Journal of Chemical Information and Modeling, Volume 46

Volume 46, Number 1, January 2006

• Dilip K. Sinha, Subhash C. Basak:
  Fourth Indo-U.S. Workshop on Mathematical Chemistry, January 8-12, 2005, Pune, Maharashtra, India. 1
  
• Matevz Pompe, Milan Randic:
  "Anticonnectivity": A Challenge for Structure-Property-Activity Studies. 2-8
  
• Douglas M. Hawkins, Subhash C. Basak, Jessica J. Kraker, Kevin T. Geiss, Frank A. Witzmann:
  Combining Chemodescriptors and Biodescriptors in Quantitative Structure-Activity Relationship Modeling. 9-16
  
• Om Prakash Pandey, Indira Ghosh:
  Developing an Antituberculosis Compounds Database and Data Mining in the Search of a Motif Responsible for the Activity of a Diverse Class of Antituberculosis Agents. 17-23
  
• Subhash Ajmani, Kamalakar Jadhav, Sudhir A. Kulkarni:
  Three-Dimensional QSAR Using the k-Nearest Neighbor Method and Its Interpretation. 24-31
  
• Marco Pintore, Christophe Wechman, Gilles Sicard, Maurice Chastrette, Nicolas Amaury, Jacques R. Chrétien:
  Comparing the Information Content of Two Large Olfactory Databases. 32-38
  
• Philip Prathipati, Anil K. Saxena:
  Evaluation of Binary QSAR Models Derived from LUDI and MOE Scoring Functions for Structure Based Virtual Screening. 39-51
  
• Yenamandra S. Prabhakar, Krishnan Balasubramanian:
  A Simple Algorithm for Unique Representation of Chemical Structures-Cyclic/Acyclic Functionalized Achiral Molecules. 52-56
  
• Milan Randic, Alexandru T. Balaban:
  Partitioning of pi-Electrons in Rings for Clar Structures of Benzenoid Hydrocarbons. 57-64
  
• Subhash C. Basak, Ramanathan Natarajan, Denise R. Mills, Douglas M. Hawkins, Jessica J. Kraker:
  Quantitative Structure-Activity Relationship Modeling of Juvenile Hormone Mimetic Compounds for Culex Pipiens Larvae, with a Discussion of Descriptor-Thinning Methods. 65-77
  
• Samrat Dutta, Poonam Singhal, Praveen Agrawal, Raju Tomer, Kritee, Ekta Khurana, B. Jayaram:
  A Physicochemical Model for Analyzing DNA Sequences. 78-85
  
• Yenamandra S. Prabhakar, Manish K. Gupta, Nobendu Roy, Yenamandra Venkateswarlu:
  A High Dimensional QSAR Study on the Aldose Reductase Inhibitory Activity of Some Flavones: Topological Descriptors in Modeling the Activity. 86-92
  
• Manish K. Gupta, Yenamandra S. Prabhakar:
  Topological Descriptors in Modeling the Antimalarial Activity of 4-(3', 5'-Disubstituted anilino)quinolines. 93-102
  
• Mamta Thakur, Abhilash Thakur, Krishnan Balasubramanian:
  QSAR and SAR Studies on the Reduction of Some Aromatic Nitro Compounds by Xanthine Oxidase. 103-110
  
• Akbar S. Khan, Cesar V. Mujer, Timothy G. Alefantis, Joseph P. Connolly, Ulrike Beate Mayr, Petra Walcher, Werner Lubitz, Vito G. DelVecchio:
  Proteomics and Bioinformatics Strategies to Design Countermeasures against Infectious Threat Agents. 111-115
  
• Milan Randic, Frank A. Witzmann, Varshna Kodali, Subhash C. Basak:
  On the Dependence of a Characterization of Proteomics Maps on the Number of Protein Spots Considered. 116-122
  
• R. Sathyapriya, K. V. Brinda, Saraswathi Vishveshwara:
  Correlation of the Side-Chain Hubs with the Functional Residues in DNA Binding Protein Structures. 123-129
  
• Marjan Vracko, Subhash C. Basak, Kevin T. Geiss, Frank A. Witzmann:
  Proteomic Maps-Toxicity Relationship of Halocarbons Studied with Similarity Index and Genetic Algorithm. 130-136
  

• Yun-De Xiao, Rebecca Harris, Ersin Bayram, Peter Santago II, Jeffrey D. Schmitt:
  Supervised Self-Organizing Maps in Drug Discovery. 2. Improvements in Descriptor Selection and Model Validation. 137-144
  
• Gemma L. Holliday, Peter Murray-Rust, Henry S. Rzepa:
  Chemical Markup, XML, and the World Wide Web. 6. CMLReact, an XML Vocabulary for Chemical Reactions. 145-157
  
• Zsolt Lepp, Takashi Kinoshita, Hiroshi Chuman:
  Screening for New Antidepressant Leads of Multiple Activities by Support Vector Machines. 158-167
  
• Anna Maria Almerico, Marco Tutone, Antonino Lauria, Patrizia Diana, Paola Barraja, Alessandra Montalbano, Girolamo Cirrincione, Gaetano Dattolo:
  A Multivariate Analysis of HIV-1 Protease Inhibitors and Resistance Induced by Mutation. 168-179
  
• Robert P. Sheridan, Peter Hunt, J. Christopher Culberson:
  Molecular Transformations as a Way of Finding and Exploiting Consistent Local QSAR. 180-192
  
• Meir Glick, Jeremy L. Jenkins, James H. Nettles, Hamilton Hitchings, John W. Davies:
  Enrichment of High-Throughput Screening Data with Increasing Levels of Noise Using Support Vector Machines, Recursive Partitioning, and Laplacian-Modified Naive Bayesian Classifiers. 193-200
  
• Andrew Smellie, Christopher J. Wilson, Shi Chung Ng:
  Visualization and Interpretation of High Content Screening Data. 201-207
  
• Nikolaus Stiefl, Ian A. Watson, Knut Baumann, Andrea Zaliani:
  ErG: 2D Pharmacophore Descriptions for Scaffold Hopping. 208-220
  

• Shinji Amari, Masahiro Aizawa, Junwei Zhang, Kaori Fukuzawa, Yuji Mochizuki, Yoshio Iwasawa, Kotoko Nakata, Hiroshi Chuman, Tatsuya Nakano:
  VISCANA: Visualized Cluster Analysis of Protein-Ligand Interaction Based on the ab Initio Fragment Molecular Orbital Method for Virtual Ligand Screening. 221-230
  
• Matthew Clark, Frank Guarnieri, Igor Shkurko, Jeff Wiseman:
  Grand Canonical Monte Carlo Simulation of Ligand-Protein Binding. 231-242
  
• Niu Huang, Chakrapani Kalyanaraman, John J. Irwin, Matthew P. Jacobson:
  Physics-Based Scoring of Protein-Ligand Complexes: Enrichment of Known Inhibitors in Large-Scale Virtual Screening. 243-253
  
• Philippe Ferrara, Alessandro Curioni, Eric Vangrevelinghe, T. Meyer, Tiziana Mordasini, Wanda Andreoni, Pierre Acklin, Edgar Jacoby:
  New Scoring Functions for Virtual Screening from Molecular Dynamics Simulations with a Quantum-Refined Force-Field (QRFF-MD). Application to Cyclin-Dependent Kinase 2. 254-263
  
• Orazio Nicolotti, Angelo Carotti:
  QSAR and QSPR Studies of a Highly Structured Physicochemical Domain. 264-276
  
• J. Christian Baber, William A. Shirley, Yinghong Gao, Miklos Feher:
  The Use of Consensus Scoring in Ligand-Based Virtual Screening. 277-288
  
• Prabha Garg, Jitender Verma:
  In Silico Prediction of Blood Brain Barrier Permeability: An Artificial Neural Network Model. 289-297
  
• Sung Jin Cho, Yaxiong Sun:
  FLAME: A Program to Flexibly Align Molecules. 298-306
  
• Douglas J. Klein, Alexandru T. Balaban:
  The Eight Classes of Positive-Curvature Graphitic Nanocones. 307-320
  
• Debojyoti Dutta, Rajarshi Guha, Peter C. Jurs, Ting Chen:
  Scalable Partitioning and Exploration of Chemical Spaces Using Geometric Hashing. 321-333
  

• Debra L. Bautista, Deanna H. Morris, Lauren Stein, Wesley Asher, Timothy Hammitt:
  A Two Model Receptor System of the Alpha_1D Adrenergic Receptor To Describe Interactions with Epinephrine and BMY7378. 334-344
  
• Osvaldo Andrade Santos-Filho, Anton J. Hopfinger:
  Structure-Based QSAR Analysis of a Set of 4-Hydroxy-5, 6-dihydropyrones as Inhibitors of HIV-1 Protease: An Application of the Receptor-Dependent (RD) 4D-QSAR Formalism. 345-354
  

• Shane D. Peterson, Wesley Schaal, Anders Karlén:
  Improved CoMFA Modeling by Optimization of Settings. 355-364
  
• Visvaldas Kairys, Miguel X. Fernandes, Michael K. Gilson:
  Screening Drug-Like Compounds by Docking to Homology Models: A Systematic Study. 365-379
  
• Akifumi Oda, Keiichi Tsuchida, Tadakazu Takakura, Noriyuki Yamaotsu, Shuichi Hirono:
  Comparison of Consensus Scoring Strategies for Evaluating Computational Models of Protein-Ligand Complexes. 380-391
  
• Minghu Song, Matthew Clark:
  Development and Evaluation of an in Silico Model for hERG Binding. 392-400
  
• Hongming Chen, Paul D. Lyne, Fabrizio Giordanetto, Timothy Lovell, Jin Li:
  On Evaluating Molecular-Docking Methods for Pose Prediction and Enrichment Factors. 401-415
  
• Tomasz Arodz, David A. Yuen, Arkadiusz Z. Dudek:
  Ensemble of Linear Models for Predicting Drug Properties. 416-423
  
• Dirk Neumann, Oliver Kohlbacher, Christian Merkwirth, Thomas Lengauer:
  A Fully Computational Model for Predicting Percutaneous Drug Absorption. 424-429
  

• Anders Wallqvist, Ruili Huang, Narmada Thanki, David G. Covell:
  Evaluating Chemical Structure Similarity as an Indicator of Cellular Growth Inhibition. 430-437
  
• Vicky Choi:
  On Updating Torsion Angles of Molecular Conformations. 438-444
  

• L. Y. Han, Hong Huang Lin, Ze-Rong Li, C. J. Zheng, Zhi Wei Cao, B. Xie, Yu Zong Chen:
  PEARLS: Program for Energetic Analysis of Receptor-Ligand System. 445-450
  

Volume 46, Number 2, March 2006

• Robert W. Snyder, Markus Wagener:
  Seventh International Conference on Chemical Structures June 5-9, 2005 Noordwijkerhout, The Netherlands. 451
  

• Muthukumarasamy Karthikeyan, Subramanian Krishnan, Anil Kumar Pandey, Andreas Bender:
  Harvesting Chemical Information from the Internet Using a Distributed Approach: ChemXtreme. 452-461
  
• Jérôme Hert, Peter Willett, David J. Wilton, Pierre Acklin, Kamal Azzaoui, Edgar Jacoby, Ansgar Schuffenhauer:
  New Methods for Ligand-Based Virtual Screening: Use of Data Fusion and Machine Learning to Enhance the Effectiveness of Similarity Searching. 462-470
  
• David J. Wilton, Robert F. Harrison, Peter Willett, John Delaney, Kevin Lawson, Graham Mullier:
  Virtual Screening Using Binary Kernel Discrimination: Analysis of Pesticide Data. 471-477
  
• Beining Chen, Robert F. Harrison, Kitsuchart Pasupa, Peter Willett, David J. Wilton, David J. Wood, Xiao Qing Lewell:
  Virtual Screening Using Binary Kernel Discrimination: Effect of Noisy Training Data and the Optimization of Performance. 478-486
  
• Egon L. Willighagen, H. M. G. W. Denissen, Ron Wehrens, Lutgarde M. C. Buydens:
  On the Use of ¹H and ¹³C 1D NMR Spectra as QSPR Descriptors. 487-494
  
• David J. Wild, Gary Wiggins:
  Videoconferencing and Other Distance Education Techniques in Chemoinformatics Teaching and Research at Indiana University. 495-502
  
• Edward J. Barker, David Buttar, David A. Cosgrove, Eleanor J. Gardiner, Paula Kitts, Peter Willett, Valerie J. Gillet:
  Scaffold Hopping Using Clique Detection Applied to Reduced Graphs. 503-511
  
• Mireille Krier, Guillaume Bret, Didier Rognan:
  Assessing the Scaffold Diversity of Screening Libraries. 512-524
  
• Ansgar Schuffenhauer, Nathan Brown, Paul Selzer, Peter Ertl, Edgar Jacoby:
  Relationships between Molecular Complexity, Biological Activity, and Structural Diversity. 525-535
  
• Modest von Korff, Thomas Sander:
  Toxicity-Indicating Structural Patterns. 536-544
  
• Eric-Wubbo Lameijer, Joost N. Kok, Thomas Bäck, Adriaan P. IJzerman:
  The Molecule Evoluator. An Interactive Evolutionary Algorithm for the Design of Drug-Like Molecules. 545-552
  
• Eric-Wubbo Lameijer, Joost N. Kok, Thomas Bäck, Adriaan P. IJzerman:
  Mining a Chemical Database for Fragment Co-occurrence: Discovery of "Chemical Clichés". 553-562
  
• György Pirok, Nóra Máté, Jeno Varga, József Szegezdi, Miklós Vargyas, Szilárd Dóránt, Ferenc Csizmadia:
  Making "Real" Molecules in Virtual Space. 563-568
  
• Sarah Rodgers, Robert C. Glen, Andreas Bender:
  Characterizing Bitterness: Identification of Key Structural Features and Development of a Classification Model. 569-576
  
• Kristian Birchall, Valerie J. Gillet, Gavin Harper, Stephen D. Pickett:
  Training Similarity Measures for Specific Activities: Application to Reduced Graphs. 577-586
  
• Nikolaus Stiefl, Andrea Zaliani:
  A Knowledge-Based Weighting Approach to Ligand-Based Virtual Screening. 587-596
  
• Jeroen Kazius, Siegfried Nijssen, Joost N. Kok, Thomas Bäck, Adriaan P. IJzerman:
  Substructure Mining Using Elaborate Chemical Representation. 597-605
  
• Ingrid M. Socorro, Jonathan M. Goodman:
  The ROBIA Program for Predicting Organic Reactivity. 606-614
  
• Nicholas Rhodes, David E. Clark, Peter Willett:
  Similarity Searching in Databases of Flexible 3D Structures Using Autocorrelation Vectors Derived from Smoothed Bounded Distance Matrices. 615-619
  
• Pekka T. Lehtovuori, Tommi H. Nyrönen:
  SOMA - Workflow for Small Molecule Property Calculations on a Multiplatform Computing Grid. 620-625
  
• Dumitru Erhan, Pierre-Jean L'Heureux, Shi Yi Yue, Yoshua Bengio:
  Collaborative Filtering on a Family of Biological Targets. 626-635
  
• Ralph Kühne, Ralf-Uwe Ebert, Gerrit Schüürmann:
  Model Selection Based on Structural Similarity-Method Description and Application to Water Solubility Prediction. 636-641
  
• Stuart Firth-Clark, Henriëtte M. G. Willems, Anthony Williams, William Harris:
  Generation and Selection of Novel Estrogen Receptor Ligands Using the De Novo Structure-Based Design Tool, SkelGen. 642-647
  
• Andreas H. Göller, Matthias Hennemann, Jörg Keldenich, Timothy Clark:
  In Silico Prediction of Buffer Solubility Based on Quantum-Mechanical and HQSAR- and Topology-Based Descriptors. 648-658
  
• Anna Maria Capelli, Aldo Feriani, Giovanna Tedesco, Alfonso Pozzan:
  Generation of a Focused Set of GSK Compounds Biased toward Ligand-Gated Ion-Channel Ligands. 659-664
  
• Tim Cheeseright, Mark Mackey, Sally Rose, Andy Vinter:
  Molecular Field Extrema as Descriptors of Biological Activity: Definition and Validation. 665-676
  
• Markus Wagener, Jos P. M. Lommerse:
  The Quest for Bioisosteric Replacements. 677-685
  
• Chidochangu P. Mpamhanga, Beining Chen, Iain M. McLay, Peter Willett:
  Knowledge-Based Interaction Fingerprint Scoring: A Simple Method for Improving the Effectiveness of Fast Scoring Functions. 686-698
  
• Uli Fechner, Gisbert Schneider:
  Flux (1): A Virtual Synthesis Scheme for Fragment-Based de Novo Design. 699-707
  
• Monika Rella, Christopher A. Rushworth, Jodie L. Guy, Anthony J. Turner, Thierry Langer, Richard M. Jackson:
  Structure-Based Pharmacophore Design and Virtual Screening for Novel Angiotensin Converting Enzyme 2 Inhibitors. 708-716
  
• Esther Kellenberger, Pascal Muller, Claire Schalon, Guillaume Bret, Nicolas Foata, Didier Rognan:
  sc-PDB: an Annotated Database of Druggable Binding Sites from the Protein Data Bank. 717-727
  
• Samuel Toba, Jayashree Srinivasan, Allister J. Maynard, Jon M. Sutter:
  Using Pharmacophore Models To Gain Insight into Structural Binding and Virtual Screening: An Application Study with CDK2 and Human DHFR. 728-735
  
• Nicola D. Gold, Richard M. Jackson:
  A Searchable Database for Comparing Protein-Ligand Binding Sites for the Analysis of Structure-Function Relationships. 736-742
  
• Linda Hirons, Eleanor J. Gardiner, Christopher A. Hunter, Peter Willett:
  Structural DNA Profiles: Single Sequence Queries. 743-752
  
• Eleanor J. Gardiner, Linda Hirons, Christopher A. Hunter, Peter Willett:
  Genomic Data Analysis Using DNA Structure: An Analysis of Conserved Nongenic Sequences and Ultraconserved Elements. 753-761
  
• Joseph L. Durant, Burton A. Leland, James G. Nourse:
  VET: A Tool for Reaction Plausibility Checking. 762-766
  

• A. Ben Wagner:
  SciFinder Scholar 2006: An Empirical Analysis of Research Topic Query Processing. 767-774
  
• Hideyuki Masui, Huixiao Hong:
  Spec2D: A Structure Elucidation System Based on ¹H NMR and H-H COSY Spectra in Organic Chemistry. 775-787
  
• Jerry Ray Dias:
  What Do We Know about C₂₈H₁₄ and C₃₀H₁₄ Benzenoid Hydrocarbons and Their Evolution to Related Polymer Strips?. 788-800
  
• Jenna L. Wang, Paul G. Mezey:
  The Electronic Structures and Properties of Open-Ended and Capped Carbon Nanoneedles. 801-807
  
• Igor V. Tetko, Vitaly P. Solov'ev, Alexey V. Antonov, Xiaojun Yao, Jean-Pierre Doucet, Bo Tao Fan, Frank Hoonakker, Denis Fourches, Piere Jost, Nicolas Lachiche, Alexandre Varnek:
  Benchmarking of Linear and Nonlinear Approaches for Quantitative Structure-Property Relationship Studies of Metal Complexation with Ionophores. 808-819
  
• W. Bradford Davis, Ray Hefferlin:
  An Atlas of Forecasted Molecular Data. 2. Vibration Frequencies of Main-Group and Transition-Metal Neutral Gas-Phase Diatomic Molecules in the Ground State. 820-825
  
• W. Michael Brown, Shawn Martin, Mark D. Rintoul, Jean-Loup Faulon:
  Designing Novel Polymers with Targeted Properties Using the Signature Molecular Descriptor. 826-835
  
• David Vidal, Michael Thormann, Miquel Pons:
  A Novel Search Engine for Virtual Screening of Very Large Databases. 836-843
  

• Scott Oloff, Shuxing Zhang, Nagamani Sukumar, Curt M. Breneman, Alexander Tropsha:
  Chemometric Analysis of Ligand Receptor Complementarity: Identifying Complementary Ligands Based on Receptor Information (CoLiBRI). 844-851
  
• Giovanni Bottegoni, Andrea Cavalli, Maurizio Recanatini:
  A Comparative Study on the Application of Hierarchical-Agglomerative Clustering Approaches to Organize Outputs of Reiterated Docking Runs. 852-862
  
• Wen Wu, Michael Daszykowski, Beata Walczak, Brian C. Sweatman, Susan C. Connor, John N. Haselden, Daniel J. Crowther, Rob W. Gill, Michael W. Lutz:
  Peak Alignment of Urine NMR Spectra Using Fuzzy Warping. 863-875
  
• John R. Goodell, Bengt Svensson, David M. Ferguson:
  Spectrophotometric Determination and Computational Evaluation of the Rates of Hydrolysis of 9-Amino-Substituted Acridines. 876-883
  
• Dimitri Gilis, Christophe Biot, Eric Buisine, Yves Dehouck, Marianne Rooman:
  Development of Novel Statistical Potentials Describing Cation-pi Interactions in Proteins and Comparison with Semiempirical and Quantum Chemistry Approaches. 884-893
  
• Rainer Brüggemann, Guillermo Restrepo, Kristina Voigt:
  Structure-Fate Relationships of Organic Chemicals Derived from the Software Packages E4CHEM and WHASSE. 894-902
  
• Andreas Kämper, Joannis Apostolakis, Matthias Rarey, Christel M. Marian, Thomas Lengauer:
  Fully Automated Flexible Docking of Ligands into Flexible Synthetic Receptors Using Forward and Inverse Docking Strategies. 903-911
  
• Natalie Fey, Stephanie E. Harris, Jeremy N. Harvey, A. Guy Orpen:
  Adding Value to Crystallographically-Derived Knowledge Bases. 912-929
  

• Hassan Modarresi, John C. Dearden, Hamid Modarress:
  QSPR Correlation of Melting Point for Drug Compounds Based on Different Sources of Molecular Descriptors. 930-936
  

Volume 46, Number 3, May 2006

• William L. Jorgensen:
  QSAR/QSPR and Proprietary Data. 937
  
• Sangtae Kim:
  Cyberinfrastructure: Enabling the Chemical Sciences. 938
  

• Kieron R. Taylor, Robert J. Gledhill, Jonathan W. Essex, Jeremy G. Frey, Stephen W. Harris, David De Roure:
  Bringing Chemical Data onto the Semantic Web. 939-952
  
• Sulev Sild, Uko Maran, Andre Lomaka, Mati Karelson:
  Open Computing Grid for Molecular Science and Engineering. 953-959
  
• Robert J. Gledhill, Sarah Kent, Brian Hudson, W. Graham Richards, Jonathan W. Essex, Jeremy G. Frey:
  A Computer-Aided Drug Discovery System for Chemistry Teaching. 960-970
  
• Thanh N. Truong, Manohar Nayak, Hung H. Huynh, Tom Cook, Priya Mahajan, LeThuy T. Tran, Jannu Bharath, Shrish Jain, Ha B. Pham, Chaiwoot Boonyasiriwat, Nhat Nguyen, Evan Andersen, Yong Kim, Suengkeol Choe, Jihoon Choi, Thomas E. Cheatham III, Julio C. Facelli:
  Computational Science and Engineering Online (CSE-Online): A Cyber-Infrastructure for Scientific Computing. 971-984
  
• Henry S. Rzepa, Andrew Wheat, Mark J. Williamson:
  ChemSem: An Extensible and Scalable RSS-Based Seminar Alerting System for Scientific Collaboration. 985-990
  
• Rajarshi Guha, Michael T. Howard, Geoffrey R. Hutchison, Peter Murray-Rust, Henry S. Rzepa, Christoph Steinbeck, Jörg K. Wegner, Egon L. Willighagen:
  The Blue Obelisk-Interoperability in Chemical Informatics. 991-998
  
• Scott P. Brown, Steven W. Muchmore:
  High-Throughput Calculation of Protein-Ligand Binding Affinities: Modification and Adaptation of the MM-PBSA Protocol to Enterprise Grid Computing. 999-1005
  
• Simon J. Coles, Jeremy G. Frey, Michael B. Hursthouse, Mark E. Light, Andrew J. Milsted, Leslie Carr, David De Roure, Christopher Gutteridge, Hugo R. Mills, Ken Meacham, Mike Surridge, Elizabeth Lyon, Rachel Heery, Monica Duke, Michael Day:
  An E-Science Environment for Service Crystallography-from Submission to Dissemination. 1006-1016
  
• Randall Bramley, Kenneth Chiu, Tharaka Devadithya, Nisha Gupta, Charles A. Hart, John C. Huffman, Kianosh Huffman, Yu Ma, Donald F. McMullen:
  Instrument Monitoring, Data Sharing, and Archiving Using Common Instrument Middleware Architecture (CIMA). 1017-1025
  
• Matt J. Harvey, D. Scott, Peter V. Coveney:
  An Integrated Instrument Control and Informatics System for Combinatorial Materials Research. 1026-1033
  
• Peter Lind, Markus Alm:
  A Database-Centric Virtual Chemistry System. 1034-1039
  

• Michael Thormann, Andreas Klamt, Martin Hornig, Michael Almstetter:
  COSMOsim: Bioisosteric Similarity Based on COSMO-RS sigma Profiles. 1040-1053
  
• Fumiyoshi Yamashita, Takayuki Itoh, Hideto Hara, Mitsuru Hashida:
  Visualization of Large-Scale Aqueous Solubility Data Using a Novel Hierarchical Data Visualization Technique. 1054-1059
  
• Bradley C. Pearce, Michael J. Sofia, Andrew C. Good, Dieter M. Drexler, David A. Stock:
  An Empirical Process for the Design of High-Throughput Screening Deck Filters. 1060-1068
  
• Ramaswamy Nilakantan, David S. Nunn, Lynne Greenblatt, Gary Walker, Kevin S. Haraki, Dominick Mobilio:
  A Family of Ring System-Based Structural Fragments for Use in Structure-Activity Studies: Database Mining and Recursive Partitioning. 1069-1077
  
• Alireza Givehchi, Andreas Bender, Robert C. Glen:
  Analysis of Activity Space by Fragment Fingerprints, 2D Descriptors, and Multitarget Dependent Transformation of 2D Descriptors. 1078-1083
  
• Surjit B. Dixit, Sergei Y. Ponomarev, David L. Beveridge:
  Root Mean Square Deviation Probability Analysis of Molecular Dynamics Trajectories on DNA. 1084-1093
  
• Jeffrey W. Godden, Jürgen Bajorath:
  A Distance Function for Retrieval of Active Molecules from Complex Chemical Space Representations. 1094-1097
  
• Dariusz Plewczynski, Stéphane A. H. Spieser, Uwe Koch:
  Assessing Different Classification Methods for Virtual Screening. 1098-1106
  
• Alex M. Clark, Paul Labute, Martin Santavy:
  2D Structure Depiction. 1107-1123
  
• Nidhi, Meir Glick, John W. Davies, Jeremy L. Jenkins:
  Prediction of Biological Targets for Compounds Using Multiple-Category Bayesian Models Trained on Chemogenomics Databases. 1124-1133
  

• Nikolay P. Todorov, Philippe H. Monthoux, Ian L. Alberts:
  The Influence of Variations of Ligand Protonation and Tautomerism on Protein-Ligand Recognition and Binding Energy Landscape. 1134-1142
  
• Mohammad Wasim, Richard G. Brereton:
  Hard Modeling Methods for the Curve Resolution of Data from Liquid Chromatography with a Diode Array Detector and On-Flow Liquid Chromatography with Nuclear Magnetic Resonance Spectroscopy. 1143-1153
  
• Anton Lindström, Fredrik Pettersson, Fredrik Almqvist, Anders Berglund, Jan Kihlberg, Anna Linusson:
  Hierarchical PLS Modeling for Predicting the Binding of a Comprehensive Set of Structurally Diverse Protein-Ligand Complexes. 1154-1167
  
• Stuart Firth-Clark, Nikolay P. Todorov, Ian L. Alberts, Anthony Williams, Timothy James, Philip M. Dean:
  Exhaustive de novo Design of Low-Molecular-Weight Fragments Against the ATP-Binding Site of DNA-Gyrase. 1168-1173
  
• Laleh Alisaraie, Lars A. Haller, Gregor Fels:
  A QXP-Based Multistep Docking Procedure for Accurate Prediction of Protein-Ligand Complexes. 1174-1187
  
• Philippa R. N. Wolohan, Lakshmi B. Akella, Roman J. Dorfman, Peter G. Nell, Stefan M. Mundt, Robert D. Clark:
  Structural Unit Analysis Identifies Lead Series and Facilitates Scaffold Hopping in Combinatorial Chemistry. 1188-1193
  
• Milan Remko, Claus-Wilhelm von der Lieth:
  Gas-Phase and Solution Conformations of the alpha-L-Iduronic Acid Structural Unit of Heparin. 1194-1200
  
• Thierry Kogej, Ola Engkvist, Niklas Blomberg, Sorel Muresan:
  Multifingerprint Based Similarity Searches for Targeted Class Compound Selection. 1201-1213
  
• Artem Cherkasov:
  Can 'Bacterial-Metabolite-Likeness' Model Improve Odds of 'in Silico' Antibiotic Discovery?. 1214-1222
  
• Alessandra Fano, David W. Ritchie, Antonio Carrieri:
  Modeling the Structural Basis of Human CCR5 Chemokine Receptor Function: From Homology Model Building and Molecular Dynamics Validation to Agonist and Antagonist Docking. 1223-1235
  
• Deepangi Pandit, Sung-Sau So, Hongmao Sun:
  Enhancing Specificity and Sensitivity of Pharmacophore-Based Virtual Screening by Incorporating Chemical and Shape Features-A Case Study of HIV Protease Inhibitors. 1236-1244
  
• Patricia de Cerqueira Lima, Alexander Golbraikh, Scott Oloff, Yunde Xiao, Alexander Tropsha:
  Combinatorial QSAR Modeling of P-Glycoprotein Substrates. 1245-1254
  
• Julio Caballero, Leyden Fernández, José Ignacio Abreu, Michael Fernández:
  Amino Acid Sequence Autocorrelation Vectors and Ensembles of Bayesian-Regularized Genetic Neural Networks for Prediction of Conformational Stability of Human Lysozyme Mutants. 1255-1268
  
• Mamoru Sakai, Kazuo Toyota, Takeji Takui:
  A Quantum and Deductive Chemical Study for All Congeners of Polybromo/Chlorodibenzo-p-dioxin and Polybromo/Chlorodibenzofuran. 1269-1275
  

• Toshiaki Matsubara, Masashi Ishikura, Misako Aida:
  A Quantum Chemical Study of the Catalysis for Cytidine Deaminase: Contribution of the Extra Water Molecule. 1276-1285
  
• Joong-Youn Shim, Allyn C. Howlett:
  WIN55212-2 Docking to the CB₁ Cannabinoid Receptor and Multiple Pathways for Conformational Induction. 1286-1300
  

• Daniela Schuster, Christian Laggner, Theodora M. Steindl, Anja Palusczak, Rolf W. Hartmann, Thierry Langer:
  Pharmacophore Modeling and in Silico Screening for New P450 19 (Aromatase) Inhibitors. 1301-1311
  
• Munikumar R. Doddareddy, Yong Seo Cho, Hun Yeong Koh, Dong Hyun Kim, Ae Nim Pae:
  In Silico Renal Clearance Model Using Classical Volsurf Approach. 1312-1320
  
• Tulay Ercanli, Donald B. Boyd:
  Exploration of the Conformational Space of a Polymeric Material that Inhibits Human Immunodeficiency Virus. 1321-1333
  
• Micael Jacobsson, Anders Karlén:
  Ligand Bias of Scoring Functions in Structure-Based Virtual Screening. 1334-1343
  
• Fabrizio Manetti, Cristina Tintori, Mercedes Armand-Ugón, Imma Clotet-Codina, Silvio Massa, Rino Ragno, José A. Esté, Maurizio Botta:
  A Combination of Molecular Dynamics and Docking Calculations to Explore the Binding Mode of ADS-J1, a Polyanionic Compound Endowed with Anti-HIV-1 Activity. 1344-1351
  
• Jun Feng, Ashish P. Sanil, S. Stanley Young:
  PharmID: Pharmacophore Identification Using Gibbs Sampling. 1352-1359
  
• Nidhi Singh, Gwénaël Chevé, Mitchell A. Avery, Christopher R. McCurdy:
  Comparative Protein Modeling of 1-Deoxy-D-xylulose-5-phosphate Reductoisomerase Enzyme from Plasmodium falciparum: A Potential Target for Antimalarial Drug Discovery. 1360-1370
  
• Katsumi Yoshida, Tomoko Niwa:
  Quantitative Structure-Activity Relationship Studies on Inhibition of HERG Potassium Channels. 1371-1378
  
• Pierre Bruneau, Nathan R. McElroy:
  logD_7.4 Modeling Using Bayesian Regularized Neural Networks. Assessment and Correction of the Errors of Prediction. 1379-1387
  
• Xavier Gironés, Robert Ponec:
  Molecular Quantum Similarity Measures from Fermi Hole Densities: Modeling Hammett Sigma Constants. 1388-1393
  
• Dhrubajyoti Biswas, Sujata Roy, Srikanta Sen:
  A Simple Approach for Indexing the Oral Druglikeness of a Compound: Discriminating Druglike Compounds from Nondruglike Ones. 1394-1401
  
• Sven Serneels, Evert De Nolf, Pierre J. Van Espen:
  Spatial Sign Preprocessing: A Simple Way To Impart Moderate Robustness to Multivariate Estimators. 1402-1409
  
• Eric Deconinck, Menghui H. Zhang, Danny Coomans, Yvan Vander Heyden:
  Classification Tree Models for the Prediction of Blood-Brain Barrier Passage of Drugs. 1410-1419
  
• Rino Ragno, Silvia Simeoni, Sergio Valente, Silvio Massa, Antonello Mai:
  3-D QSAR Studies on Histone Deacetylase Inhibitors. A GOLPE/GRID Approach on Different Series of Compounds. 1420-1430
  
• Máté Dervarics, Ferenc Ötvös, Tamás A. Martinek:
  Development of a Chirality-Sensitive Flexibility Descriptor for 3+3D-QSAR. 1431-1438
  
• Joan R. Cucarull-González, Christian Laggner, Thierry Langer:
  Influence of the Conditions in Pharmacophore Generation, Scoring, and 3D Database Search for Chemical Feature-Based Pharmacophore Models: One Application Study of ET_A- and ET_B-Selective Antagonists. 1439-1455
  
• Markus H. J. Seifert:
  Assessing the Discriminatory Power of Scoring Functions for Virtual Screening. 1456-1465
  
• Laura Maccari, Matteo Magnani, Giovannella Strappaghetti, Federico Corelli, Maurizio Botta, Fabrizio Manetti:
  A Genetic-Function-Approximation-Based QSAR Model for the Affinity of Arylpiperazines toward alpha₁ Adrenoceptors. 1466-1478
  

• Joji M. Otaki, Akihito Mori, Yoshimasa Itoh, Takashi Nakayama, Haruhiko Yamamoto:
  Alignment-Free Classification of G-Protein-Coupled Receptors Using Self-Organizing Maps. 1479-1490
  
• Channa K. Hattotuwagama, Christopher P. Toseland, Pingping Guan, Debra J. Taylor, Shelley L. Hemsley, Irini A. Doytchinova, Darren R. Flower:
  Toward Prediction of Class II Mouse Major Histocompatibility Complex Peptide Binding Affinity: in Silico Bioinformatic Evaluation Using Partial Least Squares, a Robust Multivariate Statistical Technique. 1491-1502
  
• M. Michael Gromiha, Samuel Selvaraj, A. Mary Thangakani:
  A Statistical Method for Predicting Protein Unfolding Rates from Amino Acid Sequence. 1503-1508
  
• Dimitri Gilis:
  In Silico Analysis of the Thermodynamic Stability Changes of Psychrophilic and Mesophilic alpha-Amylases upon Exhaustive Single-Site Mutations. 1509-1516
  

• Cindy Benod, Marc-André Delsuc, Jean-Luc Pons:
  CRAACK: Consensus Program for NMR Amino Acid Type Assignment. 1517-1522
  
• Salvador Sagrado, Mark T. D. Cronin:
  Diagnostic Tools to Determine the Quality of "Transparent" Regression-Based QSARs: The "Modelling Power" Plot. 1523-1532
  

Volume 46, Number 4, July 2006

• Gerald M. Maggiora:
  On Outliers and Activity Cliffs-Why QSAR Often Disappoints. 1535
  

• Jean-François Truchon, Christopher I. Bayly:
  GLARE: A New Approach for Filtering Large Reagent Lists in Combinatorial Library Design Using Product Properties. 1536-1548
  
• Justin Klekota, Erik Brauner, Frederick P. Roth, Stuart L. Schreiber:
  Using High-Throughput Screening Data To Discriminate Compounds with Single-Target Effects from Those with Side Effects. 1549-1562
  
• Alexandru T. Balaban, Thomas G. Schmalz:
  Strain-Free Sextet-Resonant Benzenoids and Their Antisextet Dualists. 1563-1579
  
• Modest von Korff, Kurt Hilpert:
  Assessing the Predictive Power of Unsupervised Visualization Techniques to Improve the Identification of GPCR-Focused Compound Libraries. 1580-1587
  
• Sara H. Fitzgerald, Michal Sabat, H. Mario Geysen:
  Diversity Space and Its Application to Library Selection and Design. 1588-1597
  
• Aleksandr Y. Sedykh, Gilles Klopman:
  A Structural Analogue Approach to the Prediction of the Octanol-Water Partition Coefficient. 1598-1603
  
• Thy-Hou Lin, Shih-Hau Chiu, Keng-Chang Tsai:
  Supervised Feature Ranking Using a Genetic Algorithm Optimized Artificial Neural Network. 1604-1614
  
• Elisabet Gregori-Puigjané, Jordi Mestres:
  SHED: Shannon Entropy Descriptors from Topological Feature Distributions. 1615-1622
  
• Hanna Eckert, Ingo Vogt, Jürgen Bajorath:
  Mapping Algorithms for Molecular Similarity Analysis and Ligand-Based Virtual Screening: Design of DynaMAD and Comparison with MAD and DMC. 1623-1634
  

• Andreas Kerzmann, Dirk Neumann, Oliver Kohlbacher:
  SLICK - Scoring and Energy Functions for Protein-Carbohydrate Interactions. 1635-1642
  
• Mikhail E. Elyashberg, Kirill A. Blinov, Antony J. Williams, Sergey G. Molodtsov, Gary E. Martin:
  Are Deterministic Expert Systems for Computer-Assisted Structure Elucidation Obsolete?. 1643-1656
  
• Joaquim Chaves Martinez, Joan M. Barroso, Patrick Bultinck, Ramon Carbó-Dorca:
  Toward an Alternative Hardness Kernel Matrix Structure in the Electronegativity Equalization Method (EEM). 1657-1665
  
• Elena Soriano, José Marco-Contelles, Cyrille Tomassi, Albert Nguyen Van Nhien, Denis Postel:
  Computational Analysis of Aza Analogues of [2', 5'-Bis-O-(tert-butyldimethylsilyl)-beta-D-ribofuranose]-3'-spiro-5' '- (4' '-amino-1' ', 2' '-oxathiole-2' ', 2' '-dioxide) (TSAO) as HIV-1 Reverse Transcriptase Inhibitors: Relevance of Conformational Properties on the Inhibitory Activity. 1666-1677
  
• Manuel Urbano-Cuadrado, Irene Luque Ruiz, Miguel Ángel Gómez-Nieto:
  A Steroids QSAR Approach Based on Approximate Similarity Measurements. 1678-1686
  
• Milan Remko, Claus-Wilhelm von der Lieth:
  Gas-Phase and Solution Conformations of Selected Dimeric Structural Units of Heparin. 1687-1694
  
• Andreas Steffen, Andreas Kämper, Thomas Lengauer:
  Flexible Docking of Ligands into Synthetic Receptors Using a Two-Sided Incremental Construction Algorithm. 1695-1703
  
• Stéphane Betzi, Karsten Suhre, Bernard Chétrit, Françoise Guerlesquin, Xavier Morelli:
  GFscore: A General Nonlinear Consensus Scoring Function for High-Throughput Docking. 1704-1712
  
• Rajarshi Guha, Debojyoti Dutta, Peter C. Jurs, Ting Chen:
  R-NN Curves: An Intuitive Approach to Outlier Detection Using a Distance Based Method. 1713-1722
  
• Paul Laffort, Pierre Héricourt:
  Solvation Parameters. 2. A Simplified Molecular Topology to Generate Easily Optimized Values. 1723-1734
  
• Michael H. Abraham, Adam Ibrahim:
  Gas to Olive Oil Partition Coefficients: A Linear Free Energy Analysis. 1735-1741
  

• Yan Li:
  Bayesian Model Based Clustering Analysis: Application to a Molecular Dynamics Trajectory of the HIV-1 Integrase Catalytic Core. 1742-1750
  
• Noel Ferro, Ana Gallegos, Patrick Bultinck, Hans-Jörg Jacobsen, Ramon Carbó-Dorca, Thomas Reinard:
  Coulomb and Overlap Self-Similarities: A Comparative Selectivity Analysis of Structure-Function Relationships for Auxin-like Molecules. 1751-1762
  
• Pooja Sharma, Nanda Ghoshal:
  Exploration of a Binding Mode of Benzothiazol-2-yl Acetonitrile Pyrimidine Core Based Derivatives as Potent c-Jun N-Terminal Kinase-3 Inhibitors and 3D-QSAR Analyses. 1763-1774
  
• Elizabeth A. Amin, William J. Welsh:
  Highly Predictive CoMFA and CoMSIA Models for Two Series of Stromelysin-1 (MMP-3) Inhibitors Elucidate S1' and S1-S2' Binding Modes. 1775-1783
  

• K. V. V. M. Sai Ram, G. Rambabu, J. A. R. P. Sarma, Gautam R. Desiraju:
  Ligand Coordinate Analysis of SC-558 from the Active Site to the Surface of COX-2: A Molecular Dynamics Study. 1784-1794
  
• Tímea Polgár, György M. Keserü:
  Ensemble Docking into Flexible Active Sites. Critical Evaluation of FlexE against JNK-3 and beta-Secretase. 1795-1805
  
• Dharmesh M. Maniyar, Ian T. Nabney, Bruce S. Williams, Andreas Sewing:
  Data Visualization during the Early Stages of Drug Discovery. 1806-1818
  
• Xiao-Lei Zhu, Li Zhang, Qiong Chen, Jian Wan, Guangfu Yang:
  Interactions of Aryloxyphenoxypropionic Acids with Sensitive and Resistant Acetyl-Coenzyme A Carboxylase by Homology Modeling and Molecular Dynamic Simulations. 1819-1826
  
• Hong Liang, Xing Wu, Lynn J. Guziec, Frank S. Guziec Jr., Kimberly K. Larson, Jennifer Lang, Jack C. Yalowich, Brian B. Hasinoff:
  A Structure-Based 3D-QSAR Study of Anthrapyrazole Analogues of the Anticancer Agents Losoxantrone and Piroxantrone. 1827-1835
  
• Rajarshi Guha, Debojyoti Dutta, Peter C. Jurs, Ting Chen:
  Local Lazy Regression: Making Use of the Neighborhood to Improve QSAR Predictions. 1836-1847
  
• Johannes Kirchmair, Gerhard Wolber, Christian Laggner, Thierry Langer:
  Comparative Performance Assessment of the Conformational Model Generators Omega and Catalyst: A Large-Scale Survey on the Retrieval of Protein-Bound Ligand Conformations. 1848-1861
  

• Alex Strizhev, Edmond J. Abrahamian, Sun Choi, Joseph M. Leonard, Philippa R. N. Wolohan, Robert D. Clark:
  The Effects of Biasing Torsional Mutations in a Conformational GA. 1862-1870
  

• Brian Palmer, Joseph F. Danzer, Kevin Hambly, Derek A. Debe:
  StructSorter: A Method for Continuously Updating a Comprehensive Protein Structure Alignment Database. 1871-1876