Determining protein structures using deep mutagenesis

Inferring protein 3D structure from deep mutation scans

(2019) Nathan J. Rollins et al.   NATURE GENETICS

Pairwise and higher-order genetic interactions during the evolution of a tRNA

(2018) Júlia Domingo et al.   NATURE

Multiplex assessment of protein variant abundance by massively parallel sequencing

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

The genetic landscape of a physical interaction

(2018) Guillaume Diss et al.   eLife

Enhancing Evolutionary Couplings with Deep Convolutional Neural Networks

(2018) Yang Liu et al.   Cell Systems

Multi-environment fitness landscapes of a tRNA gene

(2018) Chuan Li et al.   Nature Ecology & Evolution

A framework for exhaustively mapping functional missense variants

(2017) Jochen Weile et al.   Molecular Systems Biology

Alternative evolutionary histories in the sequence space of an ancient protein

(2017) Tyler N. Starr et al.   NATURE

Assessment of contact predictions in CASP12: Co-evolution and deep learning coming of age

(2017) Joerg Schaarschmidt et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

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

(2017) Gabriel J. Rocklin et al.   SCIENCE

Protein structure determination using metagenome sequence data

(2017) Sergey Ovchinnikov et al.   SCIENCE

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

(2017) Sheng Wang et al.   PLoS Computational Biology

3D RNA and Functional Interactions from Evolutionary Couplings

(2016) Caleb Weinreb et al.   CELL

Structured States of Disordered Proteins from Genomic Sequences

(2016) Agnes Toth-Petroczy et al.   CELL

Plasmid-based one-pot saturation mutagenesis

(2016) Emily E Wrenbeck et al.   NATURE METHODS

Epistasis in protein evolution

(2016) Tyler N. Starr et al.   PROTEIN SCIENCE

Network of epistatic interactions within a yeast snoRNA

(2016) O. Puchta et al.   SCIENCE

The fitness landscape of a tRNA gene

(2016) C. Li et al.   SCIENCE

bbcontacts: prediction of β -strand pairing from direct coupling patterns

(2015) Jessica Andreani et al.   BIOINFORMATICS

Massively Parallel Functional Analysis of BRCA1 RING Domain Variants

(2015) Lea M. Starita et al.   GENETICS

The I-TASSER Suite: protein structure and function prediction

(2015) Jianyi Yang et al.   NATURE METHODS

Inferring Pairwise Interactions from Biological Data Using Maximum-Entropy Probability Models

(2015) Richard R. Stein et al.   PLoS Computational Biology

Residue proximity information and protein model discrimination using saturation-suppressor mutagenesis

(2015) Anusmita Sahoo et al.   eLife

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

(2015) Sergey Ovchinnikov et al.   eLife

Massively Parallel Functional Analysis of BRCA1 RING Domain Variants

(2015) Lea M. Starita et al.   GENETICS

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

(2014) Stefan Seemayer et al.   BIOINFORMATICS

MetaPSICOV: combining coevolution methods for accurate prediction of contacts and long range hydrogen bonding in proteins

(2014) David T. Jones et al.   BIOINFORMATICS

A Comprehensive Biophysical Description of Pairwise Epistasis throughout an Entire Protein Domain

(2014) C. Anders Olson et al.   CURRENT BIOLOGY

Deep mutational scanning: a new style of protein science

(2014) Douglas M Fowler et al.   NATURE METHODS

Robust and accurate prediction of residue–residue interactions across protein interfaces using evolutionary information

(2014) Sergey Ovchinnikov et al.   eLife

High-throughput Analysis ofin vivoProtein Stability

(2013) Ikjin Kim et al.   MOLECULAR & CELLULAR PROTEOMICS

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

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

Three-Dimensional Structures of Membrane Proteins from Genomic Sequencing

(2012) Thomas A. Hopf et al.   CELL

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

PFunkel: Efficient, Expansive, User-Defined Mutagenesis

(2012) Elad Firnberg et al.   PLoS One

Genomics-aided structure prediction

(2012) J. I. Sulkowska et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

(2011) David T. Jones et al.   BIOINFORMATICS

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

Molecular mechanisms of epistasis within and between genes

(2011) Ben Lehner   TRENDS IN GENETICS

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

High-resolution mapping of protein sequence-function relationships

(2010) Douglas M Fowler et al.   NATURE METHODS

Disentangling Direct from Indirect Co-Evolution of Residues in Protein Alignments

(2010) Lukas Burger et al.   PLoS Computational Biology

Protein Sectors: Evolutionary Units of Three-Dimensional Structure

(2009) Najeeb Halabi et al.   CELL

Stability effects of mutations and protein evolvability

(2009) Nobuhiko Tokuriki et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

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