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osprey
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book
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January 2013 |
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Deep Mutational Scanning of SARS-CoV-2 Receptor Binding Domain Reveals Constraints on Folding and ACE2 Binding
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journal
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September 2020 |
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Quantitative Missense Variant Effect Prediction Using Large-Scale Mutagenesis Data
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journal
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January 2018 |
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Enhancing Evolutionary Couplings with Deep Convolutional Neural Networks
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journal
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January 2018 |
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Inferring Protein Sequence-Function Relationships with Large-Scale Positive-Unlabeled Learning
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journal
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January 2021 |
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Informed training set design enables efficient machine learning-assisted directed protein evolution
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journal
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August 2021 |
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A Comprehensive Biophysical Description of Pairwise Epistasis throughout an Entire Protein Domain
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journal
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November 2014 |
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Pervasive Pairwise Intragenic Epistasis among Sequential Mutations in TEM-1 β-Lactamase
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journal
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May 2019 |
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Molecular mechanisms of epistasis within and between genes
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journal
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August 2011 |
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TLmutation: Predicting the Effects of Mutations Using Transfer Learning
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journal
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April 2020 |
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Machine-Learning-Guided Mutagenesis for Directed Evolution of Fluorescent Proteins
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journal
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August 2018 |
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Design by Directed Evolution
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journal
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March 1998 |
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Epistasis as the primary factor in molecular evolution
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journal
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October 2012 |
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Local fitness landscape of the green fluorescent protein
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journal
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May 2016 |
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Mutation effects predicted from sequence co-variation
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journal
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January 2017 |
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Molecular evolution by staggered extension process (StEP) in vitro recombination
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journal
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March 1998 |
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A general framework for estimating the relative pathogenicity of human genetic variants
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journal
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February 2014 |
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A method and server for predicting damaging missense mutations
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journal
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April 2010 |
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Exploring protein fitness landscapes by directed evolution
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journal
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December 2009 |
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The mutational landscape of a prion-like domain
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journal
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September 2019 |
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Major antigenic site B of human influenza H3N2 viruses has an evolving local fitness landscape
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journal
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March 2020 |
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Protein design and variant prediction using autoregressive generative models
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journal
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April 2021 |
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Determining protein structures using deep mutagenesis
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journal
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June 2019 |
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Inferring protein 3D structure from deep mutation scans
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journal
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June 2019 |
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Deep generative models of genetic variation capture the effects of mutations
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journal
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September 2018 |
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Machine-learning-guided directed evolution for protein engineering
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journal
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July 2019 |
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Machine learning-guided channelrhodopsin engineering enables minimally invasive optogenetics
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journal
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October 2019 |
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Unified rational protein engineering with sequence-based deep representation learning
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journal
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October 2019 |
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Low-N protein engineering with data-efficient deep learning
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journal
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April 2021 |
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Leveraging implicit knowledge in neural networks for functional dissection and engineering of proteins
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journal
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May 2019 |
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A fundamental protein property, thermodynamic stability, revealed solely from large-scale measurements of protein function
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journal
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October 2012 |
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Navigating the protein fitness landscape with Gaussian processes
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journal
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December 2012 |
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Assessing the utility of coevolution-based residue-residue contact predictions in a sequence- and structure-rich era
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journal
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September 2013 |
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Machine learning-assisted directed protein evolution with combinatorial libraries
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journal
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April 2019 |
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Biological structure and function emerge from scaling unsupervised learning to 250 million protein sequences
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journal
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April 2021 |
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CCMpred—fast and precise prediction of protein residue–residue contacts from correlated mutations
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journal
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July 2014 |
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Exploiting ontology graph for predicting sparsely annotated gene function
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journal
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June 2015 |
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Learned protein embeddings for machine learning
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journal
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March 2018 |
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A Comprehensive, High-Resolution Map of a Gene’s Fitness Landscape
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journal
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February 2014 |
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The FoldX web server: an online force field
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journal
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July 2005 |
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CADD: predicting the deleteriousness of variants throughout the human genome
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journal
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October 2018 |
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UniProt: a worldwide hub of protein knowledge
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November 2018 |
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The Pfam protein families database in 2019
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journal
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October 2018 |
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Language models enable zero-shot prediction of the effects of mutations on protein function
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preprint
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November 2021 |
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Evaluating Protein Transfer Learning with TAPE
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preprint
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June 2019 |
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Improved contact prediction in proteins: Using pseudolikelihoods to infer Potts models
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journal
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January 2013 |
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ProtTrans: Towards Cracking the Language of Lifes Code Through Self-Supervised Deep Learning and High Performance Computing
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journal
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January 2021 |
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Learning the language of viral evolution and escape
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journal
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January 2021 |
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Learning to Forget: Continual Prediction with LSTM
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journal
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October 2000 |
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HH-suite3 for fast remote homology detection and deep protein annotation
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journal
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September 2019 |
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Deep mutational scanning of an RRM domain of the Saccharomyces cerevisiae poly(A)-binding protein
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journal
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September 2013 |
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Machine learning to design integral membrane channelrhodopsins for efficient eukaryotic expression and plasma membrane localization
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journal
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October 2017 |
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Protein 3D Structure Computed from Evolutionary Sequence Variation
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journal
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December 2011 |
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Epistasis and the Dynamics of Reversion in Molecular Evolution
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journal
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July 2016 |
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Accurate Measurement of the Effects of All Amino-Acid Mutations on Influenza Hemagglutinin
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journal
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June 2016 |
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Robust and accurate prediction of residue–residue interactions across protein interfaces using evolutionary information
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journal
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May 2014 |
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Sequence co-evolution gives 3D contacts and structures of protein complexes
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journal
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September 2014 |
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The genetic landscape of a physical interaction
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journal
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April 2018 |
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Mapping mutational effects along the evolutionary landscape of HIV envelope
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journal
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March 2018 |