Learning the protein language: Evolution, structure, and function

Learning the language of viral evolution and escape

(2021) Brian Hie et al.   SCIENCE

SARS-CoV-2 Variants of Concern in the United States—Challenges and Opportunities

(2021) Rochelle P. Walensky et al.   JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION

Revolutionary cryo-EM is taking over structural biology

(2020) Ewen Callaway   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

Computational design of closely related proteins that adopt two well-defined but structurally divergent folds

(2020) Kathy Y. Wei et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Leveraging Uncertainty in Machine Learning Accelerates Biological Discovery and Design

(2020) Brian Hie et al.   Cell Systems

CATH: increased structural coverage of functional space

(2020) Ian Sillitoe et al.   NUCLEIC ACIDS RESEARCH

Improvements to the ABSINTH forcefield for proteins based on experimentally derived amino-acid specific backbone conformational statistics

(2019) Jeong-Mo Choi et al.   Journal of Chemical Theory and Computation

BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis

(2019) Remco Bouckaert et al.   PLoS Computational Biology

End-to-End Differentiable Learning of Protein Structure

(2019) Mohammed AlQuraishi   Cell Systems

Quantification of Uncertainty in Peptide-MHC Binding Prediction Improves High-Affinity Peptide Selection for Therapeutic Design

(2019) Haoyang Zeng et al.   Cell Systems

Distance-based protein folding powered by deep learning

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

Analysis of distance‐based protein structure prediction by deep learning in CASP13

(2019) Jinbo Xu et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Antibody Complementarity Determining Region Design Using High-Capacity Machine Learning

(2019) Ge Liu et al.   BIOINFORMATICS

A survey on semi-supervised learning

(2019) Jesper E. van Engelen et al.   MACHINE LEARNING

Unified rational protein engineering with sequence-based deep representation learning

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

Deciphering protein evolution and fitness landscapes with latent space models

(2019) Xinqiang Ding et al.   Nature Communications

Learned protein embeddings for machine learning

(2018) Kevin K Yang et al.   BIOINFORMATICS

Multiplex assessment of protein variant abundance by massively parallel sequencing

(2018) Kenneth A. Matreyek et al.   NATURE GENETICS

Enhancing Evolutionary Couplings with Deep Convolutional Neural Networks

(2018) Yang Liu et al.   Cell Systems

Accurate classification of BRCA1 variants with saturation genome editing

(2018) Gregory M. Findlay et al.   NATURE

Deep generative models of genetic variation capture the effects of mutations

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

UniProt: a worldwide hub of protein knowledge

(2018)   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

SCOPe: Manual Curation and Artifact Removal in the Structural Classification of Proteins – extended Database

(2017) John-Marc Chandonia et al.   JOURNAL OF MOLECULAR BIOLOGY

A framework for exhaustively mapping functional missense variants

(2017) Jochen Weile et al.   Molecular Systems Biology

Trade-offs between enzyme fitness and solubility illuminated by deep mutational scanning

(2017) Justin R. Klesmith et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Single-mutation fitness landscapes for an enzyme on multiple substrates reveal specificity is globally encoded

(2017) Emily E. Wrenbeck et al.   Nature Communications

Machine learning to design integral membrane channelrhodopsins for efficient eukaryotic expression and plasma membrane localization

(2017) Claire N. Bedbrook et al.   PLoS Computational Biology

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

(2017) Sheng Wang et al.   PLoS Computational Biology

Deconstruction of the Ras switching cycle through saturation mutagenesis

(2017) Pradeep Bandaru et al.   eLife

A biologist’s guide to Bayesian phylogenetic analysis

(2017) Fabrícia F. Nascimento et al.   Nature Ecology & Evolution

Phenotypic Characterization of a Comprehensive Set of MAPK1 /ERK2 Missense Mutants

(2016) Lisa Brenan et al.   Cell Reports

A Primer to Single-Particle Cryo-Electron Microscopy

(2015) Yifan Cheng et al.   CELL

ImageNet Large Scale Visual Recognition Challenge

(2015) Olga Russakovsky et al.   INTERNATIONAL JOURNAL OF COMPUTER VISION

Massively parallel single-amino-acid mutagenesis

(2015) Jacob O Kitzman et al.   NATURE METHODS

The TOPCONS web server for consensus prediction of membrane protein topology and signal peptides

(2015) Konstantinos D. Tsirigos et al.   NUCLEIC ACIDS RESEARCH

Emerging methods in protein co-evolution

(2013) David de Juan et al.   NATURE REVIEWS GENETICS

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

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

(2013) Magnus Ekeberg et al.   PHYSICAL REVIEW E

Navigating the protein fitness landscape with Gaussian processes

(2013) P. A. Romero et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Capturing the mutational landscape of the beta-lactamase TEM-1

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

Activity-enhancing mutations in an E3 ubiquitin ligase identified by high-throughput mutagenesis

(2013) L. M. Starita et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Deep mutational scanning of an RRM domain of the Saccharomyces cerevisiae poly(A)-binding protein

(2013) D. Melamed et al.   RNA

The spatial architecture of protein function and adaptation

(2012) Richard N. McLaughlin Jr et al.   NATURE

Protein structure prediction from sequence variation

(2012) Debora S Marks et al.   NATURE BIOTECHNOLOGY

A fundamental protein property, thermodynamic stability, revealed solely from large-scale measurements of protein function

(2012) C. L. Araya et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2011) Michael Remmert et al.   NATURE METHODS

HMMER web server: interactive sequence similarity searching

(2011) R. D. Finn et al.   NUCLEIC ACIDS RESEARCH

Multicoil2: Predicting Coiled Coils and Their Oligomerization States from Sequence in the Twilight Zone

(2011) Jason Trigg et al.   PLoS One

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating

(2009) Nicolas Lartillot et al.   BIOINFORMATICS

GROMACS 4:  Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation

(2008) Berk Hess et al.   Journal of Chemical Theory and Computation

Sequence-similar, structure-dissimilar protein pairs in the PDB

(2007) Mickey Kosloff et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS