HDOCK: a web server for protein–protein and protein–DNA/RNA docking based on a hybrid strategy

Addressing recent docking challenges: A hybrid strategy to integrate template-based and free protein-protein docking

(2017) Yumeng Yan et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

InterEvDock: a docking server to predict the structure of protein–protein interactions using evolutionary information

(2016) Jinchao Yu et al.   NUCLEIC ACIDS RESEARCH

Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experiment

(2016) Marc F. Lensink 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

A non-redundant protein-RNA docking benchmark version 2.0

(2016) Chandran Nithin et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

A Web Interface for Easy Flexible Protein-Protein Docking with ATTRACT

(2015) Sjoerd J. de Vries et al.   BIOPHYSICAL JOURNAL

Exploring the potential of global protein–protein docking: an overview and critical assessment of current programs for automatic ab initio docking

(2015) Sheng-You Huang   DRUG DISCOVERY TODAY

pyDockSAXS: protein–protein complex structure by SAXS and computational docking

(2015) Brian Jiménez-García et al.   NUCLEIC ACIDS RESEARCH

NPDock: a web server for protein–nucleic acid docking

(2015) Irina Tuszynska et al.   NUCLEIC ACIDS RESEARCH

ZDOCK server: interactive docking prediction of protein-protein complexes and symmetric multimers

(2014) B. G. Pierce et al.   BIOINFORMATICS

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

(2014) Sheng-You Huang   DRUG DISCOVERY TODAY

A knowledge-based scoring function for protein-RNA interactions derived from a statistical mechanics-based iterative method

(2014) Sheng-You Huang et al.   NUCLEIC ACIDS RESEARCH

SwarmDock: a server for flexible protein–protein docking

(2013) Mieczyslaw Torchala et al.   BIOINFORMATICS

JSmol and the Next-Generation Web-Based Representation of 3D Molecular Structure as Applied toProteopedia

(2013) Robert M. Hanson et al.   ISRAEL JOURNAL OF CHEMISTRY

Inclusion of the orientational entropic effect and low-resolution experimental information for protein-protein docking in Critical Assessment of PRedicted Interactions (CAPRI)

(2013) Sheng-You Huang et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Sampling and scoring: A marriage made in heaven

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

A nonredundant structure dataset for benchmarking protein-RNA computational docking

(2012) Sheng-You Huang et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment

(2011) Michael Remmert et al.   NATURE METHODS

The HADDOCK web server for data-driven biomolecular docking

(2010) Sjoerd J de Vries et al.   Nature Protocols

HexServer: an FFT-based protein docking server powered by graphics processors

(2010) G. Macindoe et al.   NUCLEIC ACIDS RESEARCH

MDockPP: A hierarchical approach for protein-protein docking and its application to CAPRI rounds 15-19

(2010) Sheng-You Huang et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Protein-protein docking benchmark version 4.0

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

3D-Garden: a system for modelling protein–protein complexes based on conformational refinement of ensembles generated with the marching cubes algorithm

(2008) Victor I. Lesk et al.   BIOINFORMATICS

A protein-DNA docking benchmark

(2008) M. van Dijk et al.   NUCLEIC ACIDS RESEARCH

The RosettaDock server for local protein-protein docking

(2008) S. Lyskov et al.   NUCLEIC ACIDS RESEARCH

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

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