Ligand-biased ensemble receptor docking (LigBEnD): a hybrid ligand/receptor structure-based approach

Miscellaneous Topics in Computer-Aided Drug Design: Synthetic Accessibility and GPU Computing, and Other Topics

(2016) Yoshifumi Fukunishi et al.   CURRENT PHARMACEUTICAL DESIGN

CSAR 2014: A Benchmark Exercise Using Unpublished Data from Pharma

(2016) Heather A. Carlson et al.   Journal of Chemical Information and Modeling

Comprehensive evaluation of ten docking programs on a diverse set of protein–ligand complexes: the prediction accuracy of sampling power and scoring power

(2016) Zhe Wang et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Structure-Based Predictions of Activity Cliffs

(2015) Jarmila Husby et al.   Journal of Chemical Information and Modeling

DOCK 6: Impact of new features and current docking performance

(2015) William J. Allen et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Docking to multiple pockets or ligand fields for screening, activity prediction and scaffold hopping

(2014) Yu-Chen Chen et al.   Future Medicinal Chemistry

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

ALiBERO: Evolving a Team of Complementary Pocket Conformations Rather than a Single Leader

(2012) Manuel Rueda et al.   Journal of Chemical Information and Modeling

Docking performance of the glide program as evaluated on the Astex and DUD datasets: a complete set of glide SP results and selected results for a new scoring function integrating WaterMap and glide

(2012) Matthew P. Repasky et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Variability in docking success rates due to dataset preparation

(2012) Christopher R. Corbeil et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Surflex-Dock: Docking benchmarks and real-world application

(2012) Russell Spitzer 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

Molecular dynamics simulations and drug discovery

(2011) Jacob D Durrant et al.   BMC BIOLOGY

Systematic Exploitation of Multiple Receptor Conformations for Virtual Ligand Screening

(2011) Giovanni Bottegoni et al.   PLoS One

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

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

Spatial chemical distance based on atomic property fields

(2010) A. V. Grigoryan et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Development of a new physics-based internal coordinate mechanics force field and its application to protein loop modeling

(2010) Yelena A. Arnautova et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

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

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

Recipes for the Selection of Experimental Protein Conformations for Virtual Screening

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

AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility

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

Flexible ligand docking to multiple receptor conformations: a practical alternative

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

A new method for ligand docking to flexible receptors by dual alanine scanning and refinement (SCARE)

(2008) Giovanni Bottegoni et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Four-Dimensional Docking: A Fast and Accurate Account of Discrete Receptor Flexibility in Ligand Docking

(2008) Giovanni Bottegoni et al.   JOURNAL OF MEDICINAL CHEMISTRY