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

By Haim Ashkenazy, Elana Erez, Eric Martz, Tal Pupko, Nir Ben-Tal. Nucleic Acids Res., 2010

1,867 citations recorded by the source corpus.

It is informative to detect highly conserved positions in proteins and nucleic acid sequence/structure since they are often indicative of structural and/or functional importance. ConSurf (http://consurf.tau.ac.il) and ConSeq (http://conseq.tau.ac.il) are two well-established web servers for calculating the evolutionary conservation of amino acid positions in proteins using an empirical Bayesian inference, starting from protein structure and sequence, respectively. Here, we present the new version of the ConSurf web server that combines the two independent servers, providing an easier and more intuitive step-by-step interface, while offering the user more flexibility during the process. In addition, the new version of ConSurf calculates the evolutionary rates for nucleic acid sequences. The new version is freely available at: http://consurf.tau.ac.il/.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/ac3da0a511712add9777113030880398d203e4a3

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Citations in the corpus

Deep mutational scanning of an RRM domain of the Saccharomyces cerevisiae poly(A)-binding protein (2013, methodology): “…for natural Pab1 homologs were created by providing WebLogo a MAFFT-based multiple sequence alignment of 306 sequences selected by ConSurf server (Ashkenazy et al. 2010) from the UniRef90 database (Pruitt et al. 2011) showing a maximal 95% identity between sequences and a minimum of 35% identity…”
XRN 5’→3’ exoribonucleases: Structure, mechanisms and functions (2013, methodology): “Multiple alignment and conservation scores were calculated using ConSurf [68], which takes into account the phylogenetic distance between species.”
NGL Viewer: a web application for molecular visualization (2015, methodology): “Specifically, integration of browser-based visualizations simplifies access to results of structure-related calculations from web tools (3,4) and allows for quick depiction of entries in online structural databases (5–7).”
ConSurf 2016: an improved methodology to estimate and visualize evolutionary conservation in macromolecules (2016, background): “The protocol for the selection of homologous sequences was shaped while massive amounts of sequence data are becoming available (2,3).”
Using HHsearch to tackle proteins of unknown function: A pilot study with PH domains (2016, methodology): “The presence of this one PH-like domain was verified by demonstrating both that it has a specific targeting activity and that it is required for one aspect of the function of full length Vps13p.”
PredictProtein—an open resource for online prediction of protein structural and functional features (2014, positive): “Prediction of functional features: predicted aspects include ConSurf annotations and visualizations of functionally important sites (26,27), protein mutability landscape analysis showing the effect of point mutations on protein function predicted by SNAP2 (28), Gene Ontology (GO) terms from metastud”
FunFOLD: an improved automated method for the prediction of ligand binding residues using 3D models of proteins (2011, methodology): “The sequence-based methods rely on identifying conserved residues that may be structurally or functionally important and include methods such as fire-star (CASP9 group FN315) [4], WSsas [5], FRcons [6], ConFunc (CASP8 - FN437) [7], ConSurf [8], FPSDP (CASP8 - FN242) [9] and INTERPID [10].”