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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, Bhyravabhotla 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, Jeffrey S. 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 Alpha1D 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
- Lianyi Han, Honghuang Lin, Ze-Rong Li, C. J. Zheng, Zhi Wei Cao, B. Xie, Yuzong 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 S. 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 - Timothy J. Cheeseright, Mark D. 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, Le-Thuy 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,