Resource for Biocomputing, Visualization, and Informatics

Resource for Biocomputing, Visualization, and Informatics

Research Emphasis

The Resource for Biocomputing, Visualization, and Informatics creates innovative computational and visualization-based data analysis methods and algorithms; implements these as professional-quality, fully documented, easy-to-use software tools; and applies these tools to solve a wide range of genomic and molecular recognition problems within the complex sequence-structure-function triad. Application areas include gene characterization and interpretation, drug design, variation in drug response due to genetic factors, protein engineering, biomaterials design, and prediction of function from sequence and structure.

Current Research

Sequence analysis and bioinformatics: The characterization and interpretation of genomic data, including knowledge discovery and transfer in nucleic acid and protein sequence analysis, pharmacogenomics, and the identification of gene and regulatory motifs, protein family/superfamily relationships, and gene expression patterns.

Structural informatics: The development, application, and dissemination of analysis methodologies and software tools in computational structural biology, including algorithm development of low- and high-resolution protein structural models and their comparison, molecular visualization for structural analysis and the integration of sequence and tertiary structural information, and facilitation of collaborative research through use of high-performance network technology.

Functional informatics: Theoretical and applied research in how protein structures deliver function, including the identification and characterization of protein superfamilies, the generation of new computational-based representations of protein chemistry, and the development of structurally contextual definitions of protein function.

Resource Capabilities

Methods

A major focus of our efforts is on the development of analysis methods utilizing interactive computer graphics techniques. The powerful and affordable graphics processing units now available for desktop computers enable these methods to be accessed by any scientist.

Instruments

Instrumentation includes: 1) a high-performance cluster of symmetric multiprocessor Hewlett-Packard AlphaServer computers for performing theoretical studies on protein and nucleic acid structure and function and for storing, searching, and analyzing various sequence and structure databases; and 2) a high-performance interactive three-dimensional graphics workstations equipped with special glasses for viewing in stereo for visualization of complex molecular structures. All systems are interconnected via a high-performance network and are capable of distributed computations.

Software

Software capabilities include commercial applications for database searching and analysis and several locally developed packages disseminated as documented source code to allow others to use the resource's software, both for their own research applications and as a starting point and training tool for specialized applications. Local packages include Chimera, an advanced molecular visualization system that can easily be extended for specialized molecular modeling needs. We maintain local copies of a variety of protein and DNA sequence databases, including primary, secondary, motif, and domain databases, which are available for browsing, homology, and comparison searching. These local databases include the Protein Data Bank, the Cambridge Structural Database, and Isostar.

Training Opportunities and Workshops

Two or three workshops on the use of Chimera are usually conducted each year. Announcements of new workshops and the training materials used at past workshops are available on the Outreach & Training page of the UCSF Computer Graphics Lab Web site. In addition, extensive online training tutorials are available.

Publications

1. Huang, C. C., Ferrin, T. E., and Babbitt, P. C., Leveraging enzyme structure-function relationships for functional inference and experimental design: The structure-function linkage database. Biochemistry 45:2545–2555, 2006.

2. Couch, G. S., Hendrix, D. K., and Ferrin, T. E., Nucleic acid visualization with UCSF Chimera. Nucleic Acids Research 34:e29, 2006.

3. Goddard, T. D., Huang, C. C., and Ferrin, T. E., Software extensions to UCSF Chimera for interactive visualization of large molecular assemblies. Structure 13:473–482, 2005.

4. Pettersen, E. F., Goddard, T. D., Huang, C. C., Couch, G. S., Greenblatt, D. M., Meng, E. C., and Ferrin, T. E., UCSF Chimera—A visualization system for exploratory research and analysis. Journal of Computational Chemistry 25:1605–1612, 2004.