Biological structure and function emerge from scaling unsupervised learning to 250 million protein sequences

UDSMProt: universal deep sequence models for protein classification

(2020) Nils Strodthoff et al.   BIOINFORMATICS

Improved protein structure prediction using potentials from deep learning

(2020) Andrew W. Senior et al.   NATURE

NetSurfP-2.0: Improved prediction of protein structural features by integrated deep learning

(2019) Michael Schantz Klausen et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Revealing evolutionary constraints on proteins through sequence analysis

(2019) Shou-Wen Wang et al.   PLoS Computational Biology

Machine-learning-guided directed evolution for protein engineering

(2019) Kevin K. Yang et al.   NATURE METHODS

Unified rational protein engineering with sequence-based deep representation learning

(2019) Ethan C. Alley et al.   NATURE METHODS

Critical assessment of methods of protein structure prediction (CASP)—Round XIII

(2019) Andriy Kryshtafovych et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Modeling aspects of the language of life through transfer-learning protein sequences

(2019) Michael Heinzinger et al.   BMC BIOINFORMATICS

High precision in protein contact prediction using fully convolutional neural networks and minimal sequence features

(2018) David T Jones et al.   BIOINFORMATICS

Learned protein embeddings for machine learning

(2018) Kevin K Yang et al.   BIOINFORMATICS

Quantitative Missense Variant Effect Prediction Using Large-Scale Mutagenesis Data

(2018) Vanessa E. Gray et al.   Cell Systems

Deep generative models of genetic variation capture the effects of mutations

(2018) Adam J. Riesselman et al.   NATURE METHODS

eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses

(2018) Jaime Huerta-Cepas et al.   NUCLEIC ACIDS RESEARCH

Mutation effects predicted from sequence co-variation

(2017) Thomas A Hopf et al.   NATURE BIOTECHNOLOGY

Origins of coevolution between residues distant in protein 3D structures

(2017) Ivan Anishchenko et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Critical assessment of methods of protein structure prediction (CASP)-Round XII

(2017) John Moult 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

Uniclust databases of clustered and deeply annotated protein sequences and alignments

(2016) Milot Mirdita et al.   NUCLEIC ACIDS RESEARCH

Critical assessment of methods of protein structure prediction: Progress and new directions in round XI

(2016) John Moult et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Coevolutionary Landscape Inference and the Context-Dependence of Mutations in Beta-Lactamase TEM-1

(2015) Matteo Figliuzzi et al.   MOLECULAR BIOLOGY AND EVOLUTION

CCMpred—fast and precise prediction of protein residue–residue contacts from correlated mutations

(2014) Stefan Seemayer et al.   BIOINFORMATICS

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

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

Deep mutational scanning: a new style of protein science

(2014) Douglas M Fowler et al.   NATURE METHODS

MRFalign: Protein Homology Detection through Alignment of Markov Random Fields

(2014) Jianzhu Ma et al.   PLoS Computational Biology

SCOPe: Structural Classification of Proteins—extended, integrating SCOP and ASTRAL data and classification of new structures

(2013) Naomi K. Fox et al.   NUCLEIC ACIDS RESEARCH

Pfam: the protein families database

(2013) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

Improved contact prediction in proteins: Using pseudolikelihoods to infer Potts models

(2013) Magnus Ekeberg et al.   PHYSICAL REVIEW E

Amino acid composition of proteins reduces deleterious impact of mutations

(2013) Sahand Hormoz   Scientific Reports

Multiobjective evolutionary algorithms to identify highly autocorrelated areas: the case of spatial distribution in financially compromised farms

(2011) Carlos R. García-Alonso et al.   ANNALS OF OPERATIONS RESEARCH

PSICOV: precise structural contact prediction using sparse inverse covariance estimation on large multiple sequence alignments

(2011) David T. Jones et al.   BIOINFORMATICS

Protein sequence comparison and fold recognition: progress and good-practice benchmarking

(2011) Johannes Söding et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

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

(2011) Michael Remmert et al.   NATURE METHODS

Protein 3D Structure Computed from Evolutionary Sequence Variation

(2011) Debora S. Marks et al.   PLoS One

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

Learning generative models for protein fold families

(2010) Sivaraman Balakrishnan et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Graphical Models of Residue Coupling in Protein Families

(2008) J. Thomas et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Identification of direct residue contacts in protein-protein interaction by message passing

(2008) M. Weigt et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA