson, Rolf Larsson, Anders Isaksson, Mats G. Gustafsson:
In Vitro Drug Sensitivity-Gene Expression Correlations Involve a Tissue of Origin Dependency. 239-248
- Anselm H. C. Horn:
Introduction to Programming with Fortran: With Coverage of Fortran 90, 95, 2003 and 77. By Ian Chivers and Jane Sleightholme. Springer: London, U.K., 2005. XX+592 pp and CD-ROM. ISBN 1-84628-053-5. Softcover. U.S. $69.95, Euro 53.45. 249-250 - Stephen R. Heller:
Adobe After Effects 7.0 - Studio Techniques By Mark Christiansen. Adobe (Peachpit) Press: Berkeley, CA, 2006, 576 pp and DVD. ISBN 0-321-38552-7. Softcover. U.S. $54.99. 250 - Stephen R. Heller:
Adobe Encore DVD 2.0 - Classroom in a Book By the Adobe Creative Team. Adobe (Peachpit) Press: Berkeley, CA, 2006, 248 pp and DVD. ISBN 0-321-26795-8. Softcover. U.S. $45.00. 250 - Stephen R. Heller:
Final Cut Express HD: Digital Video Editing for Everyone (Apple Pro Training) By Diana Weynand. Adobe (Peachpit) Press: Berkeley, CA, 2006, 512 pp and DVD. ISBN 0-321-33533-3. Softcover. U.S. $49.99. 250 - Stephen R. Heller:
Adobe Premier Pro 2.0 - Studio Techniques By Jacob Rosenberg. Adobe (Peachpit) Press: Berkeley, CA, 2006, 624 pp and DVD. ISBN 0-321-38547-0. Softcover. U.S. $54.99. 250
Volume 47, Number 2, March 2007
- Thomas M. Ehrman, David J. Barlow, Peter J. Hylands:
Phytochemical Databases of Chinese Herbal Constituents and Bioactive Plant Compounds with Known Target Specificities. 254-263 - Thomas M. Ehrman, David J. Barlow, Peter J. Hylands:
Virtual Screening of Chinese Herbs with Random Forest. 264-278 - Massimo Baroni, Gabriele Cruciani, Simone Sciabola, Francesca Perruccio, Jonathan S. Mason:
A Common Reference Framework for Analyzing/Comparing Proteins and Ligands. Fingerprints for Ligands And Proteins (FLAP): Theory and Application. 279-294 - Ewgenij Proschak, Jörg K. Wegner, Andreas Schüller, Gisbert Schneider, Uli Fechner:
Molecular Query Language (MQL)A Context-Free Grammar for Substructure Matching. 295-301 - S. Joshua Swamidass, Pierre Baldi:
Bounds and Algorithms for Fast Exact Searches of Chemical Fingerprints in Linear and Sublinear Time. 302-317 - Harald Mauser, Martin Stahl:
Chemical Fragment Spaces for de novo Design. 318-324 - Ansgar Schuffenhauer, Nathan Brown, Peter Ertl, Jeremy L. Jenkins, Paul Selzer, Jacques Hamon:
Clustering and Rule-Based Classifications of Chemical Structures Evaluated in the Biological Activity Space. 325-336 - Martin Vogt, Jürgen Bajorath:
Introduction of an Information-Theoretic Method to Predict Recovery Rates of Active Compounds for Bayesian in Silico Screening: Theory and Screening Trials. 337-341 - Tobias Fink, Jean-Louis Reymond:
Virtual Exploration of the Chemical Universe up to 11 Atoms of C, N, O, F: Assembly of 26.4 Million Structures (110.9 Million Stereoisomers) and Analysis for New Ring Systems, Stereochemistry, Physicochemical Properties, Compound Classes, and Drug Discovery. 342-353 - Eleanor J. Gardiner, Valerie J. Gillet, Peter Willett, David A. Cosgrove:
Representing Clusters Using a Maximum Common Edge Substructure Algorithm Applied to Reduced Graphs and Molecular Graphs. 354-366 - Ingo Vogt, Jürgen Bajorath:
Analysis of a High-Throughput Screening Data Set Using Potency-Scaled Molecular Similarity Algorithms. 367-375 - Daniel J. Graham:
Information Content in Organic Molecules: Brownian Processing at Low Levels. 376-389
- Patrick C. Maaß, Tanja Schulz-Gasch, Martin Stahl, Matthias Rarey:
Recore: A Fast and Versatile Method for Scaffold Hopping Based on Small Molecule Crystal Structure Conformations. 390-399 - Shinji Soga, Hiroki Shirai, Masato Kobori, Noriaki Hirayama:
Use of Amino Acid Composition to Predict Ligand-Binding Sites. 400-406 - Anton Schwaighofer, Timon Schroeter, Sebastian Mika, Julian Laub, Antonius ter Laak, Detlev Sülzle, Ursula Ganzer, Nikolaus Heinrich, Klaus-Robert Müller:
Accurate Solubility Prediction with Error Bars for Electrolytes: A Machine Learning Approach. 407-424 - Wei Chen, Michael K. Gilson:
ConCept: de Novo Design of Synthetic Receptors for Targeted Ligands. 425-434 - Christopher R. Corbeil, Pablo Englebienne, Nicolas Moitessier:
Docking Ligands into Flexible and Solvated Macromolecules, 1. Development and Validation of FITTED 1.0. 435-449 - Stephen P. Jelfs, Peter Ertl, Paul Selzer:
Estimation of pKa for Druglike Compounds Using Semiempirical and Information-Based Descriptors. 450-459 - Tingjun Hou, Junmei Wang, Wei Zhang, Xiaojie Xu:
ADME Evaluation in Drug Discovery, 6. Can Oral Bioavailability in Humans Be Effectively Predicted by Simple Molecular Property-Based Rules? 460-463 - Ivan Baran, Radka Svobodová Vareková, Laavanya Parthasarathi, Simon Suchomel, Fergal P. Casey, Denis C. Shields:
Identification of Potential Small Molecule Peptidomimetics Similar to Motifs in Proteins. 464-474 - Subhendu Mukherjee, Shuchi Nagar, Sanchita Mullick, Arup Mukherjee, Achintya Saha:
Pharmacophore Mapping of Selective Binding Affinity of Estrogen Modulators through Classical and Space Modeling Approaches: Exploration of Bridged-Cyclic Compounds with Diarylethylene Linkage. 475-487 - Jean-François Truchon, Christopher I. Bayly:
Evaluating Virtual Screening Methods: Good and Bad Metrics for the "Early Recognition" Problem. 488-508 - Hongsuk Kang, Hwanho Choi, Hwangseo Park:
Prediction of Molecular Solvation Free Energy Based on the Optimization of Atomic Solvation Parameters with Genetic Algorithm. 509-514 - Tiziano Tuccinardi, Elisa Nuti, Gabriella Ortore, Claudiu T. Supuran, Armando Rossello, Adriano Martinelli:
Analysis of Human Carbonic Anhydrase II: Docking Reliability and Receptor-Based 3D-QSAR Study. 515-525 - Reiji Teramoto, Hiroaki Fukunishi:
Supervised Consensus Scoring for Docking and Virtual Screening. 526-534
- Terttu I. Hukka, Tuula T. Pakkanen:
Modeling the Interaction between Two- and Four-Ring Progestin Models and a Silicone-Based Polymer Model: A Density Functional Theory Study. 535-546 - Rafal Gieleciak, Jaroslaw Polanski:
Modeling Robust QSAR, 2. Iterative Variable Elimination Schemes for CoMSA: Application for Modeling Benzoic Acid pKa Values. 547-556 - M. Letizia Barreca, Laura De Luca, Nunzio Iraci, Angela Rao, Stefania Ferro, Giovanni Maga, Alba Chimirri:
Structure-Based Pharmacophore Identification of New Chemical Scaffolds as Non-Nucleoside Reverse Transcriptase Inhibitors. 557-562 - Theodora M. Steindl, Daniela Schuster, Christian Laggner, Karen Chuang, Rémy D. Hoffmann, Thierry Langer:
Parallel Screening and Activity Profiling with HIV Protease Inhibitor Pharmacophore Models. 563-571 - Andrea Bortolato, Stefano Moro:
In Silico Binding Free Energy Predictability by Using the Linear Interaction Energy (LIE) Method: Bromobenzimidazole CK2 Inhibitors as a Case Study. 572-582 - Scott Boyer, Catrin Hasselgren Arnby, Lars Carlsson, James Smith, Viktor Stein, Robert C. Glen:
Reaction Site Mapping of Xenobiotic Biotransformations. 583-590 - Jörn Marialke, Robert Körner, Simon Tietze, Joannis Apostolakis:
Graph-Based Molecular Alignment (GMA). 591-601 - Elodie Lescot, Jana Sopkova-de Oliveira Santos, Christophe Dubessy, Hassan Oulyadi, Aurélien Lesnard, Hubert Vaudry, Ronan Bureau, Sylvain Rault:
Definition of New Pharmacophores for Nonpeptide Antagonists of Human Urotensin-II. Comparison with the 3D-structure of Human Urotensin-II and URP. 602-612 - Jing Wei, Songqing Wang, Shaofen Gao, Xuedong Dai, Qingzhi Gao:
3D-Pharmacophore Models for Selective A2A and A2B Adenosine Receptor Antagonists. 613-625 - James L. Melville, Jonathan D. Hirst:
TMACC: Interpretable Correlation Descriptors for Quantitative Structure-Activity Relationships. 626-634 - Ajit P. Zambre, Ashok L. Ganure, Devanand Shinde, Vithal M. Kulkarni:
Perspective Assessment of COX-1 and COX-2 Selectivity of Nonsteroidal Anti-Inflammatory Drugs from Clinical Practice: Use of Genetic Function Approximation. 635-643 - Tiziano Tuccinardi, Fabrizio Manetti, Silvia Schenone, Adriano Martinelli, Maurizio Botta:
Construction and Validation of a RET TK Catalytic Domain by Homology Modeling. 644-655 - Uli Fechner, Gisbert Schneider:
Flux (2): Comparison of Molecular Mutation and Crossover Operators for Ligand-Based de Novo Design. 656-667
- Yipin Lu, Renxiao Wang, Chao-Yie Yang, Shaomeng Wang:
Analysis of Ligand-Bound Water Molecules in High-Resolution Crystal Structures of Protein-Ligand Complexes. 668-675 - Pamela L. Piotrowski, Bobby G. Sumpter, Heinrich V. Malling, John S. Wassom, Pinyi Lu, Robin A. Brothers, Gary A. Sega, Sheryl A. Martin, Morey Parang:
A Toxicity Evaluation and Predictive System Based on Neural Networks and Wavelets. 676-685
- Maciej Haranczyk, Maciej Gutowski:
Quantum Mechanical Energy-Based Screening of Combinatorially Generated Library of Tautomers. TauTGen: A Tautomer Generator Program. 686-694 - Krystian Eitner, Tomasz Gaweda, Marcin Hoffmann, Miroslawa Jura, Leszek Rychlewski, Jan Barciszewski:
eHiTS-to-VMD Interface Application. The Search for Tyrosine-tRNA Ligase Inhibitors. 695-702
- Robert E. Buntrock:
The ACS Style Guide, Third Edition: Effective Communication of Scientific Information Edited by Anne M. Coghill and Lorrin R. Garson. American Chemical Society and Oxford University Press: Washington, DC and Oxford, U.K, 2006. XIV + 430 pp. ISBN 0-8412-3999-1. Hardcover. $59.50. 703 - Robert E. Buntrock:
The Merck Index: An Encyclopedia of Chemicals, Drugs, and Biologicals, Fourteenth Edition Edited by Maryadele J. O'Neil, Patricia E. Heckelman, Cherie B. Koch, and Kristin J. Roman. Merck & Co., Inc.: Whitehouse Station, New Jersey, 2006. xiv + 1756 pp. + tables and indexes; includes CD and Internet access. ISBN 978-0-911910-00-1. Hardcover. U.S. $125.00. 703-704 - Stephen R. Heller:
Understanding Adobe Photoshop: Digital Imaging Concepts and Techniques By Richard M. Harrington. Adobe (Peachpit) Press: Berkeley, CA, 2006, 400 pages and DVD. ISBN 0-321-36898-3. Softcover. US$ 44.99. 704 - Stephen R. Heller:
Macromedia Dreamweaver 8: Training from the Source By Khristine Annwyn Page. Macromedia Press: Berkeley, CA, 2006, 608 pages and CD-ROM. ISBN 0-321-33626-7. Softcover. US$ 44.99. 704
Volume 47, Number 3, May 2007
- Jerry Ray Dias:
Mathematics of Periodic Tables for Benzenoid Hydrocarbons. 707-715 - Alexandru T. Balaban, Adrian Beteringhe, Titus Constantinescu, Petru A. Filip, Ovidiu Ivanciuc:
Four New Topological Indices Based on the Molecular Path Code. 716-731 - Dragan Marusic:
Hamilton Cycles and Paths in Fullerenes. 732-736 - Spela Zuperl, Primoz Pristovsek, Viktor Menart, Vladka Gaberc-Porekar, Marjana Novic:
Chemometric Approach in Quantification of Structural Identity/Similarity of Proteins in Biopharmaceuticals. 737-743 - Haruo Hosoya:
Important Mathematical Structures of the Topological Index Z for Tree Graphs. 744-750 - Emili Besalú, Jesús Vicente de Julián-Ortiz, Lionello Pogliani:
Trends and Plot Methods in MLR Studies. 751-760 - Guillermo Restrepo, Héber Mesa, Eugenio-José Llanos:
Three Dissimilarity Measures to Contrast Dendrograms. 761-770 - Ramanathan Natarajan, Subhash C. Basak, Terrence S. Neumann:
Novel Approach for the Numerical Characterization of Molecular Chirality. 771-775 - Ivan Gutman, Sonja Stankovic, Jelena Durdevic, Boris Furtula:
On the Cycle-Dependence of Topological Resonance Energy. 776-781 - Alan R. Katritzky, Liliana M. Pacureanu, Dimitar A. Dobchev, Mati Karelson:
QSPR Study of Critical Micelle Concentration of Anionic Surfactants Using Computational Molecular Descriptors. 782-793 - Ernesto Estrada, Adelio R. Matamala:
Generalized Topological Indices. Modeling Gas-Phase Rate Coefficients of Atmospheric Relevance. 794-804 - Adalbert Kerber, Reinhard Laue, Markus Meringer, Christoph Rücker:
Molecules in Silico: A Graph Description of Chemical Reactions. 805-817 - Aneta Jezierska, Jaroslaw J. Panek, Aleksander Filarowski:
Molecular Properties Investigation of a Substituted Aromatic Mannich Base: Dynamic and Static Models. 818-831 - Katja Balazic, Jernej Stare, Janez Mavri:
Infrared Spectrum of 4-Methoxypicolinic Acid N-Oxide: Computation of Asymmetric O-H Stretching Band. 832-839 - Jernej Stare:
First-Principle Calculation of Reduced Masses in Vibrational Analysis Using Generalized Internal Coordinates: Some Crucial Aspects and Examples. 840-850 - Todor Pavlov, Milen Todorov, Galina Stoyanova, Patricia Schmieder, Hristo T. Aladjov, Rossitsa Serafimova, Ovanes Mekenyan:
Conformational Coverage by a Genetic Algorithm: Saturation of Conformational Space. 851-863 - Mircea V. Diudea, Aniela E. Vizitiu, Dusanka Janezic:
Cluj and Related Polynomials Applied in Correlating Studies. 864-874 - Halina Szatylowicz, Tadeusz Marek Krygowski, Joanna E. Zachara-Horeglad:
Long-Distance Structural Consequences of H-Bonding. How H-Bonding Affects Aromaticity of the Ring in Variously Substituted Aniline/Anilinium/Anilide Complexes with Bases and Acids. 875-886 - Wolfgang Linert, István Lukovits:
Aromaticity of Carbon Nanotubes. 887-890 - Primoz Luksic, Tomaz Pisanski:
Growth in Catacondensed Benzenoid Graphs. 891-896 - Milan Randic, Harry W. Kroto, Damir Vukicevic:
Numerical Kekulé Structures of Fullerenes and Partitioning of π-Electrons to Pentagonal and Hexagonal Rings. 897-904 - Patrick W. Fowler, Mark Lillington:
Mellitic Trianhydride, C12O9: The Aromatic Oxide of Carbon. 905-908 - Danail Bonchev, Gregory A. Buck:
From Molecular to Biological Structure and Back. 909-917 - Zeljko Debeljak, Armin Skrbo, Ivona Jasprica, Ana Mornar, Vanda Plecko, Mihajlo Banjanac, Marica Medic-Saric:
QSAR Study of Antimicrobial Activity of Some 3-Nitrocoumarins and Related Compounds. 918-926 - Dragos Horvath, Fanny Bonachéra, Vitaly P. Solov'ev, Cédric Gaudin, Alexandre Varnek:
Stochastic versus Stepwise Strategies for Quantitative Structure-Activity Relationship GenerationHow Much Effort May the Mining for Successful QSAR Models Take? 927-939 - Janez Konc, Dusanka Janezic:
Protein-Protein Binding-Sites Prediction by Protein Surface Structure Conservation. 940-944 - Ashesh Nandy, Subhash C. Basak, Brian D. Gute:
Graphical Representation and Numerical Characterization of H5N1 Avian Flu Neuraminidase Gene Sequence. 945-951
- S. Joshua Swamidass, Pierre Baldi:
Mathematical Correction for Fingerprint Similarity Measures to Improve Chemical Retrieval. 952-964 - Chloé-Agathe Azencott, Alexandre Ksikes, S. Joshua Swamidass, Jonathan H. Chen, Liva Ralaivola, Pierre Baldi:
One- to Four-Dimensional Kernels for Virtual Screening and the Prediction of Physical, Chemical, and Biological Properties. 965-974 - Stephen E. Stein, Valeri I. Babushok, Robert L. Brown, Peter J. Linstrom:
Estimation of Kováts Retention Indices Using Group Contributions. 975-980 - Abhyuday Mandal, Kjell Johnson, C. F. Jeff Wu, Dirk Bornemeier:
Identifying Promising Compounds in Drug Discovery: Genetic Algorithms and Some New Statistical Techniques. 981-988 - Debojyoti Dutta, Rajarshi Guha, David J. Wild, Ting Chen:
Ensemble Feature Selection: Consistent Descriptor Subsets for Multiple QSAR Models. 989-997