Calculating an optimal box size for ligand docking and virtual screening against experimental and predicted binding pockets

Beware of Machine Learning-Based Scoring Functions—On the Danger of Developing Black Boxes

(2014) Joffrey Gabel et al.   Journal of Chemical Information and Modeling

Docking Ligands into Flexible and Solvated Macromolecules. 7. Impact of Protein Flexibility and Water Molecules on Docking-Based Virtual Screening Accuracy

(2014) Eric Therrien et al.   Journal of Chemical Information and Modeling

rDock: A Fast, Versatile and Open Source Program for Docking Ligands to Proteins and Nucleic Acids

(2014) Sergio Ruiz-Carmona et al.   PLoS Computational Biology

Drug repositioning by structure-based virtual screening

(2013) Dik-Lung Ma et al.   CHEMICAL SOCIETY REVIEWS

eFindSite: Improved prediction of ligand binding sites in protein models using meta-threading, machine learning and auxiliary ligands

(2013) Michal Brylinski et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Latest developments in molecular docking: 2010-2011 in review

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

Unleashing the power of meta-threading for evolution/structure-based function inference of proteins

(2013) Michal Brylinski   Frontiers in Genetics

Inverse Virtual Screening allows the discovery of the biological activity of natural compounds

(2012) Gianluigi Lauro et al.   BIOORGANIC & MEDICINAL CHEMISTRY

Surflex-Dock: Docking benchmarks and real-world application

(2012) Russell Spitzer et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Directory of Useful Decoys, Enhanced (DUD-E): Better Ligands and Decoys for Better Benchmarking

(2012) Michael M. Mysinger et al.   JOURNAL OF MEDICINAL CHEMISTRY

eThread: A Highly Optimized Machine Learning-Based Approach to Meta-Threading and the Modeling of Protein Tertiary Structures

(2012) Michal Brylinski et al.   PLoS One

Identification of cavities on protein surface using multiple computational approaches for drug binding site prediction

(2011) Z. Zhang et al.   BIOINFORMATICS

FRED Pose Prediction and Virtual Screening Accuracy

(2011) Mark McGann   Journal of Chemical Information and Modeling

DSX: A Knowledge-Based Scoring Function for the Assessment of Protein–Ligand Complexes

(2011) Gerd Neudert et al.   Journal of Chemical Information and Modeling

Open Babel: An open chemical toolbox

(2011) Noel M O'Boyle et al.   Journal of Cheminformatics

Comparison of current docking tools for the simulation of inhibitor binding by the transmembrane domain of the sarco/endoplasmic reticulum calcium ATPase

(2010) Michael Lape et al.   BIOPHYSICAL CHEMISTRY

Improved Ligand-Protein Binding Affinity Predictions Using Multiple Binding Modes

(2010) Eva Stjernschantz et al.   BIOPHYSICAL JOURNAL

Rapid Flexible Docking Using a Stochastic Rotamer Library of Ligands

(2010) Feng Ding et al.   Journal of Chemical Information and Modeling

SKATE: A docking program that decouples systematic sampling from scoring

(2010) Jianwen A. Feng et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

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

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

I-TASSER: a unified platform for automated protein structure and function prediction

(2010) Ambrish Roy et al.   Nature Protocols

Virtual Screening for HIV Protease Inhibitors: A Comparison of AutoDock 4 and Vina

(2010) Max W. Chang et al.   PLoS One

Small-angle scattering for structural biology-Expanding the frontier while avoiding the pitfalls

(2010) David A. Jacques et al.   PROTEIN SCIENCE

The protein-small-molecule database, a non-redundant structural resource for the analysis of protein-ligand binding

(2009) I. Wallach et al.   BIOINFORMATICS

Fr-TM-align: a new protein structural alignment method based on fragment alignments and the TM-score

(2009) Shashi Pandit et al.   BMC BIOINFORMATICS

AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility

(2009) Garrett M. Morris et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

I-TASSER: Fully automated protein structure prediction in CASP8

(2009) Yang Zhang   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Drug Discovery Using Chemical Systems Biology: Repositioning the Safe Medicine Comtan to Treat Multi-Drug and Extensively Drug Resistant Tuberculosis

(2009) Sarah L. Kinnings et al.   PLoS Computational Biology

Predicting Protein Ligand Binding Sites by Combining Evolutionary Sequence Conservation and 3D Structure

(2009) John A. Capra et al.   PLoS Computational Biology

Radius of gyration as an indicator of protein structure compactness

(2008) M. Yu. Lobanov et al.   MOLECULAR BIOLOGY