Limits and potential of combined folding and docking

Large-scale discovery of protein interactions at residue resolution using co-evolution calculated from genomic sequences

(2021) Anna G. Green et al.   Nature Communications

pyconsFold: a fast and easy tool for modeling and docking using distance predictions

(2021) J Lamb et al.   BIOINFORMATICS

Highly accurate protein structure prediction with AlphaFold

(2021) John Jumper et al.   NATURE

Highly accurate protein structure prediction for the human proteome

(2021) Kathryn Tunyasuvunakool et al.   NATURE

Accurate prediction of protein structures and interactions using a three-track neural network

(2021) Minkyung Baek et al.   SCIENCE

DNCON2_Inter: predicting interchain contacts for homodimeric and homomultimeric protein complexes using multiple sequence alignments of monomers and deep learning

(2021) Farhan Quadir et al.   Scientific Reports

Improved protein structure prediction using potentials from deep learning

(2020) Andrew W. Senior et al.   NATURE

Improved protein structure prediction using predicted interresidue orientations

(2020) Jianyi Yang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Distance-based protein folding powered by deep learning

(2019) Jinbo Xu   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Deep learning extends de novo protein modelling coverage of genomes using iteratively predicted structural constraints

(2019) Joe G. Greener et al.   Nature Communications

Contact Potential for Structure Prediction of Proteins and Protein Complexes from Potts Model

(2018) Ivan Anishchenko et al.   BIOPHYSICAL JOURNAL

UniProt: a worldwide hub of protein knowledge

(2018)   NUCLEIC ACIDS RESEARCH

STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets

(2018) Damian Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

Inferring interaction partners from protein sequences using mutual information

(2018) Anne-Florence Bitbol   PLoS Computational Biology

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

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

Conservation of coevolving protein interfaces bridges prokaryote–eukaryote homologies in the twilight zone

(2016) Juan Rodriguez-Rivas et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Modeling complexes of modeled proteins

(2016) Ivan Anishchenko et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Unexpected features of the dark proteome

(2015) Nelson Perdigão et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Improved Contact Predictions Using the Recognition of Protein Like Contact Patterns

(2014) Marcin J. Skwark et al.   PLoS Computational Biology

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

(2014) Sergey Ovchinnikov et al.   eLife

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

(2014) Thomas A Hopf et al.   eLife

Advances, Interactions, and Future Developments in the CNS, Phenix, and Rosetta Structural Biology Software Systems

(2013) Paul D. Adams et al.   Annual Review of Biophysics

The MIntAct project—IntAct as a common curation platform for 11 molecular interaction databases

(2013) Sandra Orchard et al.   NUCLEIC ACIDS RESEARCH

Docking, scoring, and affinity prediction in CAPRI

(2013) Marc F. Lensink et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Predicting protein residue–residue contacts using deep networks and boosting

(2012) Jesse Eickholt et al.   BIOINFORMATICS

Estimation of Residue-Residue Coevolution using Direct Coupling Analysis Identifies Many Native Contacts Across a Large Number of Domain Families

(2012) Faruck Morcos et al.   BIOPHYSICAL JOURNAL

The structural basis for the interaction between the CAF1 nuclease and the NOT1 scaffold of the human CCR4–NOT deadenylase complex

(2012) Alain-Pierre Petit et al.   NUCLEIC ACIDS RESEARCH

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

Direct-coupling analysis of residue coevolution captures native contacts across many protein families

(2011) F. Morcos et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

PyRosetta: a script-based interface for implementing molecular modeling algorithms using Rosetta

(2010) S. Chaudhury et al.   BIOINFORMATICS

Template-Based Modeling of Protein-Protein Interfaces

(2009) Petras Kundrotas et al.   BIOPHYSICAL JOURNAL

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

(2009) Srayanta Mukherjee et al.   NUCLEIC ACIDS RESEARCH

Simultaneous prediction of protein folding and docking at high resolution

(2009) Rhiju Das et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

High-resolution protein complexes from integrating genomic information with molecular simulation

(2009) Alexander Schug et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

DOCKGROUND protein-protein docking decoy set

(2008) S. Liu et al.   BIOINFORMATICS

The Universal Protein Resource (UniProt) 2009

(2008)   NUCLEIC ACIDS RESEARCH

Pcons: A neural-network-based consensus predictor that improves fold recognition

(2002) Jesper Lundström et al.   PROTEIN SCIENCE