ConSurf 2016: an improved methodology to estimate and visualize evolutionary conservation in macromolecules

Structural basis of outer membrane protein insertion by the BAM complex

(2016) Yinghong Gu et al.   NATURE

Causes of evolutionary rate variation among protein sites

(2016) Julian Echave et al.   NATURE REVIEWS GENETICS

The bacterial dicarboxylate transporter VcINDY uses a two-domain elevator-type mechanism

(2016) Christopher Mulligan et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

The bacterial dicarboxylate transporter VcINDY uses a two-domain elevator-type mechanism

(2016) Christopher Mulligan et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Wasabi: An Integrated Platform for Evolutionary Sequence Analysis and Data Visualization

(2015) Andres Veidenberg et al.   MOLECULAR BIOLOGY AND EVOLUTION

Structure and activity of tryptophan-rich TSPO proteins

(2015) Y. Guo et al.   SCIENCE

Automatic Prediction of Protein 3D Structures by Probabilistic Multi-template Homology Modeling

(2015) Armin Meier et al.   PLoS Computational Biology

FuncPatch: a web server for the fast Bayesian inference of conserved functional patches in protein 3D structures

(2014) Yi-Fei Huang et al.   BIOINFORMATICS

Computational identification of natural peptides based on analysis of molecular evolution

(2014) Amir Toporik et al.   BIOINFORMATICS

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

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

Identification of the determinants of tRNA function and susceptibility to rapid tRNA decay by high-throughput in vivo analysis

(2014) Michael P. Guy et al.   GENES & DEVELOPMENT

The RCSB Protein Data Bank: views of structural biology for basic and applied research and education

(2014) Peter W. Rose et al.   NUCLEIC ACIDS RESEARCH

Rfam 12.0: updates to the RNA families database

(2014) Eric P. Nawrocki et al.   NUCLEIC ACIDS RESEARCH

Phylogenetic Gaussian Process Model for the Inference of Functionally Important Regions in Protein Tertiary Structures

(2014) Yi-Fei Huang et al.   PLoS Computational Biology

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

ConSurf: Using Evolutionary Data to Raise Testable Hypotheses about Protein Function

(2013) Gershon Celniker et al.   ISRAEL JOURNAL OF CHEMISTRY

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

CD-HIT: accelerated for clustering the next-generation sequencing data

(2012) Limin Fu et al.   BIOINFORMATICS

jModelTest 2: more models, new heuristics and parallel computing

(2012) Diego Darriba et al.   NATURE METHODS

Cellular crowding imposes global constraints on the chemistry and evolution of proteomes

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

ViennaRNA Package 2.0

(2011) Ronny Lorenz et al.   Algorithms for Molecular Biology

ProtTest 3: fast selection of best-fit models of protein evolution

(2011) Diego Darriba et al.   BIOINFORMATICS

MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods

(2011) K. Tamura et al.   MOLECULAR BIOLOGY AND EVOLUTION

HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment

(2011) Michael Remmert et al.   NATURE METHODS

A comparative study of conservation and variation scores

(2010) Fredrik Johansson et al.   BMC BIOINFORMATICS

ConSurf 2010: calculating evolutionary conservation in sequence and structure of proteins and nucleic acids

(2010) H. Ashkenazy et al.   NUCLEIC ACIDS RESEARCH

INTREPID: a web server for prediction of functionally important residues by evolutionary analysis

(2009) S. Sankararaman et al.   NUCLEIC ACIDS RESEARCH

Sequence context-specific profiles for homology searching

(2009) A. Biegert et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

An Improved General Amino Acid Replacement Matrix

(2008) S. Q. Le et al.   MOLECULAR BIOLOGY AND EVOLUTION

Detection of Functionally Important Regions in “Hypothetical Proteins” of Known Structure

(2008) Guy Nimrod et al.   STRUCTURE