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CASTp 3.0 is a web server that computes the surface topography of proteins based on their atomic coordinates. It can identify pockets, cavities, and features on the protein surface, and provide information such as area, volume, and sequence.
- CASTp - University of Illinois Chicago
Please cite this paper if you publish or present results...
- CASTp - University of Illinois Chicago
CASTp is a web tool that computes and visualizes the surface topography of proteins based on their atomic coordinates. It can help users to identify and analyze the hydrophobic, hydrophilic, and charged regions of protein surfaces.
Please cite this paper if you publish or present results using CASTp analysis: Tian et al., Nucleic Acids Res. 2018. PMID: 29860391 DOI: 10.1093/nar/gky473. The enhanced CASTpFold server with new features for the whole protein universe is online, check here: CASTpFold.
- Introduction
- Materials and Methods
- The CASTp Server
- Input and Output
- Discussion
- Funding
Protein structures are complex and are sculpted with numerous surface pockets, internal cavities and cross channels. These topographic features provide structural basis and micro-environments for proteins to carry out their functions such as ligand binding, DNA interaction and enzymatic activity. Identification and quantification of these topograph...
The Computed Atlas of Surface Topography of proteins (CASTp) server uses the alpha shape method (4) developed in computational geometry to identify topographic features, to measure area and volume and to compute imprint (5–8). The alpha shape method has also been applied in other studies of cavities and channels in protein structures (9,10). The se...
The CASTp server aims to provide comprehensive and detailed quantitative characterization of topographic features of proteins (14,15). Since its release 15 years ago, the CASTp server has ∼45 000 visits and fulfills ∼33 000 calculation requests annually. It has been proven to be a useful tool for a wide range of studies, including investigations of...
Input
The CASTp server takes protein structures in the PDB format and a probe radius as input for topographic computation. Through the intuitive interface, users can either search for pre-computed results using a four-letter PDB ID, or submit their own protein structures to request customized computation. For pre-computed results, a default probe radius of 1.4 Å is used, which is the standard value for computing solvent accessible surface area. For customized computation request, users can specify...
Output
The CASTp server identifies all surface pockets, interior cavities and cross channels in a protein structure and provides detailed delineation of all atoms participating in their formation. It also measures their exact volumes and areas, as well as sizes of the mouth openings if exist. These metrics are calculated analytically, using both the solvent accessible surface model (Richards’ surface) (24) and the molecular surface model (Connolly’s surface) (25). In addition, the CASTp server also...
Case study
Figure 3 illustrates the adenosine triphosphate (ATP) binding pocket on the cyclin-dependent kinase 2 (CDK2, PDB ID: 2xmy) that is automatically identified by the CASTp server. CDK2 is an important enzyme that regulates cell cycle with other CDKs. Many functionally important residues are located in this pocket, including three residues Lys33, Asp86 and Asp145 in the ATP binding site, one residue Asp127 in the catalytic site, two residues Asn132 and Asp145 in Mg binding sites and one residue L...
This paper describes significant improvement of the CASTp server, including: (i) the addition of imprints of negative volumes as a visualization option; (ii) the inclusion of pre-computed results for biological assemblies, rather than reporting results for the asymmetric unit alone; (iii) an improved user interface, which contains an updated and ad...
NIH [R01CA204962]. Funding for open access charge: NIH [R01CA204962]; UIC Research Open Access Article Publishing (ROAAP) Fund. Conflict of interest statement. None declared.
- T. Andrew Binkowski, Shapor Naghibzadeh, Jie Liang
- 2003
Computer Atlas of Surface Topography of Proteins (CASTp) aims to provide comprehensive and detailed quantitative characterization of topographic features of protein, is now updated to version 3.0. Since its release in 2006, the CASTp server has ≈45000 visits and fulfills ≈33000 calculation requests annually.
Jul 2, 2018 · 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.
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Jul 1, 2003 · Computed Atlas of Surface Topography of proteins (CASTp) provides an online resource for locating, delineating and measuring concave surface regions on three-dimensional structures of proteins. These include pockets located on protein surfaces and voids buried in the interior of proteins.
