CLUB-MARTINI: Selecting Favourable Interactions amongst Available Candidates, a Coarse-Grained Simulation Approach to Scoring Docking Decoys

Protein-Protein Docking: From Interaction to Interactome

(2014) Ilya A. Vakser   BIOPHYSICAL JOURNAL

Search strategies and evaluation in protein–protein docking: principles, advances and challenges

(2014) Sheng-You Huang   DRUG DISCOVERY TODAY

A Bayesian statistical approach of improving knowledge-based scoring functions for protein-ligand interactions

(2014) Sam Z. Grinter et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

DrugScorePPI Knowledge-Based Potentials Used as Scoring and Objective Function in Protein-Protein Docking

(2014) Dennis M. Krüger et al.   PLoS One

Score_set: A CAPRI benchmark for scoring protein complexes

(2014) Marc F. Lensink et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Coarse-grained versus atomistic simulations: realistic interaction free energies for real proteins

(2013) Ali May et al.   BIOINFORMATICS

Scoring functions for protein–protein interactions

(2013) Iain H Moal et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Improving the Scoring of Protein–Ligand Binding Affinity by Including the Effects of Structural Water and Electronic Polarization

(2013) Jinfeng Liu et al.   Journal of Chemical Information and Modeling

Blind prediction of interfacial water positions in CAPRI

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

Docking, scoring, and affinity prediction in CAPRI

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

Scoring protein interaction decoys using exposed residues (SPIDER): A novel multibody interaction scoring function based on frequent geometric patterns of interfacial residues

(2012) Raed Khashan et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Integrating atom-based and residue-based scoring functions for protein-protein docking

(2011) Thom Vreven et al.   PROTEIN SCIENCE

Are Scoring Functions in Protein−Protein Docking Ready To Predict Interactomes? Clues from a Novel Binding Affinity Benchmark

(2010) Panagiotis L. Kastritis et al.   JOURNAL OF PROTEOME RESEARCH

A Guide to Simple and Informative Binding Assays

(2010) Thomas D. Pollard   MOLECULAR BIOLOGY OF THE CELL

Docking and scoring protein interactions: CAPRI 2009

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

Blind predictions of protein interfaces by docking calculations in CAPRI

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

A survey of available tools and web servers for analysis of protein-protein interactions and interfaces

(2009) N. Tuncbag et al.   BRIEFINGS IN BIOINFORMATICS

The structural basis of Arf effector specificity: the crystal structure of ARF6 in a complex with JIP4

(2009) Tatiana Isabet et al.   EMBO JOURNAL

The MARTINI Coarse-Grained Force Field: Extension to Proteins

(2008) Luca Monticelli et al.   Journal of Chemical Theory and Computation

GROMACS 4:  Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation

(2008) Berk Hess et al.   Journal of Chemical Theory and Computation