ColabFold: making protein folding accessible to all

Improved prediction of protein-protein interactions using AlphaFold2

(2022) Patrick Bryant et al.   Nature Communications

Massive expansion of human gut bacteriophage diversity

(2021) Luis F. Camarillo-Guerrero et al.   CELL

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

Critical Assessment of Methods of Protein Structure Prediction ( CASP ) – Round XIV

(2021) Andriy Kryshtafovych et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

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

(2021) Minkyung Baek et al.   SCIENCE

Metagenomic compendium of 189,680 DNA viruses from the human gut microbiome

(2021) Stephen Nayfach et al.   Nature Microbiology

MetaEuk—sensitive, high-throughput gene discovery, and annotation for large-scale eukaryotic metagenomics

(2020) Eli Levy Karin et al.   Microbiome

MMseqs2 desktop and local web server app for fast, interactive sequence searches

(2019) M Mirdita et al.   BIOINFORMATICS

HH-suite3 for fast remote homology detection and deep protein annotation

(2019) Martin Steinegger et al.   BMC BIOINFORMATICS

Clustering huge protein sequence sets in linear time

(2018) Martin Steinegger et al.   Nature Communications

UniProt: a worldwide hub of protein knowledge

(2018)   NUCLEIC ACIDS RESEARCH

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

(2017) Martin Steinegger et al.   NATURE BIOTECHNOLOGY

The ClusPro web server for protein–protein docking

(2017) Dima Kozakov et al.   Nature Protocols

OpenMM 7: Rapid development of high performance algorithms for molecular dynamics

(2017) Peter Eastman et al.   PLoS Computational Biology

Uniclust databases of clustered and deeply annotated protein sequences and alignments

(2016) Milot Mirdita et al.   NUCLEIC ACIDS RESEARCH

DockQ: A Quality Measure for Protein-Protein Docking Models

(2016) Sankar Basu et al.   PLoS One

3Dmol.js: molecular visualization with WebGL

(2014) N. Rego et al.   BIOINFORMATICS

UniRef clusters: a comprehensive and scalable alternative for improving sequence similarity searches

(2014) B. E. Suzek et al.   BIOINFORMATICS

The NCBI Taxonomy database

(2011) S. Federhen   NUCLEIC ACIDS RESEARCH

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

Improved prediction of protein side-chain conformations with SCWRL4

(2009) Georgii G. Krivov et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS