Multi-state design of flexible proteins predicts sequences optimal for conformational change

Multistate design of influenza antibodies improves affinity and breadth against seasonal viruses

(2019) Alexander M. Sevy et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Consensus sequence design as a general strategy to create hyperstable, biologically active proteins

(2019) Matt Sternke et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Bim suppresses the development of SLE by limiting myeloid inflammatory responses

(2017) FuNien Tsai et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Clustal Omega for making accurate alignments of many protein sequences

(2017) Fabian Sievers et al.   PROTEIN SCIENCE

Conserved properties of individual Ca2+-binding sites in calmodulin

(2016) D. Brent Halling et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Biophysical and computational methods to analyze amino acid interaction networks in proteins

(2016) Kathleen F. O'Rourke et al.   Computational and Structural Biotechnology Journal

PDBFlex: exploring flexibility in protein structures

(2015) Thomas Hrabe et al.   NUCLEIC ACIDS RESEARCH

Design of Protein Multi-specificity Using an Independent Sequence Search Reduces the Barrier to Low Energy Sequences

(2015) Alexander M. Sevy et al.   PLoS Computational Biology

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

Small-molecule ligand docking into comparative models with Rosetta

(2013) Steven A Combs et al.   Nature Protocols

Emerging methods in protein co-evolution

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

Improvements to Robotics-Inspired Conformational Sampling in Rosetta

(2013) Amelie Stein et al.   PLoS One

Atomic-level functional model of dengue virus Envelope protein infectivity

(2013) E. A. Christian et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Human Germline Antibody Gene Segments Encode Polyspecific Antibodies

(2013) Jordan R. Willis et al.   PLoS Computational Biology

Multistate approaches in computational protein design

(2012) James A. Davey et al.   PROTEIN SCIENCE

Prediction of Mutational Tolerance in HIV-1 Protease and Reverse Transcriptase Using Flexible Backbone Protein Design

(2012) Elisabeth Humphris-Narayanan et al.   PLoS Computational Biology

Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega

(2011) F. Sievers et al.   Molecular Systems Biology

A Generic Program for Multistate Protein Design

(2011) Andrew Leaver-Fay et al.   PLoS One

Predicting the Tolerated Sequences for Proteins and Protein Interfaces Using RosettaBackrub Flexible Backbone Design

(2011) Colin A. Smith 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

A Highly Conserved Neutralizing Epitope on Group 2 Influenza A Viruses

(2011) D. C. Ekiert et al.   SCIENCE

Viral calciomics: Interplays between Ca2+ and virus

(2009) Yubin Zhou et al.   CELL CALCIUM

Solvent accessible surface area approximations for rapid and accurate protein structure prediction

(2009) Elizabeth Durham et al.   JOURNAL OF MOLECULAR MODELING

A Correspondence Between Solution-State Dynamics of an Individual Protein and the Sequence and Conformational Diversity of its Family

(2009) Gregory D. Friedland et al.   PLoS Computational Biology

Tradeoff Between Stability and Multispecificity in the Design of Promiscuous Proteins

(2009) Menachem Fromer et al.   PLoS Computational Biology

Backrub-Like Backbone Simulation Recapitulates Natural Protein Conformational Variability and Improves Mutant Side-Chain Prediction

(2008) Colin A. Smith et al.   JOURNAL OF MOLECULAR BIOLOGY

Structure of influenza hemagglutinin in complex with an inhibitor of membrane fusion

(2008) R. J. Russell et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Recognition Dynamics Up to Microseconds Revealed from an RDC-Derived Ubiquitin Ensemble in Solution

(2008) O. F. Lange et al.   SCIENCE

A normalized root-mean-spuare distance for comparing protein three-dimensional structures

(2002) Oliviero Carugo et al.   PROTEIN SCIENCE