Tools for integrated sequence-structure analysis with UCSF Chimera

Background: Comparing related structures and viewing the structures in the context of sequence alignments are important tasks in protein structure-function research. While many programs exist for individual aspects of such work, there is a need for interactive visualization tools that: (a) provide a deep integration of sequence and structure, far beyond mapping where a sequence region falls in the structure and vice versa; (b) facilitate changing data of one type based on the other (for example, using only sequence-conserved residues to match structures, or adjusting a sequence alignment based on spatial fit); (c) can be used with a researcher's own data, including arbitrary sequence alignments and annotations, closely or distantly related sets of proteins, etc.; and (d) interoperate with each other and with a full complement of molecular graphics features. We describe enhancements to UCSF Chimera to achieve these goals. Results: The molecular graphics program UCSF Chimera includ...

• Type: Journal
• Year: 2006
• Where: BMCBI
• Authors: Elaine C. Meng, Eric F. Pettersen, Gregory S. Couch, Conrad C. Huang, Thomas E. Ferrin
• Keywords: Arbitrary Sequence Alignments, BMCBI 2006, Sequence Alignments, UCSF Chimera