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. 2018 Jul 2;46(W1):W363-W367.
doi: 10.1093/nar/gky473.

CASTp 3.0: computed atlas of surface topography of proteins

Wei Tian  1 , Chang Chen  1 , Xue Lei  1 , Jieling Zhao  2 , Jie Liang  1
Affiliations

CASTp 3.0: computed atlas of surface topography of proteins

Wei Tian et al. Nucleic Acids Res. .

Abstract

Geometric and topological properties of protein structures, including surface pockets, interior cavities and cross channels, are of fundamental importance for proteins to carry out their functions. Computed Atlas of Surface Topography of proteins (CASTp) is a web server that provides online services for locating, delineating and measuring these geometric and topological properties of protein structures. It has been widely used since its inception in 2003. In this article, we present the latest version of the web server, CASTp 3.0. CASTp 3.0 continues to provide reliable and comprehensive identifications and quantifications of protein topography. In addition, it now provides: (i) imprints of the negative volumes of pockets, cavities and channels, (ii) topographic features of biological assemblies in the Protein Data Bank, (iii) improved visualization of protein structures and pockets, and (iv) more intuitive structural and annotated information, including information of secondary structure, functional sites, variant sites and other annotations of protein residues. The CASTp 3.0 web server is freely accessible at http://sts.bioe.uic.edu/castp/.

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Figures

Figure 1.
Figure 1.
The surface of the ATP binding pocket of CDK2 (PDB ID: 2xmy), computed by CASTp 3.0.
Figure 2.
Figure 2.
The case when the asymmetric unit differs from the biological assembly. (A) Asymmetric unit in the PDB ID: 2iwv and the artificial giant pocket. The giant pocket is formed by the four channels of the four biological units and the space among them with unclear biological relevance. (B) Biological structure of 2iwv (biological assembly 1) and its channel detected by the CASTp server.
Figure 3.
Figure 3.
The main user interface of the CASTp server. (A) The pocket panel. (B) The sequence and annotation panels.
See this image and copyright information in PMC

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