1) pharmACOphore: Multiple Flexible Ligand Alignment Based on Ant Colony Optimization (Journal of Chemical Information and Modeling) Tuesday August 31st 2010 2) Setting Anchor in the Minor Groove: in Silico Investigation into Formamido N-Methylpyrrole and N-Methylimidazole Polyamides Bound by Cognate DNA Sequences (Journal of Chemical Information and Modeling) Tuesday August 31st 2010 0 comments, related, 1 Up Vote 0 comments, related, 1 Up Vote 0 comments, related, 1 Up Vote 3) TAMkin: A Versatile Package for Vibrational Analysis and Chemical Kinetics (Journal of Chemical Information and Modeling) Friday August 27th 2010 4) From Structure Diagrams to Visual Chemical Patterns (Journal of Chemical Information and Modeling) Friday August 27th 2010 5) Molecular Docking and 3D-QSAR CoMFA Studies on Indole Inhibitors of GIIA Secreted Phospholipase A2 (Journal of Chemical Information and Modeling) Friday August 27th 2010 0 comments, related, 1 Up Vote 0 comments, related, 1 Up Vote 0 comments, related, 1 Up Vote 6) GARLig: A Fully Automated Tool for Subset Selection of Large Fragment Spaces via a Self-Adaptive Genetic Algorithm (Journal of Chemical Information and Modeling) Friday August 27th 2010 7) Molecular Graph Augmentation with Rings and Functional Groups (Journal of Chemical Information and Modeling) Friday August 27th 2010 8) Molecular Dynamics Simulations and Elastic Network Analysis of Protein Kinase B (Akt/PKB) Inactivation (Journal of Chemical Information and Modeling) Wednesday August 25th 2010 0 comments, related, 1 Up Vote 0 comments, related, 1 Up Vote 0 comments, related, 1 Up Vote 9) Rapid Context-Dependent Ligand Desolvation in Molecular Docking (Journal of Chemical Information and Modeling) Wednesday August 25th 2010 10) Replacement Method and Enhanced Replacement Method Versus the Genetic Algorithm Approach for the Selection of Molecular Descriptors in QSPR/QSAR Theories (Journal of Chemical Information and Modeling) Friday August 20th 2010 11) An Open-Source Java Platform for Automated Reaction Mapping (Journal of Chemical Information and Modeling) Wednesday August 18th 2010 0 comments, related, 1 Up Vote 0 comments, related, 1 Up Vote 0 comments, related, 1 Up Vote 12) Postprocessing of Protein−Ligand Docking Poses Using Linear Response MM-PB/SA: Application to Wee1 Kinase Inhibitors (Journal of Chemical Information and Modeling) Tuesday August 17th 2010 13) Rapid Flexible Docking Using a Stochastic Rotamer Library of Ligands (Journal of Chemical Information and Modeling) Tuesday August 17th 2010 14) Reducing Docking Score Variations Arising from Input Differences (Journal of Chemical Information and Modeling) Wednesday August 11th 2010 0 comments, related, 1 Up Vote 0 comments, related, 1 Up Vote 0 comments, related, 1 Up Vote 15) Test MM-PB/SA on True Conformational Ensembles of Protein−Ligand Complexes (Journal of Chemical Information and Modeling) Tuesday August 10th 2010 16) Benchmark Performance of MultiCASE Inc. Software in Ames Mutagenicity Set (Journal of Chemical Information and Modeling) Tuesday August 10th 2010 17) Discovery of New Inhibitors of Schistosoma mansoni PNP by Pharmacophore-Based Virtual Screening (Journal of Chemical Information and Modeling) Tuesday August 10th 2010 0 comments, related, 1 Up Vote 0 comments, related, 1 Up Vote 0 comments, related, 1 Up Vote 18) Computational Modeling Toward Understanding Agonist Binding on Dopamine 3 (Journal of Chemical Information and Modeling) Tuesday August 10th 2010 19) WizePairZ: A Novel Algorithm to Identify, Encode, and Exploit Matched Molecular Pairs with Unspecified Cores in Medicinal Chemistry (Journal of Chemical Information and Modeling) Saturday August 7th 2010 20) Pocket Similarity: Are α Carbons Enough? (Journal of Chemical Information and Modeling) Saturday August 7th 2010 0 comments, related, 1 Up Vote 0 comments, related, 1 Up Vote 0 comments, related, 1 Up Vote 21) FLAP: GRID Molecular Interaction Fields in Virtual Screening. Validation using the DUD Data Set (Journal of Chemical Information and Modeling) Saturday August 7th 2010 22) Enthalpic Efficiency of Ligand Binding (Journal of Chemical Information and Modeling) Thursday August 5th 2010 23) Hashing Algorithms and Data Structures for Rapid Searches of Fingerprint Vectors (Journal of Chemical Information and Modeling) Wednesday August 4th 2010 0 comments, related, 1 Up Vote 0 comments, related, 1 Up Vote 0 comments, related, 1 Up Vote 24) Search for Complexity Generating Chemical Transformations by Combining Connectivity Analysis and Cascade Transformation Patterns (Journal of Chemical Information and Modeling) Wednesday August 4th 2010 25) Knowledge-Based Scoring Functions in Drug Design. 1. Developing a Target-Specific Method for Kinase−Ligand Interactions (Journal of Chemical Information and Modeling) Wednesday August 4th 2010 26) Inverse Frequency Weighting of Fragments for Similarity-Based Virtual Screening (Journal of Chemical Information and Modeling) Saturday July 31st 2010 0 comments, related, 1 Up Vote 0 comments, related, 1 Up Vote 0 comments, related, 1 Up Vote 27) Predicting Polypharmacology by Binding Site Similarity: From Kinases to the Protein Universe (Journal of Chemical Information and Modeling) Thursday July 29th 2010 28) Introduction of Jumping Fragments in Combination with QSARs for the Assessment of Classification in Ecotoxicology (Journal of Chemical Information and Modeling) Wednesday July 28th 2010 29) Protein Kinases: Docking and Homology Modeling Reliability (Journal of Chemical Information and Modeling) Wednesday July 28th 2010 0 comments, related, 1 Up Vote 0 comments, related, 1 Up Vote 0 comments, related, 1 Up Vote 30) Pharmacophore Modeling of Substituted 1,2,4-Trioxanes for Quantitative Prediction of their Antimalarial Activity† (Journal of Chemical Information and Modeling) Tuesday July 27th 2010 31) Evolution of Human Receptor Binding Affinity of H1N1 Hemagglutinins from 1918 to 2009 Pandemic Influenza A Virus (Journal of Chemical Information and Modeling) Tuesday July 27th 2010 32) Systematic Classification and Analysis of Themes in Protein−DNA Recognition (Journal of Chemical Information and Modeling) Saturday July 24th 2010 0 comments, related, 1 Up Vote 0 comments, related, 1 Up Vote 0 comments, related, 1 Up Vote 33) Model-Free Drug-Likeness from Fragments (Journal of Chemical Information and Modeling) Saturday July 24th 2010 34) Generation, Validation, and Utilization of a Three-Dimensional Pharmacophore Model for EP3 Antagonists (Journal of Chemical Information and Modeling) Saturday July 24th 2010 35) Molecular Interaction Fields and 3D-QSAR Studies of p53−MDM2 Inhibitors Suggest Additional Features of Ligand−Target Interaction (Journal of Chemical Information and Modeling) Monday July 19th 2010 0 comments, related, 1 Up Vote 0 comments, related, 1 Up Vote 0 comments, related, 1 Up Vote 36) Similarity−Potency Trees: A Method to Search for SAR Information in Compound Data Sets and Derive SAR Rules (Journal of Chemical Information and Modeling) Friday July 16th 2010 37) Systematic Signatures for Organic Reactions (Journal of Chemical Information and Modeling) Friday July 16th 2010 38) HIV-1 TAR RNA Spontaneously Undergoes Relevant Apo-to-Holo Conformational Transitions in Molecular Dynamics and Constrained Geometrical Simulations (Journal of Chemical Information and Modeling) Friday July 16th 2010 0 comments, related, 1 Up Vote 0 comments, related, 1 Up Vote 0 comments, related, 1 Up Vote 39) Generative Models for Chemical Structures (Journal of Chemical Information and Modeling) Friday July 16th 2010 40) Predicting Total Clearance in Humans from Chemical Structure (Journal of Chemical Information and Modeling) Friday July 16th 2010 41) Chemical Substitutions That Introduce Activity Cliffs Across Different Compound Classes and Biological Targets (Journal of Chemical Information and Modeling) Thursday July 8th 2010 0 comments, related, 1 Up Vote 0 comments, related, 2 Up Votes 0 comments, related, 1 Up Vote 42) A General Treatment of Solubility 4. Description and Analysis of a PCA Model for Ostwald Solubility Coefficients (Journal of Chemical Information and Modeling) Friday July 2nd 2010 43) NovoFLAP: A Ligand-Based De Novo Design Approach for the Generation of Medicinally Relevant Ideas (Journal of Chemical Information and Modeling) Wednesday June 30th 2010 44) Tautomer Identification and Tautomer Structure Generation Based on the InChI Code (Journal of Chemical Information and Modeling) Wednesday June 30th 2010 0 comments, related, 1 Up Vote 0 comments, related, 1 Up Vote 0 comments, related, 1 Up Vote 45) One Concept, Three Implementations of 3D Pharmacophore-Based Virtual Screening: Distinct Coverage of Chemical Search Space (Journal of Chemical Information and Modeling) Tuesday June 29th 2010 46) Selection of In Silico Drug Screening Results by Using Universal Active Probes (UAPs) (Journal of Chemical Information and Modeling) Saturday June 26th 2010 47) Trust, But Verify: On the Importance of Chemical Structure Curation in Cheminformatics and QSAR Modeling Research (Journal of Chemical Information and Modeling) Friday June 25th 2010 0 comments, related, 1 Up Vote 0 comments, related, 1 Up Vote 0 comments, related, 1 Up Vote 48) In Silico Binary Classification QSAR Models Based on 4D-Fingerprints and MOE Descriptors for Prediction of hERG Blockage (Journal of Chemical Information and Modeling) Tuesday June 22nd 2010 49) When is Chemical Similarity Significant? The Statistical Distribution of Chemical Similarity Scores and Its Extreme Values (Journal of Chemical Information and Modeling) Tuesday June 15th 2010 50) Assessing Synthetic Accessibility of Chemical Compounds Using Machine Learning Methods (Journal of Chemical Information and Modeling) Friday June 11th 2010 0 comments, related, 1 Up Vote 0 comments, related, 1 Up Vote 0 comments, related, 1 Up Vote 51) Comparative Evaluation of 3D Virtual Ligand Screening Methods: Impact of the Molecular Alignment on Enrichment (Journal of Chemical Information and Modeling) Wednesday June 9th 2010 52) Pharmaceutical Perspectives of Nonlinear QSAR Strategies (Journal of Chemical Information and Modeling) Tuesday June 8th 2010 53) Computational Study on the Interaction of N1 Substituted Pyrazole Derivatives with B-Raf Kinase: An Unusual Water Wire Hydrogen-Bond Network and Novel Interactions at the Entrance of the Active Site (Journal of Chemical Information and Modeling) Saturday June 5th 2010 0 comments, related, 1 Up Vote 0 comments, related, 1 Up Vote 0 comments, related, 1 Up Vote 54) Proteochemometric Recognition of Stable Kinase Inhibition Complexes Using Topological Autocorrelation and Support Vector Machines (Journal of Chemical Information and Modeling) Saturday June 5th 2010 55) Tautomer Preference in PDB Complexes and its Impact on Structure-Based Drug Discovery (Journal of Chemical Information and Modeling) Wednesday June 2nd 2010 56) Similarity Perception of Reactions Catalyzed by Oxidoreductases and Hydrolases Using Different Classification Methods (Journal of Chemical Information and Modeling) Wednesday June 2nd 2010 0 comments, related, 1 Up Vote 0 comments, related, 1 Up Vote 0 comments, related, 1 Up Vote 57) SCISSORS: A Linear-Algebraical Technique to Rapidly Approximate Chemical Similarities (Journal of Chemical Information and Modeling) Saturday May 29th 2010 58) Ligand-Based Virtual Screening Using Bayesian Networks (Journal of Chemical Information and Modeling) Thursday May 27th 2010 59) Efficient Virtual Screening Using Multiple Protein Conformations Described as Negative Images of the Ligand-Binding Site (Journal of Chemical Information and Modeling) Thursday May 27th 2010 0 comments, related, 1 Up Vote 0 comments, related, 1 Up Vote 0 comments, related, 1 Up Vote 60) Affinity of Sulfamates and Sulfamides to Carbonic Anhydrase II Isoform: Experimental and Molecular Modeling Approaches (Journal of Chemical Information and Modeling) Thursday May 20th 2010 61) Accuracy Assessment of Protein-Based Docking Programs against RNA Targets (Journal of Chemical Information and Modeling) Thursday May 20th 2010 62) MORPH: A New Tool for Ligand Design (Journal of Chemical Information and Modeling) Wednesday May 19th 2010 0 comments, related, 1 Up Vote 0 comments, related, 1 Up Vote 0 comments, related, 1 Up Vote 63) Estimation of ADME Properties with Substructure Pattern Recognition (Journal of Chemical Information and Modeling) Wednesday May 19th 2010 64) Insights for Predicting Blood-Brain Barrier Penetration of CNS Targeted Molecules Using QSPR Approaches (Journal of Chemical Information and Modeling) Wednesday May 19th 2010 65) Rationalization of the Performance and Target Dependence of Similarity Searching Incorporating Protein−Ligand Interaction Information (Journal of Chemical Information and Modeling) Saturday May 15th 2010 0 comments, related, 1 Up Vote 0 comments, related, 1 Up Vote 0 comments, related, 1 Up Vote 66) A 3D Model of CYP1B1 Explains the Dominant 4-Hydroxylation of Estradiol (Journal of Chemical Information and Modeling) Thursday May 13th 2010 67) Virtual Fragment Docking by Glide: a Validation Study on 190 Protein−Fragment Complexes (Journal of Chemical Information and Modeling) Wednesday May 12th 2010 68) Probing Interaction Requirements in PTP1B Inhibitors: A Comparative Molecular Dynamics Study (Journal of Chemical Information and Modeling) Tuesday May 11th 2010 0 comments, related, 1 Up Vote 0 comments, related, 1 Up Vote 0 comments, related, 1 Up Vote 69) Large-Scale Systematic Analysis of 2D Fingerprint Methods and Parameters to Improve Virtual Screening Enrichments (Journal of Chemical Information and Modeling) Saturday May 8th 2010 70) Rationalizing Three-Dimensional Activity Landscapes and the Influence of Molecular Representations on Landscape Topology and the Formation of Activity Cliffs (Journal of Chemical Information and Modeling) Thursday May 6th 2010 71) Molecular Dynamics Studies on T1 Lipase: Insight into a Double-Flap Mechanism (Journal of Chemical Information and Modeling) Thursday May 6th 2010 0 comments, related, 1 Up Vote 0 comments, related, 1 Up Vote 0 comments, related, 1 Up Vote 72) Gaussian Processes for Classification: QSAR Modeling of ADMET and Target Activity (Journal of Chemical Information and Modeling) Saturday May 1st 2010 73) Model Tool to Describe Chemical Structures in XML Format Utilizing Structural Fragments and Chemical Ontology (Journal of Chemical Information and Modeling) Friday April 30th 2010 74) LowModeMD—Implicit Low-Mode Velocity Filtering Applied to Conformational Search of Macrocycles and Protein Loops (Journal of Chemical Information and Modeling) Friday April 30th 2010 0 comments, related, 1 Up Vote 0 comments, related, 1 Up Vote 0 comments, related, 1 Up Vote 75) Ranking Using the Copeland Score: A Comparison with the Hasse Diagram (Journal of Chemical Information and Modeling) Friday April 30th 2010 76) Structure-based Design of Novel Small-Molecule Inhibitors of Plasmodium falciparum (Journal of Chemical Information and Modeling) Thursday April 29th 2010 77) Extended-Connectivity Fingerprints (Journal of Chemical Information and Modeling) Thursday April 29th 2010 0 comments, related, 1 Up Vote 0 comments, related, 2 Up Votes 0 comments, related, 1 Up Vote 78) Drug-like Bioactive Structures and Conformational Coverage with the LigPrep/ConfGen Suite: Comparison to Programs MOE and Catalyst (Journal of Chemical Information and Modeling) Wednesday April 28th 2010 79) Comparison of Three Preprocessing Filters Efficiency in Virtual Screening: Identification of New Putative LXRβ Regulators As a Test Case (Journal of Chemical Information and Modeling) Tuesday April 27th 2010 80) ParaDockS: A Framework for Molecular Docking with Population-Based Metaheuristics (Journal of Chemical Information and Modeling) Tuesday April 27th 2010 0 comments, related, 1 Up Vote 0 comments, related, 1 Up Vote 0 comments, related, 1 Up Vote 81) Branch-and-Bound Algorithms for Enumerating Treelike Chemical Graphs with Given Path Frequency Using Detachment-Cut (Journal of Chemical Information and Modeling) Tuesday April 27th 2010 82) Correlation Analyses on Binding Affinity of Substituted Benzenesulfonamides with Carbonic Anhydrase Using ab Initio MO Calculations on Their Complex Structures (Journal of Chemical Information and Modeling) Saturday April 24th 2010 83) A Semantic Web Ontology for Small Molecules and Their Biological Targets (Journal of Chemical Information and Modeling) Thursday April 22nd 2010 0 comments, related, 1 Up Vote 0 comments, related, 1 Up Vote 0 comments, related, 1 Up Vote 84) Classification and Virtual Screening of Androgen Receptor Antagonists (Journal of Chemical Information and Modeling) Wednesday April 21st 2010 85) Are There Differences between Launched Drugs, Clinical Candidates, and Commercially Available Compounds? (Journal of Chemical Information and Modeling) Friday April 16th 2010 86) A Novel Evaluation of Residue and Protein Volumes by Means of Laguerre Tessellation (Journal of Chemical Information and Modeling) Thursday April 15th 2010 0 comments, related, 1 Up Vote 0 comments, related, 1 Up Vote 0 comments, related, 1 Up Vote 87) Targeting the BH3 Domain Mediated Protein−Protein Interaction of Bcl-xL through Virtual Screening (Journal of Chemical Information and Modeling) Thursday April 15th 2010 88) Ranking Chemical Structures for Drug Discovery: A New Machine Learning Approach (Journal of Chemical Information and Modeling) Wednesday April 14th 2010 89) Accurate Ensemble Molecular Dynamics Binding Free Energy Ranking of Multidrug-Resistant HIV-1 Proteases (Journal of Chemical Information and Modeling) Tuesday April 13th 2010 0 comments, related, 1 Up Vote 0 comments, related, 1 Up Vote 0 comments, related, 1 Up Vote 90) ConfGen: A Conformational Search Method for Efficient Generation of Bioactive Conformers (Journal of Chemical Information and Modeling) Thursday April 8th 2010 91) Quantum Chemical Associations Ligand−Residue: Their Role to Predict Flavonoid Binding Sites in Proteins (Journal of Chemical Information and Modeling) Thursday April 8th 2010 92) Molecular Scaffolds with High Propensity to Form Multi-Target Activity Cliffs (Journal of Chemical Information and Modeling) Saturday April 3rd 2010 0 comments, related, 1 Up Vote 0 comments, related, 1 Up Vote 0 comments, related, 2 Up Votes 93) HPPD: Ligand- and Target-Based Virtual Screening on a Herbicide Target (Journal of Chemical Information and Modeling) Friday April 2nd 2010 94) Assessment of a Novel Scoring Method Based on Solvent Accessible Surface Area Descriptors (Journal of Chemical Information and Modeling) Thursday April 1st 2010 95) Binding of Pollutant Aromatics on Carbon Nanotubes and Graphite (Journal of Chemical Information and Modeling) Thursday April 1st 2010 0 comments, related, 1 Up Vote 0 comments, related, 1 Up Vote 0 comments, related, 1 Up Vote 96) Multiple Pharmacophore Models Combined with Molecular Docking: A Reliable Way for Efficiently Identifying Novel PDE4 Inhibitors with High Structural Diversity (Journal of Chemical Information and Modeling) Wednesday March 31st 2010 97) Drug- and Lead-likeness, Target Class, and Molecular Diversity Analysis of 7.9 Million Commercially Available Organic Compounds Provided by 29 Suppliers (Journal of Chemical Information and Modeling) Friday March 19th 2010 98) Conformer Generation with OMEGA: Algorithm and Validation Using High Quality Structures from the Protein Databank and Cambridge Structural Database (Journal of Chemical Information and Modeling) Thursday March 18th 2010 0 comments, related, 1 Up Vote 0 comments, related, 1 Up Vote 0 comments, related, 1 Up Vote View: prev | next

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