Software and resources for computational medicinal chemistry

In-Silico ADME Models: A General Assessment of their Utility in Drug Discovery Applications

(2011) M. Paul Gleeson et al.   CURRENT TOPICS IN MEDICINAL CHEMISTRY

Structure-Based Discovery of Natural-Product-like TNF-α Inhibitors

(2010) Daniel Shiu-Hin Chan et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Tautomerism and Magnesium Chelation of HIV-1 Integrase Inhibitors: A Theoretical Study

(2010) Chenzhong Liao et al.   ChemMedChem

Pharmacophore Based Drug Design Approach as a Practical Process in Drug Discovery

(2010) Qingzhi Gao et al.   Current Computer-Aided Drug Design

QSAR in the Pharmaceutical Research Setting: QSAR Models for Broad, Large Problems

(2010) D.G. Sprous et al.   CURRENT TOPICS IN MEDICINAL CHEMISTRY

Successful Applications of Computer Aided Drug Discovery: Moving Drugs from Concept to the Clinic

(2010) Tanaji Talele et al.   CURRENT TOPICS IN MEDICINAL CHEMISTRY

Pharmacophore modeling and applications in drug discovery: challenges and recent advances

(2010) Sheng-Yong Yang   DRUG DISCOVERY TODAY

Computer tools in the discovery of HIV-1 integrase inhibitors

(2010) Chenzhong Liao et al.   Future Medicinal Chemistry

Can we trust docking results? Evaluation of seven commonly used programs on PDBbind database

(2010) Dariusz Plewczynski et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Evaluation of the performance of four molecular docking programs on a diverse set of protein-ligand complexes

(2010) Xun Li et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Tautomerism in large databases

(2010) Markus Sitzmann et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Discovery of Novel Fibroblast Growth Factor Receptor 1 Kinase Inhibitors by Structure-Based Virtual Screening

(2010) Krishna P. Ravindranathan et al.   JOURNAL OF MEDICINAL CHEMISTRY

Virtual Screening for the Identification of Novel Nonsteroidal Glucocorticoid Modulators

(2010) Valeria Onnis et al.   JOURNAL OF MEDICINAL CHEMISTRY

ThePthaladyns: GTP Competitive Inhibitors of Dynamin I and II GTPase Derived from Virtual Screening

(2010) Luke R. Odell et al.   JOURNAL OF MEDICINAL CHEMISTRY

Discovery of Non-Glycoside Sodium-Dependent Glucose Co-Transporter 2 (SGLT2) Inhibitors by Ligand-Based Virtual Screening

(2010) Jian-Sung Wu et al.   JOURNAL OF MEDICINAL CHEMISTRY

Novel Inhibitors of Dengue Virus Methyltransferase: Discovery by in Vitro-Driven Virtual Screening on a Desktop Computer Grid

(2010) Michael Podvinec et al.   JOURNAL OF MEDICINAL CHEMISTRY

Design, Synthesis, Enzyme-Inhibitory Activity, and Effect on Human Cancer Cells of a Novel Series of Jumonji Domain-Containing Protein 2 Histone Demethylase Inhibitors

(2010) Shohei Hamada et al.   JOURNAL OF MEDICINAL CHEMISTRY

Discovery of Novel GSK-3β Inhibitors with Potent in Vitro and in Vivo Activities and Excellent Brain Permeability Using Combined Ligand- and Structure-Based Virtual Screening

(2010) Mohammad A. Khanfar et al.   JOURNAL OF MEDICINAL CHEMISTRY

Selection of Evodiamine as a Novel Topoisomerase I Inhibitor by Structure-Based Virtual Screening and Hit Optimization of Evodiamine Derivatives as Antitumor Agents

(2010) Guoqiang Dong et al.   JOURNAL OF MEDICINAL CHEMISTRY

Discovery of Mitogen-Activated Protein Kinase-Interacting Kinase 1 Inhibitors by a Comprehensive Fragment-Oriented Virtual Screening Approach

(2010) Julen Oyarzabal et al.   JOURNAL OF MEDICINAL CHEMISTRY

Fragment-Based Drug Discovery Applied to Hsp90. Discovery of Two Lead Series with High Ligand Efficiency

(2010) Christopher W. Murray et al.   JOURNAL OF MEDICINAL CHEMISTRY

Complementarity Between a Docking and a High-Throughput Screen in Discovering New Cruzain Inhibitors

(2010) Rafaela S. Ferreira et al.   JOURNAL OF MEDICINAL CHEMISTRY

Novel Carbamates as Orally Active Acetylcholinesterase Inhibitors Found to Improve Scopolamine-Induced Cognition Impairment: Pharmacophore-Based Virtual Screening, Synthesis, and Pharmacology†

(2010) Shailendra S. Chaudhaery et al.   JOURNAL OF MEDICINAL CHEMISTRY

Quo Vadis, Virtual Screening? A Comprehensive Survey of Prospective Applications

(2010) Peter Ripphausen et al.   JOURNAL OF MEDICINAL CHEMISTRY

Optimized Hydrophobic Interactions and Hydrogen Bonding at the Target-Ligand Interface Leads the Pathways of Drug-Designing

(2010) Rohan Patil et al.   PLoS One

Probing Binding Modes of Small Molecule Inhibitors to the Polo-Box Domain of Human Polo-like Kinase 1

(2010) Chenzhong Liao et al.   ACS Medicinal Chemistry Letters

Identification of a New Series of STAT3 Inhibitors by Virtual Screening

(2010) Kenji Matsuno et al.   ACS Medicinal Chemistry Letters

Indolyl-pyrrolone as a new scaffold for Pim1 inhibitors

(2009) Stefania Olla et al.   BIOORGANIC & MEDICINAL CHEMISTRY LETTERS

Long-timescale molecular dynamics simulations of protein structure and function

(2009) John L Klepeis et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Prospective Ligand- and Target-Based 3D QSAR: State of the Art 2008

(2009) Robert Clark   CURRENT TOPICS IN MEDICINAL CHEMISTRY

Homology modeling in drug discovery: current trends and applications

(2009) Claudio N. Cavasotto et al.   DRUG DISCOVERY TODAY

Pharmacophoric model building for antitubercular activity of the individual Schiff bases of small combinatorial library

(2009) Wesam S. Abdel-Aal et al.   EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY

Novel Inhibitors of Human Histone Deacetylase (HDAC) Identified by QSAR Modeling of Known Inhibitors, Virtual Screening, and Experimental Validation

(2009) Hao Tang et al.   Journal of Chemical Information and Modeling

Optical Structure Recognition Software To Recover Chemical Information: OSRA, An Open Source Solution

(2009) Igor V. Filippov et al.   Journal of Chemical Information and Modeling

Comparative Assessment of Scoring Functions on a Diverse Test Set

(2009) Tiejun Cheng et al.   Journal of Chemical Information and Modeling

Comparison of Several Molecular Docking Programs: Pose Prediction and Virtual Screening Accuracy

(2009) Jason B. Cross et al.   Journal of Chemical Information and Modeling

ChEMBL. An interview with John Overington, team leader, chemogenomics at the European Bioinformatics Institute Outstation of the European Molecular Biology Laboratory (EMBL-EBI)

(2009) Wendy A. Warr   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Directed Discovery of Agents Targeting the Met Tyrosine Kinase Domain by Virtual Screening

(2009) Megan L. Peach et al.   JOURNAL OF MEDICINAL CHEMISTRY

Integration of Ligand and Structure-Based Virtual Screening for the Identification of the First Dual Targeting Agent for Heat Shock Protein 90 (Hsp90) and Tubulin

(2009) Andrew J. S. Knox et al.   JOURNAL OF MEDICINAL CHEMISTRY

Discovery of Potent and Selective Inhibitors of the Mammalian Target of Rapamycin (mTOR) Kinase

(2009) Pawel Nowak et al.   JOURNAL OF MEDICINAL CHEMISTRY

Generation of Ligand-Based Pharmacophore Model and Virtual Screening for Identification of Novel Tubulin Inhibitors with Potent Anticancer Activity

(2009) Yi-Kun Chiang et al.   JOURNAL OF MEDICINAL CHEMISTRY

Synthesis, Biological Evaluation, and Three-Dimensional in Silico Pharmacophore Model for σ1Receptor Ligands Based on a Series of Substituted Benzo[d]oxazol-2(3H)-one Derivatives

(2009) Daniele Zampieri et al.   JOURNAL OF MEDICINAL CHEMISTRY

Discovery of Geranylgeranyltransferase-I Inhibitors with Novel Scaffolds by the Means of Quantitative Structure−Activity Relationship Modeling, Virtual Screening, and Experimental Validation

(2009) Yuri K. Peterson et al.   JOURNAL OF MEDICINAL CHEMISTRY

Pursuing Aldose Reductase Inhibitors through in Situ Cross-Docking and Similarity-Based Virtual Screening

(2009) Sandro Cosconati et al.   JOURNAL OF MEDICINAL CHEMISTRY

Discovery of New Inhibitors of ResistantStreptococcus pneumoniaePenicillin Binding Protein (PBP) 2x by Structure-Based Virtual Screening

(2009) Laurence Miguet et al.   JOURNAL OF MEDICINAL CHEMISTRY

Modeling of the Aryl Hydrocarbon Receptor (AhR) Ligand Binding Domain and Its Utility in Virtual Ligand Screening to Predict New AhR Ligands

(2009) William H. Bisson et al.   JOURNAL OF MEDICINAL CHEMISTRY

Flaviviral Protease Inhibitors Identified by Fragment-Based Library Docking into a Structure Generated by Molecular Dynamics

(2009) Dariusz Ekonomiuk et al.   JOURNAL OF MEDICINAL CHEMISTRY

Inhibitors for Human Glutaminyl Cyclase by Structure Based Design and Bioisosteric Replacement

(2009) Mirko Buchholz et al.   JOURNAL OF MEDICINAL CHEMISTRY

Identification of Enoxacin as an Inhibitor of Osteoclast Formation and Bone Resorption by Structure-Based Virtual Screening

(2009) David A. Ostrov et al.   JOURNAL OF MEDICINAL CHEMISTRY

Development of a Novel Virtual Screening Cascade Protocol to Identify Potential Trypanothione Reductase Inhibitors

(2009) Rolando Perez-Pineiro et al.   JOURNAL OF MEDICINAL CHEMISTRY

Synthesis, Activity, and Pharmacophore Development for Isatin-β-thiosemicarbazones with Selective Activity toward Multidrug-Resistant Cells

(2009) Matthew D. Hall et al.   JOURNAL OF MEDICINAL CHEMISTRY

Virtual Screening Approach for the Identification of New Rac1 Inhibitors

(2009) Nicola Ferri et al.   JOURNAL OF MEDICINAL CHEMISTRY

Modern Homology Modeling of G-Protein Coupled Receptors: Which Structural Template to Use?

(2009) Juan Carlos Mobarec et al.   JOURNAL OF MEDICINAL CHEMISTRY

Identification of Death-Associated Protein Kinases Inhibitors Using Structure-Based Virtual Screening

(2009) Masako Okamoto et al.   JOURNAL OF MEDICINAL CHEMISTRY

Novel Organic Proteasome Inhibitors Identified by Virtual and in Vitro Screening

(2009) Nicolas Basse et al.   JOURNAL OF MEDICINAL CHEMISTRY

Three-Dimensional Pharmacophore Methods in Drug Discovery

(2009) Andrew R. Leach et al.   JOURNAL OF MEDICINAL CHEMISTRY

An overview of the PubChem BioAssay resource

(2009) Yanli Wang et al.   NUCLEIC ACIDS RESEARCH

Chemical Entities of Biological Interest: an update

(2009) Paula de Matos et al.   NUCLEIC ACIDS RESEARCH

DOCK 6: Combining techniques to model RNA-small molecule complexes

(2009) P. T. Lang et al.   RNA

Combining docking with pharmacophore filtering for improved virtual screening

(2009) Megan L Peach et al.   Journal of Cheminformatics

Pharmacophore-Based Virtual Screening

(2008) Hongmao Sun   CURRENT MEDICINAL CHEMISTRY

Limitations and lessons in the use of X-ray structural information in drug design

(2008) A DAVIS et al.   DRUG DISCOVERY TODAY

Structure-based virtual screening for identification of novel 11β-HSD1 inhibitors

(2008) Huaiyu Yang et al.   EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY

Mold2, Molecular Descriptors from 2D Structures for Chemoinformatics and Toxicoinformatics

(2008) Huixiao Hong et al.   Journal of Chemical Information and Modeling

An improved relaxed complex scheme for receptor flexibility in computer-aided drug design

(2008) Rommie E. Amaro et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

On the Applicability of GPCR Homology Models to Computer-Aided Drug Discovery: A Comparison between In Silico and Crystal Structures of the β2-Adrenergic Receptor

(2008) Stefano Costanzi   JOURNAL OF MEDICINAL CHEMISTRY

Recent Developments in Fragment-Based Drug Discovery

(2008) Miles Congreve et al.   JOURNAL OF MEDICINAL CHEMISTRY

Discovery of Novel Nitrobenzothiazole Inhibitors forMycobacterium tuberculosisATP Phosphoribosyl Transferase (HisG) through Virtual Screening

(2008) Yoonsang Cho et al.   JOURNAL OF MEDICINAL CHEMISTRY

Methyl (11aS)-1,2,3,5,11,11a-Hexahydro-3,3-dimethyl-1-oxo-6H-imidazo-[3′,4′:1,2]pyridin[3,4-b]indol-2-Substituted Acetates: Synthesis and Three-Dimensional Quantitative Structure−Activity Relationship Investigation as a Class of Novel Vasodilators

(2008) Jiawang Liu et al.   JOURNAL OF MEDICINAL CHEMISTRY

Virtual Screening, Identification, and Biochemical Characterization of Novel Inhibitors of the Reverse Transcriptase of Human Immunodeficiency Virus Type-1

(2008) Alon Herschhorn et al.   JOURNAL OF MEDICINAL CHEMISTRY

Discovery of Novel Cdc25 Phosphatase Inhibitors with Micromolar Activity Based on the Structure-Based Virtual Screening

(2008) Hwangseo Park et al.   JOURNAL OF MEDICINAL CHEMISTRY

Virtual Screening to Successfully Identify Novel Janus Kinase 3 Inhibitors: A Sequential Focused Screening Approach

(2008) Xin Chen et al.   JOURNAL OF MEDICINAL CHEMISTRY

Novel γ-Aminobutyric Acid ρ1Receptor Antagonists; Synthesis, Pharmacological Activity and Structure−Activity Relationships

(2008) Rohan J. Kumar et al.   JOURNAL OF MEDICINAL CHEMISTRY

Ensemble-Based Virtual Screening Reveals Potential Novel Antiviral Compounds for Avian Influenza Neuraminidase

(2008) Lily S. Cheng et al.   JOURNAL OF MEDICINAL CHEMISTRY

Is Quantum Mechanics Necessary for Predicting Binding Free Energy?

(2008) Ting Zhou et al.   JOURNAL OF MEDICINAL CHEMISTRY

Discovery of Novel Human Histamine H4 Receptor Ligands by Large-Scale Structure-Based Virtual Screening

(2008) Róbert Kiss et al.   JOURNAL OF MEDICINAL CHEMISTRY

Discovery of Novel Chemotypes to a G-Protein-Coupled Receptor through Ligand-Steered Homology Modeling and Structure-Based Virtual Screening

(2008) Claudio N. Cavasotto et al.   JOURNAL OF MEDICINAL CHEMISTRY

Target Flexibility: An Emerging Consideration in Drug Discovery and Design†

(2008) Pietro Cozzini et al.   JOURNAL OF MEDICINAL CHEMISTRY

Identification of Novel Cannabinoid CB1 Receptor Antagonists by Using Virtual Screening with a Pharmacophore Model

(2008) Hongwu Wang et al.   JOURNAL OF MEDICINAL CHEMISTRY

Fast Three Dimensional Pharmacophore Virtual Screening of New Potent Non-Steroid Aromatase Inhibitors

(2008) Marco A. C. Neves et al.   JOURNAL OF MEDICINAL CHEMISTRY

Discovery of Novel CB2Receptor Ligands by a Pharmacophore-Based Virtual Screening Workflow

(2008) Patrick Markt et al.   JOURNAL OF MEDICINAL CHEMISTRY

PharmaGist: a webserver for ligand-based pharmacophore detection

(2008) D. Schneidman-Duhovny et al.   NUCLEIC ACIDS RESEARCH

HMDB: a knowledgebase for the human metabolome

(2008) D. S. Wishart et al.   NUCLEIC ACIDS RESEARCH

Towards the development of universal, fast and highly accurate docking/scoring methods: a long way to go

(2007) N Moitessier et al.   BRITISH JOURNAL OF PHARMACOLOGY

Molecule-pharmacophore superpositioning and pattern matching in computational drug design

(2007) G WOLBER   DRUG DISCOVERY TODAY