Efficient consideration of coordinated water molecules improves computational protein-protein and protein-ligand docking discrimination

Water molecules in protein–ligand interfaces. Evaluation of software tools and SAR comparison

(2019) Eva Nittinger et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

The Rosetta All-Atom Energy Function for Macromolecular Modeling and Design

(2017) Rebecca F. Alford et al.   Journal of Chemical Theory and Computation

Simultaneous Optimization of Biomolecular Energy Functions on Features from Small Molecules and Macromolecules

(2016) Hahnbeom Park et al.   Journal of Chemical Theory and Computation

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

Combined Covalent-Electrostatic Model of Hydrogen Bonding Improves Structure Prediction with Rosetta

(2015) Matthew J. O’Meara et al.   Journal of Chemical Theory and Computation

Towards Ligand Docking Including Explicit Interface Water Molecules

(2013) Gordon Lemmon et al.   PLoS One

Blind prediction of interfacial water positions in CAPRI

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

Intuitive, but not simple: Including explicit water molecules in protein-protein docking simulations improves model quality

(2013) Hardik I. Parikh et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Probing the role of interfacial waters in protein-DNA recognition using a hybrid implicit/explicit solvation model

(2013) Shen Li et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Are Protein Force Fields Getting Better? A Systematic Benchmark on 524 Diverse NMR Measurements

(2012) Kyle A. Beauchamp et al.   Journal of Chemical Theory and Computation

Placevent: An algorithm for prediction of explicit solvent atom distribution-Application to HIV-1 protease and F-ATP synthase

(2012) Daniel J. Sindhikara et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Rapid and Accurate Prediction and Scoring of Water Molecules in Protein Binding Sites

(2012) Gregory A. Ross et al.   PLoS One

Extensive protein and DNA backbone sampling improves structure-based specificity prediction for C2H2 zinc fingers

(2011) Chen Yanover et al.   NUCLEIC ACIDS RESEARCH

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

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

How Fast-Folding Proteins Fold

(2011) K. Lindorff-Larsen et al.   SCIENCE

Three-Dimensional Molecular Theory of Solvation Coupled with Molecular Dynamics in Amber

(2010) Tyler Luchko et al.   Journal of Chemical Theory and Computation

Protein-protein docking benchmark version 4.0

(2010) Howook Hwang et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Empirical Scoring Functions for Advanced Protein−Ligand Docking with PLANTS

(2009) Oliver Korb et al.   Journal of Chemical Information and Modeling

Sampling Rotation Groups by Successive Orthogonal Images

(2008) Julie C. Mitchell   SIAM JOURNAL ON SCIENTIFIC COMPUTING