Score_set: A CAPRI benchmark for scoring protein complexes

Collective variable driven molecular dynamics to improve protein–protein docking scoring

(2014) Diego Masone et al.   COMPUTATIONAL BIOLOGY AND CHEMISTRY

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

InterEvScore: a novel coarse-grained interface scoring function using a multi-body statistical potential coupled to evolution

(2013) Jessica Andreani et al.   BIOINFORMATICS

SwarmDock: a server for flexible protein–protein docking

(2013) Mieczyslaw Torchala et al.   BIOINFORMATICS

The scoring of poses in protein-protein docking: current capabilities and future directions

(2013) Iain H Moal et al.   BMC 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

Selection of Specific Protein Binders for Pre-Defined Targets from an Optimized Library of Artificial Helicoidal Repeat Proteins (alphaRep)

(2013) Asma Guellouz et al.   PLoS One

Sampling and scoring: A marriage made in heaven

(2013) Sandor Vajda et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Community-wide evaluation of methods for predicting the effect of mutations on protein-protein interactions

(2013) Rocco Moretti 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

Structure of the Ultra-High-Affinity Colicin E2 DNase–Im2 Complex

(2012) Justyna Aleksandra Wojdyla et al.   JOURNAL OF MOLECULAR BIOLOGY

Prediction of protein-protein binding free energies

(2012) Thom Vreven et al.   PROTEIN SCIENCE

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

Scoring Function Based on Weighted Residue Network

(2011) Xiong Jiao et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Scoring by Intermolecular Pairwise Propensities of Exposed Residues (SIPPER): A New Efficient Potential for Protein−Protein Docking

(2011) Carles Pons et al.   Journal of Chemical Information and Modeling

Energy design for protein-protein interactions

(2011) D. V. S. Ravikant et al.   JOURNAL OF CHEMICAL PHYSICS

Community-Wide Assessment of Protein-Interface Modeling Suggests Improvements to Design Methodology

(2011) Sarel J. Fleishman et al.   JOURNAL OF MOLECULAR BIOLOGY

Mechanism of activation of methyltransferases involved in translation by the Trm112 ‘hub’ protein

(2011) Dominique Liger et al.   NUCLEIC ACIDS RESEARCH

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

(2011) Thom Vreven et al.   PROTEIN SCIENCE

A structure-based benchmark for protein-protein binding affinity

(2011) Panagiotis L. Kastritis et al.   PROTEIN SCIENCE

Computational Design of Proteins Targeting the Conserved Stem Region of Influenza Hemagglutinin

(2011) S. J. Fleishman et al.   SCIENCE

Accounting for conformational changes during protein–protein docking

(2010) Martin Zacharias   CURRENT OPINION IN STRUCTURAL BIOLOGY

Putting an N-terminal end to the Clostridium thermocellum xylanase Xyn10B story: Crystal structure of the CBM22-1–GH10 modules complexed with xylohexaose

(2010) Shabir Najmudin et al.   JOURNAL OF STRUCTURAL BIOLOGY

Protein–protein docking tested in blind predictions: the CAPRI experiment

(2010) Joël Janin   Molecular BioSystems

Scoring functions and their evaluation methods for protein–ligand docking: recent advances and future directions

(2010) Sheng-You Huang et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

The structural and energetic basis for high selectivity in a high-affinity protein-protein interaction

(2010) N. A. G. Meenan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Docking and scoring protein interactions: CAPRI 2009

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

Protein-protein docking benchmark version 4.0

(2010) Howook Hwang 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

Convergence and combination of methods in protein–protein docking

(2009) Sandor Vajda et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

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 Ternary Structure of the Double-headed Arrowhead Protease Inhibitor API-A Complexed with Two Trypsins Reveals a Novel Reactive Site Conformation

(2009) Rui Bao et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

DOCKGROUND protein-protein docking decoy set

(2008) S. Liu et al.   BIOINFORMATICS

Amino acid network and its scoring application in protein–protein docking

(2008) Shan Chang et al.   BIOPHYSICAL CHEMISTRY

Predicting 3D Structures of Protein-Protein Complexes

(2008) Ilya Vakser et al.   CURRENT PHARMACEUTICAL BIOTECHNOLOGY

Recognition-induced Conformational Changes in Protein-Protein Docking

(2008) M. Lensink et al.   CURRENT PHARMACEUTICAL BIOTECHNOLOGY

Structural and Mutational Analyses of the Interaction between the Barley α-Amylase/Subtilisin Inhibitor and the Subtilisin Savinase Reveal a Novel Mode of Inhibition

(2008) Pernille Ollendorff Micheelsen et al.   JOURNAL OF MOLECULAR BIOLOGY

A combination of rescoring and refinement significantly improves protein docking performance

(2008) Brian Pierce et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Structure of the Yeast tRNA m7G Methylation Complex

(2008) Nicolas Leulliot et al.   STRUCTURE