ConSurf: an algorithmic tool for the identification of functional regions in proteins by surface mapping of phylogenetic information.

By Aharon Armon, Dan-Ovidiu Graur, Nir Ben-Tal. Journal of Molecular Biology, 2001

541 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/3000c5bc45291052eb1321c31b2319046e1c4a8b

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Citations in the corpus

Graphical Models of Residue Coupling in Protein Families (2008, methodology): “While the above discussion deals with the confounding role of phylogeny, techniques such as Evolutionary Trace [20] and ConSurf [1] exploit phylogenetic information in order to identify possible functional sites.”
OpenStructure: an integrated software framework for computational structural biology (2013, methodology): “Conservation of columns in an alignment may be calculated with a variation of the algorithm from ConSurf (Armon et al., 2001), which considers the pairwise physicochemical similarity of residues in each alignment column (for an example, see Biasini et al., 2010).”
Rate4Site: an algorithmic tool for the identification of functional regions in proteins by surface mapping of evolutionary determinants within their homologues (2002, methodology): “, 1996) and ‘ConSurf’ (Armon et al., 2001), which was based on the maximum parsimony approach (MP-ConSurf), is that the slow evolution rate of surface residues is the result of constraints due to binding, e.”
Q-SiteFinder: an energy-based method for the prediction of protein-ligand binding sites (2005, background): “…which often * To whom correspondence should be addressed. uses protein evolutionary information (Lichtarge et al., 1996; Aloy et al., 2001; Armon et al., 2001; Landgraf et al., 2001) or by structural comparisons of functional sites (Artymiuk et al., 1994; Wallace et al., 1997; Stark and…”
Scoring residue conservation (2002, unknown): “The score of Armon et al. 27 does account for gaps.”
Sustainability and Stewardship of Glyphosate and Glyphosate-resistant Crops (2007, methodology): “…can be visualized through a tool called ConSurf, where the conservation score (Rate4Site; vide supra) is painted on a known x-ray crystal structure (Armon et al. 2001; Glaser et al. 2003) allowing us to see the binding site; for example, the acetolactate synthase (ALS) enzyme herbicide binding…”
LIGSITEcsc: predicting ligand binding sites using the Connolly surface and degree of conservation (2006, methodology): “Conservation has been widely used for function site prediction [26-28] and protein-protein interaction interface prediction [29-32], combined with other physiochemical properties.”
Using evolutionary data to make sense of macromolecules with a “face‐lifted” ConSurf (2023, methodology): “ConSurf (Armon et al. 2001) and related methodologies (Huang & Golding 2014; Huang & Golding 2015; Morgan et al. 2006) are superior to such methods as they account for the evolutionary relationships between homologues represented as a phylogenetic tree.”
Network analysis of protein structures identifies functional residues. (2004, background): “13,19,20,52 Here we report that the combination of centrality and solvent accessibility already enabled us to identify active site residues in 70% of the proteins within a data set of 178 representative enzymes generated by Bartlett et al .”
Protein–protein interaction and quaternary structure (2008, methodology): “Valdar & Thornton (2001) and Armon et al. (2001) use a similar approach with more elaborate measures of the evolutionary divergence that take into account observed mutation rates, in order to predict binding sites.”
Crystal Structure of the SPOC Domain of the Arabidopsis Flowering Regulator FPA (2016, background): “An analysis of the SPOC domain indicates a large surface patch near strands β1, β3, β5 and β6 that is conserved among plant FPA homologs (Fig 4A) [26].”
All-atom 3D structure prediction of transmembrane β-barrel proteins from sequences (2015, background): “In addition, three conserved (36) proline residues (P231, P246, and P261) are predicted to lie on three adjacent β-strands (Fig.”
Graphical models of protein–protein interaction specificity from correlated mutations and interaction data (2009, methodology): “guiding docking,13 another study tested a number of typical coupling metrics and found them not to be indicative of intermolecular contacts.14 A recent large-scale study did find co-evolving pairs to be in general closer than other pairs.17 Another indirect manifestation of cross-coupling is in diff”
ISIS: interaction sites identified from sequence (2007, background): “Note that all estimates were derived for the test set too distant for homology-based predictions ( Aloy and Russell, 2002 ).”