Connecting the Sequence-Space of Bacterial Signaling Proteins to Phenotypes Using Coevolutionary Landscapes

Causes of evolutionary rate variation among protein sites

(2016) Julian Echave et al.   NATURE REVIEWS GENETICS

Inter-Protein Sequence Co-Evolution Predicts Known Physical Interactions in Bacterial Ribosomes and the Trp Operon

(2016) Christoph Feinauer et al.   PLoS One

Evolution, energy landscapes and the paradoxes of protein folding

(2015) Peter G. Wolynes   BIOCHIMIE

Capturing coevolutionary signals inrepeat proteins

(2015) Rocío Espada et al.   BMC BIOINFORMATICS

Evolving New Protein-Protein Interaction Specificity through Promiscuous Intermediates

(2015) Christopher D. Aakre et al.   CELL

Structural and Functional Impact of Parkinson Disease-Associated Mutations in the E3 Ubiquitin Ligase Parkin

(2015) Fabienne C. Fiesel et al.   HUMAN MUTATION

A many-body term improves the accuracy of effective potentials based on protein coevolutionary data

(2015) A. Contini et al.   JOURNAL OF CHEMICAL PHYSICS

Coevolutionary Landscape Inference and the Context-Dependence of Mutations in Beta-Lactamase TEM-1

(2015) Matteo Figliuzzi et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Relationship between dN/dS and Scaled Selection Coefficients

(2015) Stephanie J. Spielman et al.   MOLECULAR BIOLOGY AND EVOLUTION

Synthetic biology of cell signaling

(2015) Jonathan Hansen et al.   Natural Computing

MMB-GUI: a fast morphing method demonstrates a possible ribosomal tRNA translocation trajectory

(2015) Alex Tek et al.   NUCLEIC ACIDS RESEARCH

From residue coevolution to protein conformational ensembles and functional dynamics

(2015) Ludovico Sutto et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Constructing sequence-dependent protein models using coevolutionary information

(2015) Ryan R. Cheng et al.   PROTEIN SCIENCE

Predicting protein folding rate change upon point mutation using residue-level coevolutionary information

(2015) Saurav Mallik et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Pervasive degeneracy and epistasis in a protein-protein interface

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

Dimeric interactions and complex formation using direct coevolutionary couplings

(2015) Ricardo N. dos Santos et al.   Scientific Reports

Large-Scale Conformational Transitions and Dimerization Are Encoded in the Amino-Acid Sequences of Hsp70 Chaperones

(2015) Duccio Malinverni et al.   PLoS Computational Biology

Synthetic biology of cell signaling

(2015) Jonathan Hansen et al.   Natural Computing

Biophysics of protein evolution and evolutionary protein biophysics

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

Toward rationally redesigning bacterial two-component signaling systems using coevolutionary information

(2014) Ryan R. Cheng et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Coevolutionary information, protein folding landscapes, and the thermodynamics of natural selection

(2014) F. Morcos et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A multiscale approach to predicting affinity changes in protein-protein interfaces

(2014) Daniel F. A. R. Dourado et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Frustration in biomolecules

(2014) Diego U. Ferreiro et al.   QUARTERLY REVIEWS OF BIOPHYSICS

Refactoring and Optimization of Light-Switchable Escherichia coli Two-Component Systems

(2014) Sebastian R. Schmidl et al.   ACS Synthetic Biology

Phosphorylation by PINK1 Releases the UBL Domain and Initializes the Conformational Opening of the E3 Ubiquitin Ligase Parkin

(2014) Thomas R. Caulfield et al.   PLoS Computational Biology

Determinants of specificity in two-component signal transduction

(2013) Anna I Podgornaia et al.   CURRENT OPINION IN MICROBIOLOGY

Translating HIV Sequences into Quantitative Fitness Landscapes Predicts Viral Vulnerabilities for Rational Immunogen Design

(2013) Andrew L. Ferguson et al.   IMMUNITY

Engineered fumarate sensing Escherichia coli based on novel chimeric two-component system

(2013) Irisappan Ganesh et al.   JOURNAL OF BIOTECHNOLOGY

The network of stabilizing contacts in proteins studied by coevolutionary data

(2013) Sara Lui et al.   JOURNAL OF CHEMICAL PHYSICS

Emerging methods in protein co-evolution

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

Fast fitting to low resolution density maps: elucidating large-scale motions of the ribosome

(2013) Samuel Coulbourn Flores   NUCLEIC ACIDS RESEARCH

Pfam: the protein families database

(2013) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

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

(2013) Magnus Ekeberg et al.   PHYSICAL REVIEW E

Coevolutionary signals across protein lineages help capture multiple protein conformations

(2013) F. Morcos et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Evolution of Two-Component Signal Transduction Systems

(2012) Emily J. Capra et al.   Annual Review of Microbiology

Protein structure prediction from sequence variation

(2012) Debora S Marks et al.   NATURE BIOTECHNOLOGY

Structural basis of histidine kinase autophosphorylation deduced by integrating genomics, molecular dynamics, and mutagenesis

(2012) A. E. Dago et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genomics-aided structure prediction

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

Engineering robust control of two-component system phosphotransfer using modular scaffolds

(2012) W. R. Whitaker et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2011) A. U. Tamuri et al.   GENETICS

Dissecting the Specificity of Protein-Protein Interaction in Bacterial Two-Component Signaling: Orphans and Crosstalks

(2011) Andrea Procaccini 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

Interaction fidelity in two-component signaling

(2010) Hendrik Szurmant et al.   CURRENT OPINION IN MICROBIOLOGY

The mechanism of signal transduction by two-component systems

(2010) Patricia Casino et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Fast Flexible Modeling of RNA Structure Using Internal Coordinates

(2010) S. C. Flores et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Multichromatic Control of Gene Expression in Escherichia coli

(2010) Jeffrey J. Tabor et al.   JOURNAL OF MOLECULAR BIOLOGY

Turning limited experimental information into 3D models of RNA

(2010) S. C. Flores et al.   RNA

Systematic Dissection and Trajectory-Scanning Mutagenesis of the Molecular Interface That Ensures Specificity of Two-Component Signaling Pathways

(2010) Emily J. Capra et al.   PLoS Genetics

Structural Insight into Partner Specificity and Phosphoryl Transfer in Two-Component Signal Transduction

(2009) Patricia Casino et al.   CELL

High-resolution protein complexes from integrating genomic information with molecular simulation

(2009) Alexander Schug et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Rewiring the Specificity of Two-Component Signal Transduction Systems

(2008) Jeffrey M. Skerker et al.   CELL

Accurate prediction of protein–protein interactions from sequence alignments using a Bayesian method

(2008) Lukas Burger et al.   Molecular Systems 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