Challenges and opportunities of automated protein‐protein docking: HDOCK server vs human predictions in CAPRI Rounds 38‐46

Structural mechanisms of phospholipid activation of the human TPC2 channel

(2019) Ji She et al.   eLife

Blind prediction of homo‐ and hetero‐protein complexes: The CASP13‐CAPRI experiment

(2019) Marc F. Lensink et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Pushing the accuracy limit of shape complementarity for protein-protein docking

(2019) Yumeng Yan et al.   BMC BIOINFORMATICS

Modeling protein‐protein, protein‐peptide, and protein‐oligosaccharide complexes: CAPRI 7th edition

(2019) Marc F. Lensink et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Helicobacter pylori adhesin HopQ disrupts trans dimerization in human CEACAMs

(2018) Kristof Moonens et al.   EMBO JOURNAL

Structural Activation of Pro-inflammatory Human Cytokine IL-23 by Cognate IL-23 Receptor Enables Recruitment of the Shared Receptor IL-12Rβ1

(2018) Yehudi Bloch et al.   IMMUNITY

Hierarchical Flexible Peptide Docking by Conformer Generation and Ensemble Docking of Peptides

(2018) Pei Zhou et al.   Journal of Chemical Information and Modeling

HPEPDOCK: a web server for blind peptide–protein docking based on a hierarchical algorithm

(2018) Pei Zhou et al.   NUCLEIC ACIDS RESEARCH

Type IX secretion system PorM and gliding machinery GldM form arches spanning the periplasmic space

(2018) Philippe Leone et al.   Nature Communications

High-affinity heterotetramer formation between the large myelin-associated glycoprotein and the dynein light chain DYNLL1

(2018) Matti Myllykoski et al.   JOURNAL OF NEUROCHEMISTRY

PubChem 2019 update: improved access to chemical data

(2018) Sunghwan Kim et al.   NUCLEIC ACIDS RESEARCH

The ClusPro web server for protein–protein docking

(2017) Dima Kozakov et al.   Nature Protocols

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

(2017) Yumeng Yan et al.   NUCLEIC ACIDS RESEARCH

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

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

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

Efficient conformational ensemble generation of protein-bound peptides

(2017) Yumeng Yan et al.   Journal of Cheminformatics

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

(2016) Jinchao Yu et al.   NUCLEIC ACIDS RESEARCH

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

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

Helicobacter pylori adhesin HopQ engages in a virulence-enhancing interaction with human CEACAMs

(2016) Anahita Javaheri et al.   Nature Microbiology

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

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

The I-TASSER Suite: protein structure and function prediction

(2015) Jianyi Yang et al.   NATURE METHODS

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

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

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

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

(2014) Sheng-You Huang   DRUG DISCOVERY TODAY

SwarmDock: a server for flexible protein–protein docking

(2013) Mieczyslaw Torchala et al.   BIOINFORMATICS

Template-based structure modeling of protein–protein interactions

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

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

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

Sampling and scoring: A marriage made in heaven

(2013) Sandor Vajda 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

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

(2012) Qiangfeng Cliff Zhang et al.   NATURE

Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega

(2011) F. Sievers et al.   Molecular Systems Biology

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

(2011) Michael Remmert et al.   NATURE METHODS

Open Babel: An open chemical toolbox

(2011) Noel M O'Boyle et al.   Journal of Cheminformatics

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

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

Blind predictions of protein interfaces by docking calculations in CAPRI

(2010) Marc F. Lensink 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

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