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

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

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

Beyond blob-ology

(2014) M. T. J. Smith et al.   SCIENCE

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

(2014) Sergey Ovchinnikov et al.   eLife

Template-based structure modeling of protein–protein interactions

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

Trendspotting in the Protein Data Bank

(2013) Helen M. Berman et al.   FEBS LETTERS

CASP prediction center infrastructure and evaluation measures in CASP10 and CASP ROLL

(2013) Andriy Kryshtafovych et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Blind prediction of interfacial water positions in CAPRI

(2013) Marc F. Lensink 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

Integrative Structural Biology

(2013) A. B. Ward et al.   SCIENCE

Intertwined Associations in Structures of Homooligomeric Proteins

(2013) Stephen S. MacKinnon et al.   STRUCTURE

High-Resolution Comparative Modeling with RosettaCM

(2013) Yifan Song et al.   STRUCTURE

Optimization of affinity, specificity and function of designed influenza inhibitors using deep sequencing

(2012) Timothy A Whitehead et al.   NATURE BIOTECHNOLOGY

Protein structure prediction from sequence variation

(2012) Debora S Marks et al.   NATURE BIOTECHNOLOGY

Template-based protein structure modeling using the RaptorX web server

(2012) Morten Källberg et al.   Nature Protocols

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

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

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

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

(2011) Michael Remmert et al.   NATURE METHODS

Fast and accurate modeling of protein-protein interactions by combining template-interface-based docking with flexible refinement

(2011) Nurcan Tuncbag et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

The Subunit Interfaces of Weakly Associated Homodimeric Proteins

(2010) Sucharita Dey et al.   JOURNAL OF MOLECULAR BIOLOGY

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

Docking and scoring protein interactions: CAPRI 2009

(2010) Marc F. Lensink 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

Robust, high-throughput solution structural analyses by small angle X-ray scattering (SAXS)

(2009) Greg L Hura et al.   NATURE METHODS

MM-align: a quick algorithm for aligning multiple-chain protein complex structures using iterative dynamic programming

(2009) Srayanta Mukherjee et al.   NUCLEIC ACIDS RESEARCH

Evaluation of template-based models in CASP8 with standard measures

(2009) Domenico Cozzetto et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Fast and accurate automatic structure prediction with HHpred

(2009) Andrea Hildebrand et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Proteome Organization in a Genome-Reduced Bacterium

(2009) S. Kuhner et al.   SCIENCE

Recent Progress and Future Directions in Protein-Protein Docking

(2008) David Ritchie   CURRENT PROTEIN & PEPTIDE SCIENCE

The RosettaDock server for local protein-protein docking

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