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

De novo design of potent and selective mimics of IL-2 and IL-15

(2019) Daniel-Adriano Silva et al.   NATURE

Assessment of protein assembly prediction in CASP13

(2019) Dmytro Guzenko et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

A Completely Reimplemented MPI Bioinformatics Toolkit with a New HHpred Server at its Core

(2018) Lukas Zimmermann et al.   JOURNAL OF MOLECULAR BIOLOGY

HSYMDOCK: a docking web server for predicting the structure of protein homo-oligomers with Cn or Dn symmetry

(2018) Yumeng Yan et al.   NUCLEIC ACIDS RESEARCH

Automated evaluation of quaternary structures from protein crystals

(2018) Spencer Bliven et al.   PLoS Computational Biology

The ClusPro web server for protein–protein docking

(2017) Dima Kozakov et al.   Nature Protocols

Integrative structure modeling with the Integrative Modeling Platform

(2017) Benjamin Webb et al.   PROTEIN SCIENCE

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

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

Assessment of protein assembly prediction in CASP12

(2017) Aleix Lafita et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

VoroMQA: Assessment of protein structure quality using interatomic contact areas

(2017) Kliment Olechnovič et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Modeling CAPRI targets 110-120 by template-based and free docking using contact potential and combined scoring function

(2017) Petras J. Kundrotas et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Protein structure determination using metagenome sequence data

(2017) Sergey Ovchinnikov et al.   SCIENCE

Modeling disordered protein interactions from biophysical principles

(2017) Lenna X. Peterson et al.   PLoS Computational Biology

Accurate De Novo Prediction of Protein Contact Map by Ultra-Deep Learning Model

(2017) Sheng Wang et al.   PLoS Computational Biology

DockQ: A Quality Measure for Protein-Protein Docking Models

(2016) Sankar Basu et al.   PLoS One

Modeling and minimizing CAPRI round 30 symmetrical protein complexes from CASP-11 structural models

(2016) Marwa El Houasli et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

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

Improved de novo structure prediction in CASP11 by incorporating coevolution information into Rosetta

(2016) Sergey Ovchinnikov 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

Spherical polar Fourier assembly of protein complexes with arbitrary point group symmetry

(2016) David W. Ritchie et al.   JOURNAL OF APPLIED CRYSTALLOGRAPHY

How cryo-EM is revolutionizing structural biology

(2015) Xiao-chen Bai et al.   TRENDS IN BIOCHEMICAL SCIENCES

CONSRANK: a server for the analysis, comparison and ranking of docking models based on inter-residue contacts

(2014) E. Chermak et al.   BIOINFORMATICS

MetaPSICOV: combining coevolution methods for accurate prediction of contacts and long range hydrogen bonding in proteins

(2014) David T. Jones et al.   BIOINFORMATICS

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

Trendspotting in the Protein Data Bank

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

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

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

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

Multi-LZerD: Multiple protein docking for asymmetric complexes

(2012) Juan Esquivel-Rodríguez et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

GOAP: A Generalized Orientation-Dependent, All-Atom Statistical Potential for Protein Structure Prediction

(2011) Hongyi Zhou et al.   BIOPHYSICAL JOURNAL

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

Statistical mechanics-based method to extract atomic distance-dependent potentials from protein structures

(2011) Sheng-You Huang et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

The Subunit Interfaces of Weakly Associated Homodimeric Proteins

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

Network medicine: a network-based approach to human disease

(2010) Albert-László Barabási et al.   NATURE REVIEWS GENETICS

An integrated suite of fast docking algorithms

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

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

Fast and accurate automatic structure prediction with HHpred

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

Recent Progress and Future Directions in Protein-Protein Docking

(2008) David Ritchie   CURRENT PROTEIN & PEPTIDE SCIENCE

How Proteins Get in Touch: Interface Prediction in the Study of Biomolecular Complexes

(2008) Sjoerd de Vries et al.   CURRENT PROTEIN & PEPTIDE SCIENCE

Protein networks in disease

(2008) T. Ideker et al.   GENOME RESEARCH

Statistical Analysis of Interface Similarity in Crystals of Homologous Proteins

(2008) Qifang Xu et al.   JOURNAL OF MOLECULAR BIOLOGY

Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction

(2002) Hongyi Zhou et al.   PROTEIN SCIENCE