CASTp: computed atlas of surface topography of proteins with structural and topographical mapping of functionally annotated residues

TLDR

Protein surface cavities and specific amino acid positioning generate the physicochemical properties required for protein function. The updated CASTp version incorporates functional annotations of specific residues on protein structures. CASTp locates and measures pockets and voids on 3D protein structures, annotating residues from PDB, Swiss‑Prot, and OMIM and mapping them to surface pockets or voids via semi‑global pairwise sequence alignment. The updated CASTp web server enables the study of surface features, functional regions, and the specific roles of key residues in proteins.

Abstract

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 ( http://cast.engr.uic.edu ) 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.