Detection and sequence/structure mapping of biophysical constraints to protein variation in saturated mutational libraries and protein sequence alignments with a dedicated server

Optimization of Conformational Dynamics in an Epistatic Evolutionary Trajectory

(2016) Mariano M. González et al.   MOLECULAR BIOLOGY AND EVOLUTION

Causes of evolutionary rate variation among protein sites

(2016) Julian Echave et al.   NATURE REVIEWS GENETICS

Editorial

(2016) Daniel N.A. Bolon et al.   PROTEIN SCIENCE

Evolvability as a Function of Purifying Selection in TEM-1 β-Lactamase

(2015) Michael A. Stiffler et al.   CELL

Site-Specific Amino Acid Preferences Are Mostly Conserved in Two Closely Related Protein Homologs

(2015) Michael B. Doud et al.   MOLECULAR BIOLOGY AND EVOLUTION

How Structural and Physicochemical Determinants Shape Sequence Constraints in a Functional Enzyme

(2015) Luciano A. Abriata et al.   PLoS One

Dissecting enzyme function with microfluidic-based deep mutational scanning

(2015) Philip A. Romero et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mistranslation drives the evolution of robustness in TEM-1 β-lactamase

(2015) Sinisa Bratulic et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Pervasive degeneracy and epistasis in a protein-protein interface

(2015) A. I. Podgornaia et al.   SCIENCE

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

(2015) Sergey Ovchinnikov et al.   eLife

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

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

Biophysics of protein evolution and evolutionary protein biophysics

(2014) T. Sikosek et al.   Journal of the Royal Society Interface

An Experimentally Informed Evolutionary Model Improves Phylogenetic Fit to Divergent Lactamase Homologs

(2014) Jesse D. Bloom   MOLECULAR BIOLOGY AND EVOLUTION

Amino Acid Metabolism Conflicts with Protein Diversity

(2014) Teresa Krick et al.   MOLECULAR BIOLOGY AND EVOLUTION

A Comprehensive, High-Resolution Map of a Gene’s Fitness Landscape

(2014) Elad Firnberg et al.   MOLECULAR BIOLOGY AND EVOLUTION

Deep mutational scanning: a new style of protein science

(2014) Douglas M Fowler et al.   NATURE METHODS

Measuring the activity of protein variants on a large scale using deep mutational scanning

(2014) Douglas M Fowler et al.   Nature Protocols

Comprehensive mutational scanning of a kinasein vivoreveals substrate-dependent fitness landscapes

(2014) Alexandre Melnikov et al.   NUCLEIC ACIDS RESEARCH

High-throughput profiling of point mutations across the HIV-1 genome

(2014) Laith Q Al-Mawsawi et al.   Retrovirology

The inherent mutational tolerance and antigenic evolvability of influenza hemagglutinin

(2014) Bargavi Thyagarajan et al.   eLife

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

(2014) Sergey Ovchinnikov et al.   eLife

JSmol and the Next-Generation Web-Based Representation of 3D Molecular Structure as Applied toProteopedia

(2013) Robert M. Hanson et al.   ISRAEL JOURNAL OF CHEMISTRY

News from the Protein Mutability Landscape

(2013) Maximilian Hecht et al.   JOURNAL OF MOLECULAR BIOLOGY

What Makes a Protein Fold Amenable to Functional Innovation? Fold Polarity and Stability Trade-offs

(2013) Eynat Dellus-Gur et al.   JOURNAL OF MOLECULAR BIOLOGY

Analyses of the Effects of All Ubiquitin Point Mutants on Yeast Growth Rate

(2013) Benjamin P. Roscoe et al.   JOURNAL OF MOLECULAR BIOLOGY

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

Assessing the utility of coevolution-based residue-residue contact predictions in a sequence- and structure-rich era

(2013) H. Kamisetty 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 Hidden Codes That Shape Protein Evolution

(2013) R. J. Weatheritt et al.   SCIENCE

Three-Dimensional Structures of Membrane Proteins from Genomic Sequencing

(2012) Thomas A. Hopf et al.   CELL

Sequence-function-stability relationships in proteins from datasets of functionally annotated variants: The case of TEM β-lactamases

(2012) Luciano A. Abriata et al.   FEBS LETTERS

On the Statistical Interpretation of Site-Specific Variables in Phylogeny-Based Substitution Models

(2012) N. Rodrigue   GENETICS

Deep Sequencing of Systematic Combinatorial Libraries Reveals β-Lactamase Sequence Constraints at High Resolution

(2012) Zhifeng Deng et al.   JOURNAL OF MOLECULAR BIOLOGY

Integrating Sequence Variation and Protein Structure to Identify Sites under Selection

(2012) Austin G. Meyer et al.   MOLECULAR BIOLOGY AND EVOLUTION

Fitness analyses of all possible point mutations for regions of genes in yeast

(2012) Ryan Hietpas et al.   Nature Protocols

Molecular basis of the structure and function of H1 hemagglutinin of influenza virus

(2012) Nongluk SRIWILAIJAROEN et al.   PROCEEDINGS OF THE JAPAN ACADEMY SERIES B-PHYSICAL AND BIOLOGICAL SCIENCES

Amino acid coevolution induces an evolutionary Stokes shift

(2012) D. D. Pollock et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The interface of protein structure, protein biophysics, and molecular evolution

(2012) David A. Liberles et al.   PROTEIN SCIENCE

Influenza Virus-Mediated Membrane Fusion: Determinants of Hemagglutinin Fusogenic Activity and Experimental Approaches for Assessing Virus Fusion

(2012) Brian S. Hamilton et al.   Viruses-Basel

Estimating the Distribution of Selection Coefficients from Phylogenetic Data Using Sitewise Mutation-Selection Models

(2011) A. U. Tamuri et al.   GENETICS

Structural Characterization of an Early Fusion Intermediate of Influenza Virus Hemagglutinin

(2011) R. Xu et al.   JOURNAL OF VIROLOGY

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

Deep mutational scanning: assessing protein function on a massive scale

(2011) Carlos L. Araya et al.   TRENDS IN BIOTECHNOLOGY

Cell entry of enveloped viruses

(2011) Richard K Plemper   Current Opinion in Virology

High-resolution mapping of protein sequence-function relationships

(2010) Douglas M Fowler et al.   NATURE METHODS

The Lactamase Engineering Database: a critical survey of TEM sequences in public databases

(2009) Quan Thai et al.   BMC GENOMICS