RRDistMaps: a UCSF Chimera tool for viewing and comparing protein distance maps | Zendy

Jonathan E. Chen | Zendy; Conrad C. Huang | Zendy; Thomas E. Ferrin | Zendy

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RRDistMaps: a UCSF Chimera tool for viewing and comparing protein distance maps

Author(s) -

Jonathan E. Chen,

Conrad C. Huang,

Thomas E. Ferrin

Publication year - 2014

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/btu841

Subject(s) - chimera (genetics) , pairwise comparison , computer science , binary number , computer graphics (images) , algorithm , artificial intelligence , mathematics , biology , genetics , arithmetic , gene

Contact maps are a convenient method for the structural biologists to identify structural features through two-dimensional simplification. Binary (yes/no) contact maps with a single cutoff distance can be generalized to show continuous distance ranges. We have developed a UCSF Chimera tool, RRDistMaps, to compute such generalized maps in order to analyze pairwise variations in intramolecular contacts. An interactive utility, RRDistMaps, visualizes conformational changes, both local (e.g. binding-site residues) and global (e.g. hinge motion), between unbound and bound proteins through distance patterns. Users can target residue pairs in RRDistMaps for further navigation in Chimera. The interface contains the unique features of identifying long-range residue motion and aligning sequences to simultaneously compare distance maps.

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