Protein–ligand docking using FFT based sampling: D3R case study

A Hybrid Knowledge-Based and Empirical Scoring Function for Protein–Ligand Interaction: SMoG2016

(2017) Théau Debroise et al.   Journal of Chemical Information and Modeling

Focused grid-based resampling for protein docking and mapping

(2016) Artem B. Mamonov et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Improving scoring-docking-screening powers of protein-ligand scoring functions using random forest

(2016) Cheng Wang et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Predicting binding poses and affinities for protein - ligand complexes in the 2015 D3R Grand Challenge using a physical model with a statistical parameter estimation

(2016) Sergei Grudinin et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

CSM-lig: a web server for assessing and comparing protein–small molecule affinities

(2016) Douglas E.V. Pires et al.   NUCLEIC ACIDS RESEARCH

Modeling protein-protein and protein-peptide complexes: CAPRI 6th edition

(2016) Marc F. Lensink et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

The Impact of Side-Chain Packing on Protein Docking Refinement

(2015) Mohammad Moghadasi et al.   Journal of Chemical Information and Modeling

Iterative Knowledge-Based Scoring Functions Derived from Rigid and Flexible Decoy Structures: Evaluation with the 2013 and 2014 CSAR Benchmarks

(2015) Chengfei Yan et al.   Journal of Chemical Information and Modeling

Energy Minimization on Manifolds for Docking Flexible Molecules

(2015) Hanieh Mirzaei et al.   Journal of Chemical Theory and Computation

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: 1. Compilation of the Test Set

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

Docking, scoring, and affinity prediction in CAPRI

(2013) Marc F. Lensink et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

How good is automated protein docking?

(2013) Dima Kozakov et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Systematic placement of structural water molecules for improved scoring of protein-ligand interactions

(2011) D. J. Huggins et al.   PROTEIN ENGINEERING DESIGN & SELECTION

A Smoothed Backbone-Dependent Rotamer Library for Proteins Derived from Adaptive Kernel Density Estimates and Regressions

(2011) Maxim V. Shapovalov et al.   STRUCTURE

Confab - Systematic generation of diverse low-energy conformers

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

Docking and scoring protein interactions: CAPRI 2009

(2010) Marc F. Lensink et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Comparative Assessment of Scoring Functions on a Diverse Test Set

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

DARS (Decoys As the Reference State) Potentials for Protein-Protein Docking

(2008) Gwo-Yu Chuang et al.   BIOPHYSICAL JOURNAL