Structural Genomics

By Marco F. Ramoni. 2005

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TANKBind: Trigonometry-Aware Neural NetworKs for Drug-Protein Binding Structure Prediction (2022, background): “Biologically, the functional regions of proteins tend to be more conserved and closely associated with binding [15, 16], allowing the model to learn critical information and generalize better to unseen proteins.”
ConSurf 2010: calculating evolutionary conservation in sequence and structure of proteins and nucleic acids (2010, background): “ConSurf (1,2) and ConSeq (3) are web servers for calculating the evolutionary rate of each position of the protein and for identifying structurally and functionally important regions within proteins.”
PDBsum more: new summaries and analyses of the known 3D structures of proteins and nucleic acids (2004, methodology): “The conservation of each residue is computed by the ConSurf (13) program, which uses multiple sequence alignments of the protein chain against homologues in the sequence databases.”
Network analysis of protein structures identifies functional residues. (2004, background): “‡ 60 The server calculated the conservation for 91% of the 178 analyzed chains, not identifying enough homologs for the following 16 structures: 1c3j, 2thi, 1gog, 2plc, 3csm, 4kbp, 1chk, 1d8h, 1pya, 1coy, 1fui, 1pgs, 1ps1, 1vnc, 2cpo, and 1uox.”
Comparison of site-specific rate-inference methods for protein sequences: empirical Bayesian methods are superior. (2004, methodology): “Rate4Site was embedded in the ConSurf server (Glaser et al. 2003; http://consurf.tau.ac.il) and successfully identi-ﬁed functional residues at the contact interface of several proteins (Donaudy et al. 2003; Mella et al. 2003; Ramelot et al. 2003; RamShankar et al. 2003).”
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.”
Exploiting sequence and structure homologs to identify protein–protein binding sites (2005, unknown): “The predictions were also compared with those predicted by predictor 1 and by the ConSurf server.(25) As previously mentioned, predictor 1 used only sequence profile and accessible surface area, which are common input features used by previous studies.”
ConSurf 2016: an improved methodology to estimate and visualize evolutionary conservation in macromolecules (2016, methodology): “ConSurf is a widely used tool for revealing functional regions in macromolecules by analysing the evolutionary dynamics of amino / nucleic acids substitutions among homologous sequences (1–4).”
Sustainability and Stewardship of Glyphosate and Glyphosate-resistant Crops (2007, methodology): “…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 site depicted in…”
Advances in Protein Chemistry and Structural Biology (2010, methodology): “U N C O R R E C T E D P R O O F to be very effective (Binkowski et al., 2003a; Glaser et al., 2003; Gold and Jackson, 2006; Laskowski et al., 2005; Najmanovich et al., 2005; Pazos and Sternberg, 2004; Russell, 1998; Torrance et al., 2005; Tseng and Liang, 2006).”
ConSurf 2005: the projection of evolutionary conservation scores of residues on protein structures (2005, background): “ConSurf is a web server for mapping the level of evolutionary conservation of each of the amino acid positions of a protein onto its 3D structure (1).”
Residue centrality, functionally important residues, and active site shape: Analysis of enzyme and non‐enzyme families (2006, background): “using the ConSurf server (Glaser et al. 2003). where”