Evaluation of CONSRANK-Like Scoring Functions for Rescoring Ensembles of Protein–Protein Docking Poses

An overview of data‐driven HADDOCK strategies in CAPRI rounds 38‐45

(2019) Panagiotis I. Koukos et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Introducing a Clustering Step in a Consensus Approach for the Scoring of Protein-Protein Docking Models

(2016) Edrisse Chermak et al.   PLoS One

Rescore protein-protein docked ensembles with an interface contact statistics

(2016) Mihaly Mezei   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Lessons from (co-)evolution in the docking of proteins and peptides for CAPRI Rounds 28-35

(2016) Jinchao Yu et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

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

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

DOCKSCORE: a webserver for ranking protein-protein docked poses

(2015) Sony Malhotra et al.   BMC BIOINFORMATICS

Analysis and Ranking of Protein-Protein Docking Models Using Inter-Residue Contacts and Inter-Molecular Contact Maps

(2015) Romina Oliva et al.   MOLECULES

CONSRANK: a server for the analysis, comparison and ranking of docking models based on inter-residue contacts

(2014) E. Chermak et al.   BIOINFORMATICS

MEGADOCK 4.0: an ultra–high-performance protein–protein docking software for heterogeneous supercomputers

(2014) Masahito Ohue et al.   BIOINFORMATICS

Protein-Protein Docking: From Interaction to Interactome

(2014) Ilya A. Vakser   BIOPHYSICAL JOURNAL

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

(2013) Jessica Andreani 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

Using a consensus approach based on the conservation of inter-residue contacts to rank CAPRI models

(2013) Anna Vangone et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Ranking multiple docking solutions based on the conservation of inter-residue contacts

(2013) Romina Oliva 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

Accelerating Protein Docking in ZDOCK Using an Advanced 3D Convolution Library

(2011) Brian G. Pierce et al.   PLoS One

On the analysis of protein-protein interactions via knowledge-based potentials for the prediction of protein-protein docking

(2011) Elisenda Feliu et al.   PROTEIN SCIENCE

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

(2011) Thom Vreven et al.   PROTEIN SCIENCE

Next challenges in protein-protein docking: from proteome to interactome and beyond

(2011) Adrien S.J. Melquiond et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

Ultra-fast FFT protein docking on graphics processors

(2010) David W. Ritchie et al.   BIOINFORMATICS

SwarmDock and the Use of Normal Modes in Protein-Protein Docking

(2010) Iain H. Moal et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Performance of ZDOCK and ZRANK in CAPRI rounds 13-19

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

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

A combination of rescoring and refinement significantly improves protein docking performance

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

An iterative knowledge-based scoring function for protein-protein recognition

(2008) Sheng-You Huang et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Consensus scoring for enriching near-native structures from protein-protein docking decoys

(2008) Shide Liang et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS