Optimization of Compound Ranking for Structure-Based Virtual Ligand Screening Using an Established FRED-Surflex Consensus Approach

Latest developments in molecular docking: 2010-2011 in review

(2013) Elizabeth Yuriev et al.   JOURNAL OF MOLECULAR RECOGNITION

PDB_REDO: constructive validation, more than just looking for errors

(2012) Robbie P. Joosten et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Protein dynamics and conformational selection in bidirectional signal transduction

(2012) Ruth Nussinov et al.   BMC BIOLOGY

Virtual Screening Methods as Tools for Drug Lead Discovery from Large Chemical Libraries

(2012) X. H. Ma et al.   CURRENT MEDICINAL CHEMISTRY

In Search of Allosteric Modulators of α7-nAChR by Solvent Density Guided Virtual Screening

(2012) Raja Dey et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

ZINC: A Free Tool to Discover Chemistry for Biology

(2012) John J. Irwin et al.   Journal of Chemical Information and Modeling

Conformer Generation with OMEGA: Learning from the Data Set and the Analysis of Failures

(2012) Paul C. D. Hawkins et al.   Journal of Chemical Information and Modeling

Pose prediction and virtual screening performance of GOLD scoring functions in a standardized test

(2012) John W. Liebeschuetz et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Docking and scoring with ICM: the benchmarking results and strategies for improvement

(2012) Marco A. C. Neves et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Exploring Protein Flexibility: Incorporating Structural Ensembles From Crystal Structures and Simulation into Virtual Screening Protocols

(2012) David J. Osguthorpe et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Structure-based ligand discovery for the protein-protein interface of chemokine receptor CXCR4

(2012) M. M. Mysinger et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The assessment of computationally derived protein ensembles in protein-ligand docking

(2012) Barbara Sander et al.   Journal of Cheminformatics

Strategies in the Rational Drug Design

(2011) T. Mavromoustakos et al.   CURRENT MEDICINAL CHEMISTRY

Rapid Shape-Based Ligand Alignment and Virtual Screening Method Based on Atom/Feature-Pair Similarities and Volume Overlap Scoring

(2011) G. Madhavi Sastry et al.   Journal of Chemical Information and Modeling

FRED Pose Prediction and Virtual Screening Accuracy

(2011) Mark McGann   Journal of Chemical Information and Modeling

Tyrosine Kinase Syk Non-Enzymatic Inhibitors and Potential Anti-Allergic Drug-Like Compounds Discovered by Virtual and In Vitro Screening

(2011) Bruno O. Villoutreix et al.   PLoS One

Systematic Exploitation of Multiple Receptor Conformations for Virtual Ligand Screening

(2011) Giovanni Bottegoni et al.   PLoS One

How to choose relevant multiple receptor conformations for virtual screening: a test case of Cdk2 and normal mode analysis

(2010) Olivier Sperandio et al.   EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS

Comparative Evaluation of 3D Virtual Ligand Screening Methods: Impact of the Molecular Alignment on Enrichment

(2010) David Giganti et al.   Journal of Chemical Information and Modeling

Drug- and Lead-likeness, Target Class, and Molecular Diversity Analysis of 7.9 Million Commercially Available Organic Compounds Provided by 29 Suppliers

(2010) Alexander Chuprina et al.   Journal of Chemical Information and Modeling

Ensemble Docking into Multiple Crystallographically Derived Protein Structures: An Evaluation Based on the Statistical Analysis of Enrichments

(2010) Ian R. Craig et al.   Journal of Chemical Information and Modeling

Conformer Generation with OMEGA: Algorithm and Validation Using High Quality Structures from the Protein Databank and Cambridge Structural Database

(2010) Paul C. D. Hawkins et al.   Journal of Chemical Information and Modeling

VoteDock: Consensus docking method for prediction of protein-ligand interactions

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

Challenges and advances in computational docking: 2009 in review

(2010) Elizabeth Yuriev et al.   JOURNAL OF MOLECULAR RECOGNITION

MS-DOCK: Accurate multiple conformation generator and rigid docking protocol for multi-step virtual ligand screening

(2009) Nicolas Sauton et al.   BMC BIOINFORMATICS

Ligand scaffold hopping combining 3D maximal substructure search and molecular similarity

(2009) Flavien Quintus et al.   BMC BIOINFORMATICS

Structure-Based Virtual Ligand Screening: Recent Success Stories

(2009) Bruno Villoutreix et al.   COMBINATORIAL CHEMISTRY & HIGH THROUGHPUT SCREENING

Managing protein flexibility in docking and its applications

(2009) Chandrika B-Rao et al.   DRUG DISCOVERY TODAY

Rational drug design

(2009) Soma Mandal et al.   EUROPEAN JOURNAL OF PHARMACOLOGY

Recipes for the Selection of Experimental Protein Conformations for Virtual Screening

(2009) Manuel Rueda et al.   Journal of Chemical Information and Modeling

Ultrafast shape recognition: Evaluating a new ligand-based virtual screening technology

(2009) Pedro J. Ballester et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING

Proteins in Motion

(2009) V. J. Vinson   SCIENCE

Flexible ligand docking to multiple receptor conformations: a practical alternative

(2008) Maxim Totrov et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

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

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

MADAMM: A multistaged docking with an automated molecular modeling protocol

(2008) N. M. F. S. A. Cerqueira et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Receptor-Based Virtual Ligand Screening for the Identification of Novel CDC25 Phosphatase Inhibitors

(2007) Matthieu Montes et al.   Journal of Chemical Information and Modeling