PPI4DOCK: large scale assessment of the use of homology models in free docking over more than 1000 realistic targets

A benchmark testing ground for integrating homology modeling and protein docking

(2016) Tanggis Bohnuud et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Progress and challenges in predicting protein interfaces

(2015) Reyhaneh Esmaielbeiki et al.   BRIEFINGS IN BIOINFORMATICS

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

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

Protein models docking benchmark 2

(2015) Ivan Anishchenko et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

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

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

Protein-Protein Docking: From Interaction to Interactome

(2014) Ilya A. Vakser   BIOPHYSICAL JOURNAL

UniProt: a hub for protein information

(2014)   NUCLEIC ACIDS RESEARCH

Assessing the Applicability of Template-Based Protein Docking in the Twilight Zone

(2014) Jacopo Negroni et al.   STRUCTURE

Template-based structure modeling of protein–protein interactions

(2013) Andras Szilagyi et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Protein models: The Grand Challenge of protein docking

(2013) Ivan Anishchenko et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Defining the limits of homology modeling in information-driven protein docking

(2013) J. P. G. L. M. Rodrigues et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Assessment of template-free modeling in CASP10 and ROLL

(2013) Chin-Hsien Tai 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

How good is automated protein docking?

(2013) Dima Kozakov et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

High-Resolution Comparative Modeling with RosettaCM

(2013) Yifan Song et al.   STRUCTURE

Interactome3D: adding structural details to protein networks

(2012) Roberto Mosca et al.   NATURE METHODS

InterEvol database: exploring the structure and evolution of protein complex interfaces

(2011) Guilhem Faure et al.   NUCLEIC ACIDS RESEARCH

iAlign: a method for the structural comparison of protein–protein interfaces

(2010) Mu Gao et al.   BIOINFORMATICS

The HADDOCK web server for data-driven biomolecular docking

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

I-TASSER: a unified platform for automated protein structure and function prediction

(2010) Ambrish Roy et al.   Nature Protocols

Protein-protein docking benchmark version 4.0

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