CASTp 3.0: computed atlas of surface topography of proteins

Wei Tian; Chang Chen; Xue Lei; Jieling Zhao; Jie Liang

doi:10.1093/nar/gky473

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/.

Keywords

Atlas (anatomy)VisualizationBiologyProtein Data BankWeb serverComputational biologySurface (topology)Protein structureComputer scienceBioinformaticsWorld Wide WebGeometryData miningThe InternetAnatomyMathematicsBiochemistry

MeSH Terms

AlgorithmsBinding SitesDatabasesProteinInternetModelsMolecularProtein ConformationProteinsSoftware

Affiliated Institutions

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Publication Info

Year: 2018
Type: article
Volume: 46
Issue: W1
Pages: W363-W367
Citations: 2203
Access: Closed

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APA Style

                            
                                
                                    Wei Tian, 
                                
                                    Chang Chen, 
                                
                                    Xue Lei
                                
                                et al.
                            
                            (2018). 
                            CASTp 3.0: computed atlas of surface topography of proteins. 
                            Nucleic Acids Research
                            , 46
                            (W1)
                            , W363-W367.
                            https://doi.org/10.1093/nar/gky473
                        

Identifiers

DOI: 10.1093/nar/gky473
PMID: 29860391
PMCID: PMC6031066

Data Quality

Data completeness: 90%