Unified rational protein engineering with sequence-based deep representation learning

End-to-End Differentiable Learning of Protein Structure

(2019) Mohammed AlQuraishi   Cell Systems

ProteinNet: a standardized data set for machine learning of protein structure

(2019) Mohammed AlQuraishi   BMC BIOINFORMATICS

Learned protein embeddings for machine learning

(2018) Kevin K Yang et al.   BIOINFORMATICS

Multiplexed gene synthesis in emulsions for exploring protein functional landscapes

(2018) Calin Plesa et al.   SCIENCE

Quantitative Missense Variant Effect Prediction Using Large-Scale Mutagenesis Data

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

Automatic Chemical Design Using a Data-Driven Continuous Representation of Molecules

(2018) Rafael Gómez-Bombarelli et al.   ACS Central Science

De novo design of a fluorescence-activating β-barrel

(2018) Jiayi Dou et al.   NATURE

Deep generative models of genetic variation capture the effects of mutations

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

Soft Ngram Representation and Modeling for Protein Remote Homology Detection

(2017) Pietro Lovato et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

The Rosetta All-Atom Energy Function for Macromolecular Modeling and Design

(2017) Rebecca F. Alford et al.   Journal of Chemical Theory and Computation

Computational protein design: a review

(2017) Ivan Coluzza   JOURNAL OF PHYSICS-CONDENSED MATTER

Programming molecular self-assembly of intrinsically disordered proteins containing sequences of low complexity

(2017) Joseph R. Simon et al.   Nature Chemistry

Global analysis of protein folding using massively parallel design, synthesis, and testing

(2017) Gabriel J. Rocklin et al.   SCIENCE

Tree Alignment Based on Needleman-Wunsch Algorithm for Sensor Selection in Smart Homes

(2017) et al.   SENSORS

The Growing and Glowing Toolbox of Fluorescent and Photoactive Proteins

(2017) Erik A. Rodriguez et al.   TRENDS IN BIOCHEMICAL SCIENCES

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

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

Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life

(2017) Donovan H. Parks et al.   Nature Microbiology

STRUM: structure-based prediction of protein stability changes upon single-point mutation

(2016) Lijun Quan et al.   BIOINFORMATICS

Simultaneous Optimization of Biomolecular Energy Functions on Features from Small Molecules and Macromolecules

(2016) Hahnbeom Park et al.   Journal of Chemical Theory and Computation

Local fitness landscape of the green fluorescent protein

(2016) Karen S. Sarkisyan et al.   NATURE

The coming of age of de novo protein design

(2016) Po-Ssu Huang et al.   NATURE

OrthoDB v9.1: cataloging evolutionary and functional annotations for animal, fungal, plant, archaeal, bacterial and viral orthologs

(2016) Evgeny M. Zdobnov et al.   NUCLEIC ACIDS RESEARCH

Engineering an allosteric transcription factor to respond to new ligands

(2015) Noah D Taylor et al.   NATURE METHODS

Methods for the directed evolution of proteins

(2015) Michael S. Packer et al.   NATURE REVIEWS GENETICS

Large-scale determination of previously unsolved protein structures using evolutionary information

(2015) Sergey Ovchinnikov et al.   eLife

Continuous Distributed Representation of Biological Sequences for Deep Proteomics and Genomics

(2015) Ehsaneddin Asgari et al.   PLoS One

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

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

A Model of Substitution Trajectories in Sequence Space and Long-Term Protein Evolution

(2014) Dinara R. Usmanova et al.   MOLECULAR BIOLOGY AND EVOLUTION

Multiplex single-molecule interaction profiling of DNA-barcoded proteins

(2014) Liangcai Gu et al.   NATURE

Stabilizing biocatalysts

(2013) Andreas S. Bommarius et al.   CHEMICAL SOCIETY REVIEWS

Insights into the phylogeny and coding potential of microbial dark matter

(2013) Christian Rinke et al.   NATURE

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

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

Epistasis as the primary factor in molecular evolution

(2012) Michael S. Breen et al.   NATURE

Direct measurement of DNA affinity landscapes on a high-throughput sequencing instrument

(2011) Razvan Nutiu et al.   NATURE BIOTECHNOLOGY

Stability of Protein Pharmaceuticals: An Update

(2010) Mark Cornell Manning et al.   PHARMACEUTICAL RESEARCH

Exploring protein fitness landscapes by directed evolution

(2009) Philip A. Romero et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Diversity and Evolution of Coral Fluorescent Proteins

(2008) Naila O. Alieva et al.   PLoS One