Highly accurate protein structure prediction with AlphaFold

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

(2021) Alexander Rives et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Deducing high-accuracy protein contact-maps from a triplet of coevolutionary matrices through deep residual convolutional networks

(2021) Yang Li et al.   PLoS Computational Biology

Deep learning techniques have significantly impacted protein structure prediction and protein design

(2021) Robin Pearce et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Highly accurate protein structure prediction for the human proteome

(2021) Kathryn Tunyasuvunakool et al.   NATURE

High‐accuracy protein structure prediction in CASP14

(2021) Joana Pereira et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

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

Structural basis for loading and inhibition of a bacterial T6 SS phospholipase effector by the VgrG spike

(2020) Nicolas Flaugnatti et al.   EMBO JOURNAL

An embedded lipid in the multidrug transporter LmrP suggests a mechanism for polyspecificity

(2020) Vincent Debruycker et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

The structure of human CST reveals a decameric assembly bound to telomeric DNA

(2020) Ci Ji Lim et al.   SCIENCE

MrpH, a new class of metal-binding adhesin, requires zinc to mediate biofilm formation

(2020) Wanghsu Jiang et al.   PLoS Pathogens

Array programming with NumPy

(2020) Charles R. Harris et al.   NATURE

Structure and function of virion RNA polymerase of a crAss-like phage

(2020) Arina V. Drobysheva et al.   NATURE

UniProt: the universal protein knowledgebase in 2021

(2020) et al.   NUCLEIC ACIDS RESEARCH

Structure of SARS-CoV-2 ORF8, a rapidly evolving immune evasion protein

(2020) Thomas G. Flower et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Protein storytelling through physics

(2020) Emiliano Brini et al.   SCIENCE

End-to-End Differentiable Learning of Protein Structure

(2019) Mohammed AlQuraishi   Cell Systems

Protein-level assembly increases protein sequence recovery from metagenomic samples manyfold

(2019) Martin Steinegger et al.   NATURE METHODS

A further leap of improvement in tertiary structure prediction in CASP13 prompts new routes for future assessments

(2019) Luciano A. Abriata et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Deep‐learning contact‐map guided protein structure prediction in CASP13

(2019) Wei Zheng et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Analysis of several key factors influencing deep learning-based inter-residue contact prediction

(2019) Tianqi Wu et al.   BIOINFORMATICS

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

(2019) Martin Steinegger et al.   BMC BIOINFORMATICS

Advances in protein structure prediction and design

(2019) Brian Kuhlman et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

rawMSA: End-to-end Deep Learning using raw Multiple Sequence Alignments

(2019) Claudio Mirabello et al.   PLoS One

Unified rational protein engineering with sequence-based deep representation learning

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

Protein structure prediction using multiple deep neural networks in the 13th Critical Assessment of Protein Structure Prediction (CASP13)

(2019) Andrew W. Senior et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

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

Clustering huge protein sequence sets in linear time

(2018) Martin Steinegger et al.   Nature Communications

An Interface-Driven Design Strategy Yields a Novel, Corrugated Protein Architecture

(2018) Mohammad ElGamacy et al.   ACS Synthetic Biology

Protein Data Bank: the single global archive for 3D macromolecular structure data

(2018) et al.   NUCLEIC ACIDS RESEARCH

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

(2017) Martin Steinegger et al.   NATURE BIOTECHNOLOGY

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

(2017) Sheng Wang et al.   PLoS Computational Biology

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

FAMSA: Fast and accurate multiple sequence alignment of huge protein families

(2016) Sebastian Deorowicz et al.   Scientific Reports

How cryo-EM is revolutionizing structural biology

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

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

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

A brief history of macromolecular crystallography, illustrated by a family tree and its Nobel fruits

(2014) Mariusz Jaskolski et al.   FEBS Journal

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

(2013) Valerio Mariani et al.   BIOINFORMATICS

Protein structure prediction from sequence variation

(2012) Debora S Marks et al.   NATURE BIOTECHNOLOGY

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

(2011) David T. Jones et al.   BIOINFORMATICS

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

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

Hidden Markov model speed heuristic and iterative HMM search procedure

(2010) L Steven Johnson et al.   BMC BIOINFORMATICS

I-TASSER: a unified platform for automated protein structure and function prediction

(2010) Ambrish Roy et al.   Nature Protocols

Auto-Context and Its Application to High-Level Vision Tasks and 3D Brain Image Segmentation

(2009) Zhuowen Tu et al.   IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE

The Protein Folding Problem

(2008) Ken A. Dill et al.   Annual Review of Biophysics

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