Representing and comparing protein structures as paths in three-dimensional space.

TitleRepresenting and comparing protein structures as paths in three-dimensional space.
Publication TypeJournal Article
Year of Publication2006
AuthorsZhi D, Krishna SS, Cao H, Pevzner P, Godzik A
JournalBMC Bioinformatics
Volume7
Pagination460
Date Published2006
ISSN1471-2105
KeywordsAlgorithms, Amino Acid Sequence, Computer Simulation, Models, Chemical, Models, Molecular, Molecular Sequence Data, Protein Conformation, Proteins, Sequence Alignment, Sequence Analysis, Protein
Abstract

BACKGROUND: Most existing formulations of protein structure comparison are based on detailed atomic level descriptions of protein structures and bypass potential insights that arise from a higher-level abstraction.

RESULTS: We propose a structure comparison approach based on a simplified representation of proteins that describes its three-dimensional path by local curvature along the generalized backbone of the polypeptide. We have implemented a dynamic programming procedure that aligns curvatures of proteins by optimizing a defined sum turning angle deviation measure.

CONCLUSION: Although our procedure does not directly optimize global structural similarity as measured by RMSD, our benchmarking results indicate that it can surprisingly well recover the structural similarity defined by structure classification databases and traditional structure alignment programs. In addition, our program can recognize similarities between structures with extensive conformation changes that are beyond the ability of traditional structure alignment programs. We demonstrate the applications of procedure to several contexts of structure comparison. An implementation of our procedure, CURVE, is available as a public webserver.

DOI10.1186/1471-2105-7-460
PubMed URLhttp://www.ncbi.nlm.nih.gov/pubmed/17052359?dopt=Abstract
PMCPMC1626488
Alternate TitleBMC Bioinformatics
PubMed ID17052359