Tools for integrated sequence-structure analysis with UCSF Chimera |
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Authors: | Elaine C Meng Eric F Pettersen Gregory S Couch Conrad C Huang and Thomas E Ferrin |
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Institution: | (1) Computer Graphics Laboratory, University of California San Francisco, 600 16th Street, San Francisco, CA 94143-2440, USA |
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Abstract: | 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. |
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Keywords: | |
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