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

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

Structural basis for haem piracy from host haemopexin by Haemophilus influenzae

(2016) Silvia Zambolin et al.   Nature Communications

Specific GFP-binding artificial proteins ( Rep): a new tool for in vitro to live cell applications

(2015) A. Chevrel et al.   BIOSCIENCE REPORTS

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

Interaction with Single-stranded DNA-binding Protein StimulatesEscherichia coliRibonuclease HI Enzymatic Activity

(2015) Christine Petzold et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Structure of UBE2Z Enzyme Provides Functional Insight into Specificity in the FAT10 Protein Conjugation Machinery

(2015) Julien Schelpe et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Structures of the Ultra-High-Affinity Protein–Protein Complexes of Pyocins S2 and AP41 and Their Cognate Immunity Proteins from Pseudomonas aeruginosa

(2015) Amar Joshi et al.   JOURNAL OF MOLECULAR BIOLOGY

Mechanism of UCH-L5 Activation and Inhibition by DEUBAD Domains in RPN13 and INO80G

(2015) Danny D. Sahtoe et al.   MOLECULAR CELL

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

(2014) Sheng-You Huang   DRUG DISCOVERY TODAY

Crystal structure of the PRC1 ubiquitylation module bound to the nucleosome

(2014) Robert K. McGinty et al.   NATURE

Sequence co-evolution gives 3D contacts and structures of protein complexes

(2014) Thomas A Hopf et al.   eLife

Evaluating template-based and template-free protein-protein complex structure prediction

(2013) T. Vreven et al.   BRIEFINGS IN BIOINFORMATICS

Computational design of protein–protein interactions

(2013) Gideon Schreiber et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Template-based structure modeling of protein–protein interactions

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

Structural and Biochemical Basis for Ubiquitin Ligase Recruitment by Arrestin-related Domain-containing Protein-3 (ARRDC3)

(2013) Shiqian Qi et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Mapping Monomeric Threading to Protein–Protein Structure Prediction

(2013) Aysam Guerler et al.   Journal of Chemical Information and Modeling

Structural mechanisms of PriA-mediated DNA replication restart

(2013) B. Bhattacharyya et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Performance of ZDOCK in CAPRI rounds 20-26

(2013) Thom Vreven et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Expanding the frontiers of protein-protein modeling: From docking and scoring to binding affinity predictions and other challenges

(2013) Chiara Pallara et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Global and local structural similarity in protein-protein complexes: Implications for template-based docking

(2013) Petras J. Kundrotas et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Improved flexible refinement of protein docking in CAPRI rounds 22-27

(2013) Yang Shen   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Sampling and scoring: A marriage made in heaven

(2013) Sandor Vajda 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

Using the concept of transient complex for affinity predictions in CAPRI rounds 20-27 and beyond

(2013) Sanbo Qin et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Flexible docking and refinement with a coarse-grained protein model using ATTRACT

(2013) Sjoerd de Vries et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

A Markov-chain model description of binding funnels to enhance the ranking of docked solutions

(2013) Mieczyslaw Torchala 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

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

Protein-protein Docking and Hot-spot Prediction for Drug Discovery

(2012) Solene Grosdidier et al.   CURRENT PHARMACEUTICAL DESIGN

Structure-based prediction of protein–protein interactions on a genome-wide scale

(2012) Qiangfeng Cliff Zhang et al.   NATURE

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

Spatial clustering of protein binding sites for template based protein docking

(2011) Anisah W. Ghoorah et al.   BIOINFORMATICS

Recognition of UbcH5c and the nucleosome by the Bmi1/Ring1b ubiquitin ligase complex

(2011) Matthew L Bentley et al.   EMBO JOURNAL

The structural basis of Edc3- and Scd6-mediated activation of the Dcp1:Dcp2 mRNA decapping complex

(2011) Simon A Fromm et al.   EMBO JOURNAL

Predicting protein-protein interactions on a proteome scale by matching evolutionary and structural similarities at interfaces using PRISM

(2011) Nurcan Tuncbag et al.   Nature Protocols

Protein-Protein Complex Structure Predictions by Multimeric Threading and Template Recombination

(2011) Srayanta Mukherjee et al.   STRUCTURE

Accounting for conformational changes during protein–protein docking

(2010) Martin Zacharias   CURRENT OPINION IN STRUCTURAL BIOLOGY

Protein–protein docking tested in blind predictions: the CAPRI experiment

(2010) Joël Janin   Molecular BioSystems

Selection of near-native poses in CAPRI rounds 13-19

(2010) Sanbo Qin et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

An integrated suite of fast docking algorithms

(2010) Efrat Mashiach et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

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

Blind predictions of protein interfaces by docking calculations in CAPRI

(2010) Marc F. Lensink et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

SSB as an Organizer/Mobilizer of Genome Maintenance Complexes

(2008) Robert D. Shereda et al.   CRITICAL REVIEWS IN BIOCHEMISTRY AND MOLECULAR BIOLOGY

Recent Progress and Future Directions in Protein-Protein Docking

(2008) David Ritchie   CURRENT PROTEIN & PEPTIDE SCIENCE

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

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

Principles of flexible protein-protein docking

(2008) Nelly Andrusier et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS