Publication:
CCRXP: exploring clusters of conserved residues in protein structures

Thumbnail Image

School / College / Institute

Program

KU-Authors

KU Authors

Co-Authors

Ahmad, Shandar
Mizuguchi, Kenji
Sarai, Akinori
Nussinov, Ruth

Publication Date

Language

Embargo Status

NO

Journal Title

Journal ISSN

Volume Title

Alternative Title

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.

Source

Publisher

Oxford University Press (OUP)

Subject

Biochemistry and molecular biology

Citation

Has Part

Source

Nucleic Acids Research

Book Series Title

Edition

DOI

10.1093/nar/gkq360

item.page.datauri

Link

Rights

Copyrights Note

Endorsement

Review

Supplemented By

Referenced By

0

Views

3

Downloads

View PlumX Details