Template‐based modeling by ClusPro in CASP13 and the potential for using co‐evolutionary information in docking

What method to use for protein–protein docking?

(2019) Kathryn A Porter et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

ClusPro FMFT-SAXS: Ultra-fast Filtering Using Small-Angle X-ray Scattering Data in Protein Docking

(2018) Mikhail Ignatov et al.   JOURNAL OF MOLECULAR BIOLOGY

A Completely Reimplemented MPI Bioinformatics Toolkit with a New HHpred Server at its Core

(2018) Lukas Zimmermann et al.   JOURNAL OF MOLECULAR BIOLOGY

ClusPro-DC: Dimer Classification by the Cluspro Server for Protein–Protein Docking

(2017) Christine Yueh et al.   JOURNAL OF MOLECULAR BIOLOGY

The ClusPro web server for protein–protein docking

(2017) Dima Kozakov et al.   Nature Protocols

New additions to the ClusPro server motivated by CAPRI

(2017) Sandor Vajda et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

The challenge of modeling protein assemblies: the CASP12-CAPRI experiment

(2017) Marc F. Lensink et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Accounting for pairwise distance restraints in FFT-based protein–protein docking

(2016) Bing Xia et al.   BIOINFORMATICS

Cryo electron microscopy to determine the structure of macromolecular complexes

(2016) Marta Carroni et al.   METHODS

Protein–protein docking by fast generalized Fourier transforms on 5D rotational manifolds

(2016) Dzmitry Padhorny et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

Accounting for observed small angle X-ray scattering profile in the protein-protein docking server cluspro

(2015) Bing Xia et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Updates to the Integrated Protein–Protein Interaction Benchmarks: Docking Benchmark Version 5 and Affinity Benchmark Version 2

(2015) Thom Vreven et al.   JOURNAL OF MOLECULAR BIOLOGY

Robust and accurate prediction of residue–residue interactions across protein interfaces using evolutionary information

(2014) Sergey Ovchinnikov et al.   eLife

Correction for Kamisetty et al., Assessing the utility of coevolution-based residue-residue contact predictions in a sequence- and structure-rich era

(2013)   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Docking, scoring, and affinity prediction in CAPRI

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

Templates are available to model nearly all complexes of structurally characterized proteins

(2012) P. J. Kundrotas et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

HHfrag: HMM-based fragment detection using HHpred

(2011) Ivan Kalev et al.   BIOINFORMATICS

Protein-protein docking benchmark version 4.0

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

Learning generative models for protein fold families

(2010) Sivaraman Balakrishnan et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

CHARMM: The biomolecular simulation program

(2009) B. R. Brooks et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY