Benchmarking AlphaFold for protein complex modeling reveals accuracy determinants

ColabFold: making protein folding accessible to all

(2022) Milot Mirdita et al.   NATURE METHODS

Improved prediction of protein-protein interactions using AlphaFold2

(2022) Patrick Bryant et al.   Nature Communications

An expanded benchmark for antibody-antigen docking and affinity prediction reveals insights into antibody recognition determinants

(2021) Johnathan D. Guest et al.   STRUCTURE

Highly accurate protein structure prediction with AlphaFold

(2021) John Jumper et al.   NATURE

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

(2021) Minkyung Baek et al.   SCIENCE

AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space with high-accuracy models

(2021) Mihaly Varadi et al.   NUCLEIC ACIDS RESEARCH

Applying and improving AlphaFold at CASP14

(2021) John Jumper et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Computed structures of core eukaryotic protein complexes

(2021) Ian R. Humphreys et al.   SCIENCE

Macromolecular modeling and design in Rosetta: recent methods and frameworks

(2020) Julia Koehler Leman et al.   NATURE METHODS

Advances to tackle backbone flexibility in protein docking

(2020) Ameya Harmalkar et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

TCR3d: The T cell receptor structural repertoire database

(2019) Ragul Gowthaman et al.   BIOINFORMATICS

Prediction of interresidue contacts with DeepMetaPSICOV in CASP13

(2019) Shaun M. Kandathil et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Integrating ab initio and template-based algorithms for protein–protein complex structure prediction

(2019) Sweta Vangaveti et al.   BIOINFORMATICS

TCRpMHCmodels: Structural modelling of TCR-pMHC class I complexes

(2019) Kamilla Kjærgaard Jensen et al.   Scientific Reports

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

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

ComplexContact: a web server for inter-protein contact prediction using deep learning

(2018) Hong Zeng et al.   NUCLEIC ACIDS RESEARCH

The Rosetta All-Atom Energy Function for Macromolecular Modeling and Design

(2017) Rebecca F. Alford et al.   Journal of Chemical Theory and Computation

MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets

(2017) Martin Steinegger et al.   NATURE BIOTECHNOLOGY

Complex heatmaps reveal patterns and correlations in multidimensional genomic data

(2016) Zuguang Gu et al.   BIOINFORMATICS

T Cell Antigen Receptor Recognition of Antigen-Presenting Molecules

(2015) Jamie Rossjohn et al.   Annual Review of Immunology

Updates to the Integrated Protein–Protein Interaction Benchmarks: Docking Benchmark Version 5 and Affinity Benchmark Version 2

(2015) Thom Vreven et al.   JOURNAL OF MOLECULAR BIOLOGY

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

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

T cell receptor bias for MHC: co-evolution or co-receptors?

(2014) Sneha Rangarajan et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Developmental pathway for potent V1V2-directed HIV-neutralizing antibodies

(2014) Nicole A. Doria-Rose et al.   NATURE

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

(2014) Thomas A Hopf et al.   eLife

lDDT: a local superposition-free score for comparing protein structures and models using distance difference tests

(2013) Valerio Mariani et al.   BIOINFORMATICS

SwarmDock: a server for flexible protein–protein docking

(2013) Mieczyslaw Torchala et al.   BIOINFORMATICS

Co-evolution of a broadly neutralizing HIV-1 antibody and founder virus

(2013) Hua-Xin Liao et al.   NATURE

SAbDab: the structural antibody database

(2013) James Dunbar et al.   NUCLEIC ACIDS RESEARCH

Assessing the utility of coevolution-based residue-residue contact predictions in a sequence- and structure-rich era

(2013) H. Kamisetty et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

CD-HIT: accelerated for clustering the next-generation sequencing data

(2012) Limin Fu et al.   BIOINFORMATICS

Protein structure prediction from sequence variation

(2012) Debora S Marks et al.   NATURE BIOTECHNOLOGY

Design of a binding scaffold based on variable lymphocyte receptors of jawless vertebrates by module engineering

(2012) S.-C. Lee et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

A flexible docking approach for prediction of T cell receptor-peptide-MHC complexes

(2012) Brian G. Pierce et al.   PROTEIN SCIENCE

Clustering biomolecular complexes by residue contacts similarity

(2012) João P. G. L. M. Rodrigues et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

pROC: an open-source package for R and S+ to analyze and compare ROC curves

(2011) Xavier Robin et al.   BMC BIOINFORMATICS

Accelerating Protein Docking in ZDOCK Using an Advanced 3D Convolution Library

(2011) Brian G. Pierce et al.   PLoS One

Algorithm discovery by protein folding game players

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

Integrating atom-based and residue-based scoring functions for protein-protein docking

(2011) Thom Vreven et al.   PROTEIN SCIENCE

Ultra-fast FFT protein docking on graphics processors

(2010) David W. Ritchie et al.   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

The RCSB Protein Data Bank: redesigned web site and web services

(2010) P. W. Rose et al.   NUCLEIC ACIDS RESEARCH

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Structure of a lamprey variable lymphocyte receptor in complex with a protein antigen

(2009) C Alejandro Velikovsky et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

A combination of rescoring and refinement significantly improves protein docking performance

(2008) Brian Pierce et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS