Docking pose selection by interaction pattern graph similarity: application to the D3R grand challenge 2015

Three-Dimensional Similarity in Molecular Docking: Prioritizing Ligand Poses on the Basis of Experimental Binding Modes

(2016) Andrew Anighoro et al.   Journal of Chemical Information and Modeling

Machine learning in computational docking

(2015) Mohamed A. Khamis et al.   ARTIFICIAL INTELLIGENCE IN MEDICINE

Knowledge-Based Strategy to Improve Ligand Pose Prediction Accuracy for Lead Optimization

(2015) Cen Gao et al.   Journal of Chemical Information and Modeling

CSAR Benchmark Exercise 2013: Evaluation of Results from a Combined Computational Protein Design, Docking, and Scoring/Ranking Challenge

(2015) Richard D. Smith et al.   Journal of Chemical Information and Modeling

POSIT: Flexible Shape-Guided Docking For Pose Prediction

(2015) Brian P. Kelley et al.   Journal of Chemical Information and Modeling

Application of Shape Similarity in Pose Selection and Virtual Screening in CSARdock2014 Exercise

(2015) Ashutosh Kumar et al.   Journal of Chemical Information and Modeling

Case-specific performance of MM-PBSA, MM-GBSA, and SIE in virtual screening

(2015) Salla I. Virtanen et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING

Improvements, trends, and new ideas in molecular docking: 2012-2013 in review

(2015) Elizabeth Yuriev et al.   JOURNAL OF MOLECULAR RECOGNITION

Beware of docking!

(2015) Yu-Chian Chen   TRENDS IN PHARMACOLOGICAL SCIENCES

Does a More Precise Chemical Description of Protein–Ligand Complexes Lead to More Accurate Prediction of Binding Affinity?

(2014) Pedro J. Ballester et al.   Journal of Chemical Information and Modeling

Comparative Assessment of Scoring Functions on an Updated Benchmark: 2. Evaluation Methods and General Results

(2014) Yan Li et al.   Journal of Chemical Information and Modeling

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

sc-PDB: a 3D-database of ligandable binding sites—10 years on

(2014) Jérémy Desaphy et al.   NUCLEIC ACIDS RESEARCH

UniProt: a hub for protein information

(2014)   NUCLEIC ACIDS RESEARCH

Protoss: a holistic approach to predict tautomers and protonation states in protein-ligand complexes

(2014) Stefan Bietz et al.   Journal of Cheminformatics

Protein-Ligand Docking in the New Millennium – A Retrospective of 10 Years in the Field

(2013) S.F. Sousa et al.   CURRENT MEDICINAL CHEMISTRY

Scoring Functions for Prediction of Protein-Ligand Interactions

(2013) Jui-Chih Wang et al.   CURRENT PHARMACEUTICAL DESIGN

CSAR Benchmark Exercise 2011–2012: Evaluation of Results from Docking and Relative Ranking of Blinded Congeneric Series

(2013) Kelly L. Damm-Ganamet et al.   Journal of Chemical Information and Modeling

SFCscoreRF: A Random Forest-Based Scoring Function for Improved Affinity Prediction of Protein–Ligand Complexes

(2013) David Zilian et al.   Journal of Chemical Information and Modeling

Encoding Protein–Ligand Interaction Patterns in Fingerprints and Graphs

(2013) Jérémy Desaphy et al.   Journal of Chemical Information and Modeling

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

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

Design strategies to target crystallographic waters applied to the Hsp90 molecular chaperone

(2011) Pei-Pei Kung et al.   BIOORGANIC & MEDICINAL CHEMISTRY LETTERS

Structure-Based Discovery of Allosteric Modulators of Two Related Class B G-Protein-Coupled Receptors

(2011) Chris de Graaf et al.   ChemMedChem

CSAR Scoring Challenge Reveals the Need for New Concepts in Estimating Protein–Ligand Binding Affinity

(2011) Fedor N. Novikov et al.   Journal of Chemical Information and Modeling

Support Vector Regression Scoring of Receptor–Ligand Complexes for Rank-Ordering and Virtual Screening of Chemical Libraries

(2011) Liwei Li et al.   Journal of Chemical Information and Modeling

Crystal Structure-Based Virtual Screening for Fragment-like Ligands of the Human Histamine H1Receptor

(2011) Chris de Graaf et al.   JOURNAL OF MEDICINAL CHEMISTRY

Assessing the Performance of the MM/PBSA and MM/GBSA Methods. 1. The Accuracy of Binding Free Energy Calculations Based on Molecular Dynamics Simulations

(2010) Tingjun Hou et al.   Journal of Chemical Information and Modeling

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

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

Estrogen Receptor Alpha as a Key Target of Red Wine Polyphenols Action on the Endothelium

(2010) Matthieu Chalopin et al.   PLoS One

Assessment of Scaffold Hopping Efficiency by Use of Molecular Interaction Fingerprints

(2008) Jennifer Venhorst et al.   JOURNAL OF MEDICINAL CHEMISTRY