ConSurf 2005: the projection of evolutionary conservation scores of residues on protein structures

By M. Landau, Itay Mayrose, Yossi Rosenberg, Fabian Glaser, Eric Martz, Tal Pupko, Nir Ben-Tal. Nucleic Acids Res., 2005

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Key amino acid positions that are important for maintaining the 3D structure of a protein and/or its function(s), e.g. catalytic activity, binding to ligand, DNA or other proteins, are often under strong evolutionary constraints. Thus, the biological importance of a residue often correlates with its level of evolutionary conservation within the protein family. ConSurf () is a web-based tool that automatically calculates evolutionary conservation scores and maps them on protein structures via a user-friendly interface. Structurally and functionally important regions in the protein typically appear as patches of evolutionarily conserved residues that are spatially close to each other. We present here version 3.0 of ConSurf. This new version includes an empirical Bayesian method for scoring conservation, which is more accurate than the maximum-likelihood method that was used in the earlier release. Various additional steps in the calculation can now be controlled by a number of advanced options, thus further improving the accuracy of the calculation. Moreover, ConSurf version 3.0 also includes a measure of confidence for the inferred amino acid conservation scores.

Subfields: Materials Chemistry, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/d4329aea517a0c8ce41d702601c64263d2cf4d2c

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Citations in the corpus

Development of an epitope conservancy analysis tool to facilitate the design of epitope-based diagnostics and vaccines (2007, methodology): “Landau M, Mayrose I, Rosenberg Y, Glaser F, Martz E, Pupko T, BenTal N: ConSurf 2005: the projection of evolutionary conservation scores of residues on protein structures.”
Selecton 2007: advanced models for detecting positive and purifying selection using a Bayesian inference approach (2007, background): “Various other web servers are available for analyzing the evolutionary forces operating on a gene, including servers which perform analyses only on an amino-acid alignment (e.g. 11,12–14), and servers which perform analyses of positive selection in codon-based alignments (15–18).”
ConSurf 2010: calculating evolutionary conservation in sequence and structure of proteins and nucleic acids (2010, methodology): “(2) A text file that summarizes for each position the normalized score calculated, the assigned color, the reliability estimation (for the Bayesian method) and the amino acids/nucleotides observed in the respective MSA column.”
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).”
Predicting Protein Ligand Binding Sites by Combining Evolutionary Sequence Conservation and 3D Structure (2009, methodology): “ConSurf [39] provides a visualization of sequence conservation values on the surface of a protein structure, and the recent PatchFinder [40] method automates the prediction of functional surface patches from ConSurf.”
Molecular Mechanism for LAMP1 Recognition by Lassa Virus (2015, methodology): “To identify possible alternative sites for receptor binding, we analyzed the structure of GP1LASV using the ConSurf server (22) (Fig.”
Title: Mosaic nanoparticles elicit cross-reactive immune responses to zoonotic coronaviruses in mice (2020, neutral): “Middle and right: Sequence conservation of 12 RBDs calculated by the ConSurf Database (49) plotted on a surface representation of the RBD structure (PDB 7BZ5).”
GUIDANCE: a web server for assessing alignment confidence scores (2010, background): “For example, site-specific rate inference, as in the Consurf web server (15), is usually robust to a few badly aligned residues in a column, because a column corresponding to a conserved site will still be inferred as conserved as long as most of the data are correctly aligned.”
Crystal structure of the TLR4-MD-2 complex with bound endotoxin antagonist Eritoran. (2007, methodology): “Conservation scores were calculated by the Bayesian method using the Consurf server (Landau et al., 2005).”
Structures of Human Antibodies Bound to SARS-CoV-2 Spike Reveal Common Epitopes and Recurrent Features of Antibodies (2020, neutral): “Conservationwas calculated byConSurf Database (Landau et al., 2005) and displayed using a surface representation of the structure of the SARS-CoV-2 S protein (PDB: 6VXX). ll OPEN ACCESSArticle SARS-CoV-2 and common cold coronavirus S proteins are even lower, varying between 25% and 30%.”