CASTp: computed atlas of surface topography of proteins with structural and topographical mapping of functionally annotated residues
By J. Dundas, Ouyang Zheng, Jeffery Tseng, A. Binkowski, Y. Turpaz, Jie Liang. Nucleic Acids Res., 2006
579 citations recorded by the source corpus.
Cavities on a proteins surface as well as specific amino acid positioning within it create the physicochemical properties needed for a protein to perform its function. CASTp () is an online tool that locates and measures pockets and voids on 3D protein structures. This new version of CASTp includes annotated functional information of specific residues on the protein structure. The annotations are derived from the Protein Data Bank (PDB), Swiss-Prot, as well as Online Mendelian Inheritance in Man (OMIM), the latter contains information on the variant single nucleotide polymorphisms (SNPs) that are known to cause disease. These annotated residues are mapped to surface pockets, interior voids or other regions of the PDB structures. We use a semi-global pair-wise sequence alignment method to obtain sequence mapping between entries in Swiss-Prot, OMIM and entries in PDB. The updated CASTp web server can be used to study surface features, functional regions and specific roles of key residues of proteins.
Subfields: Materials Chemistry, Molecular Biology
View Paper: https://www.semanticscholar.org/paper/f9a490fcde8bd02b4e11dd1a2d10270b3a18680c
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In Materials Chemistry
In Molecular Biology
- O. Schueler‐Furman
- Barak Raveh
- Nir London
- Eyal Cohen
- Guy Fathi
- V. Guilloux
- Pierre Tufféry
- Peter Schmidtke
Citations in the corpus
- Fpocket: An open source platform for ligand pocket detection (2009, background): “Another In terms of availability, several of these approaches can be accessed via web servers (e.g. [34-36]), but very few packages are available for distribution.”
- Rosetta FlexPepDock web server—high resolution modeling of peptide–protein interactions (2011, background): “These include CASTp (26), which aims at detecting pockets on protein surfaces [we previously showed that this feature correlates with peptide binding sites (5)], and PepSite (27), which predicts peptide binding sites and provides a coarse prediction of specific peptide residue locations.”
- Advances in Protein Chemistry and Structural Biology (2010, methodology): “This database is part of the CASTp database (Binkowski et al., 2003b; Dundas et al., 2006).”
- CASTp 3.0: computed atlas of surface topography of proteins (2018, unknown): “The CASTp server aims to provide comprehensive and detailed quantitative characterization of topographic features of proteins [4, 5].”
- Role of computer-aided drug design in modern drug discovery (2015, unknown): “Jackson 2005), CASTp (Dundas et al. 2006), LIGSITEcsc (Huang and Schroeder 2006), SiteMap (Halgren 2009), FPocket (Le Guilloux et al.”