title: CCRXP: exploring clusters of conserved residues in protein structures.
abstract: Conserved residues forming tightly packed clusters have been shown to be energy hot spots in both protein-protein and protein-DNA complexes. A number of analyses on these clusters of conserved residues (CCRs) have been reported, all pointing to a crucial role that these clusters play in protein function, especially protein-protein and protein-DNA interactions. However, currently there is no publicly available tool to automatically detect such clusters. Here, we present a web server that takes a coordinate file in PDB format as input and automatically executes all the steps to identify CCRs in protein structures. In addition, it calculates the structural properties of each residue and of the CCRs. We also present statistics to show that CCRs, determined by these procedures, are significantly enriched in 'hot spots' in protein-protein and protein-RNA complexes, which supplements our more detailed similar results on protein-DNA complexes. We expect that CCRXP web server will be useful in studies of protein structures and their interactions and selecting mutagenesis targets. The web server can be accessed at http://ccrxp.netasa.org.
authors.affiliation: National Institute of Biomedical Innovation, 7-6-8, Saito-asagi, Ibaraki, Osaka 5670085, Japan. shandar@nibio.go.jp
authors.forename: Shandar
authors.initials: S
authors.lastname: Ahmad
authors.forename: Ozlem
authors.initials: O
authors.lastname: Keskin
authors.forename: Kenji
authors.initials: K
authors.lastname: Mizuguchi
authors.forename: Akinori
authors.initials: A
authors.lastname: Sarai
authors.forename: Ruth
authors.initials: R
authors.lastname: Nussinov
mesh_terms: D004268:DNA-Binding Proteins / Q000737:chemistry / Q000235:genetics; D020407:Internet; D046912:Multiprotein Complexes / Q000737:chemistry / Q000235:genetics; D009154:Mutation; D011506:Proteins / Q000737:chemistry* / Q000235:genetics; D016601:RNA-Binding Proteins / Q000737:chemistry / Q000235:genetics; D012984:Software
chemical_list: D004268:DNA-Binding Proteins; D046912:Multiprotein Complexes; D011506:Proteins; D016601:RNA-Binding Proteins
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