Thomas E. Ferrin, Ph.D.

Professor of Pharmaceutical Chemistry
and Biopharmaceutical Sciences
Chair, Biological and Medical Informatics Graduate Program
Director, Resource for Biocomputing, Visualization, and Informatics
and the UCSF Computer Graphics Laboratory

Address:

Computer Graphics Laboratory
University of California
San Francisco, CA 94143-0446

Phone: (415) 476-2299
Fax: (415) 502-1755
Email: tef@cgl.ucsf.edu

Education/Affiliations:

• B.Sc. University of Minnesota, Electrical Engineering and Computer Science, 1971
• Ph.D. University of California, San Francisco, Medical Information Science, 1986
• Professor, Departments of Pharmaceutical Chemistry and Biopharmaceutical Sciences, UCSF
• Chair, UCSF Biological and Medical Informatics Graduate Program
• Vice Chair, Department of Biopharmaceutical Sciences
• Member, UCSF Chemistry and Chemical Biology Graduate Program
• Member, UCSF Pharmaceutical Sciences and Pharmacogenomics Graduate Program
• Member, UCSF Biophysics Graduate Program
• Member, UCSF/UCB Bioengineering Graduate Program
• Member, Molecular Design Institute
• Member, UCSF Cancer Center

Research Activities:

My work focuses on computational approaches for comprehending the structure and function of large biological molecules using three-dimensional computer graphics and data mining techniques. Interactive visualization and manipulation of nucleic acids, proteins, and protein-ligand complexes is a highly effective research tool, especially when coupled to fast computers employing numerical analysis techniques. Complementary to these structure-based approaches to studying macromolecular function, the vast quantities of genomic data now available requires new theoretical constructs and computational approaches for turning this data into scientific understanding. Innovative computational methods such as genetic algorithms, neural networks, and hidden Markov models are providing powerful new software paradigms to relate sequence, structure, and functional information on a genomic scale. Making this information available to the scientific community through facile web-based interfaces is a considerable challenge, but crucial if others are to benefit from and build on our work, and hence constructing searchable and extensible databases using, for example, object-oriented programming techniques are required. We are incorporating these approaches and others into integrated systems for molecular recognition in applications such as drug design, protein engineering, biomaterials design, and bioremediation.

We encourage collaborative interdisciplinary research projects with scientists at UCSF, other academic institutions, and industry. Research is conducted by a diverse group whose backgrounds range from computer science to bioinformatics to structural biology and molecular biology.

Recent Awards:

• Academic Senate University Service Award for outstanding contributions to the UCSF network.

Selected Publications:

• R. Lewis, D. Roe, C.C. Huang, T.E. Ferrin, R. Langridge, and I.D. Kuntz, `` Automated Site-Directed Drug Design Using Molecular Lattices,'' J. Mol. Graphics, 10(2):66-78, 1992.
• C.C. Huang, E.F. Pettersen, T.E. Klein, T.E. Ferrin, and R. Langridge, `` Conic - A Fast Renderer for Space-Filling Molecules with Shadows,'' J. Mol. Graphics, 9(4):230-236 and 242, 1991.
• T.E. Ferrin, G.S. Couch, C.C. Huang, E.F. Pettersen, and R. Langridge, `` An Affordable Approach to Interactive Desktop Molecular Modeling,'' J. Mol. Graphics, 9(1):27-32 and 37-38, 1991.
• T.E. Klein, C.C. Huang, E.F. Pettersen, G.S. Couch, T.E. Ferrin, and R. Langridge, `` A Real-Time Malleable Molecular Surface,'' J. Mol. Graphics, 8(1):16-24 and 26-27, 1990.
• G.S. Couch, E.F. Pettersen, C.C. Huang, T.E. Ferrin, `` Annotating PDB Files with Scene Information,'' J. Mol. Graphics, 13(3):153-158, 1995.
• T.E. Ferrin, C.C. Huang, G.S. Couch, and E.F. Pettersen, `` Unified Access to Macromolecular Data,'' in: Proceedings of the NSF Scientific Database Projects, W. Chu, A. Cardenas, and R. Taira, eds., pp. 29-33, National Science Foundation, 1993.
• T.E. Ferrin and T.E. Klein, `` Comuter Graphics and Molecular Modeling,'' in: The Encyclopedia of Computational Chemistry, P.v.R. Schleyer, N.L. Allinger, T. Clark, J. Gasteigeer, H.F. Schaefer III, and P.R. Schreiner, eds., pp. 463-474, John Wiley & Sons, 1998.
• E.T. Kraemer and T.E. Ferrin, ``Molecules to Maps: Tools for Visualization and Interaction in Support of Computational Biology,'' Bioinformatics, 14(9):764-771, 1998.
• C.C. Huang, W.R. Novak, P.C. Babbitt, A.I. Jewett, T.E. Ferrin, and T.E. Klein, ``Integrated Tools for Structural and Sequence Alignment and Analysis,'' Pacific Symposium on Biocomputing 2000, R.B. Altman, A.K. Dunker, L. Hunter, T.E. Klein, and K. Lauderdale eds., pp. 230-241, World Scientific Publishing, 2000.
• D.E. Konerding, C.C. Huang, and T.E. Ferrin, "Chimera: Affordable Desktop Molecular Modeling On Linux Workstations," Proceedings of the 5th Annual Linux Showcase & Conference, Usenix Association, November 2001.
• A.I. Jewett, C.C. Huang, and T.E. Ferrin, "MINRMS: An Efficient Algorithm for Determining Protein Structure Similarity Using Root-Mean Squared-Distance," submitted.

Recent Invited Lectures and Seminars:

• "High Performance Network Applications at UCSF." Presented at the Consortium for Education Network Initiatives in California (CENIC) Retreat in Indian Wells, CA on June 12, 1997.
• "A Prototype Collaboratory for Structure-Based Drug Design Based on the Next Generation Internet." Presented at NETAMORPHOSIS in Washington, D.C. March 11-13, 1998 and sponsored by the White House Office of Science and Technology Policy and the White House National Economic Council.
• "Collaboratory Developments at the UCSF Computer Graphics Lab." Presented at the National Center for Microscopy and Imaging Research Joint Collaboratory Workshop in San Diego, CA on September 13, 1999.
• "Integrated Software Tools for Functional Genomics." Presented at the ACS Symposium on Bioinformatics as part of the American Chemical Society National Meeting in San Francisco, CA on March 28, 2000.
• "Visualization Tools for Integrating Sequence and Structural Information." Presented at Bioinformatics in the Post-Genomic Era, a symposium sponsored by Genentech and Compaq Computer in South San Francisco, CA on April 14, 2000.
• "Informatics and Visualization Tools for Pharmacogenetics Research." Presented at 21st Century Life Science Technology Revolution, a symposium sponsored by the Whitehead Institute and HP in Cambridge, MA on June 11, 2002.
• "The Chimera Collaboratory." Presented at Data and Collaboratories in the Biomedical Community, a workshop sponsored by the National Center for Research Resources in Ballston, VA on September 16-18, 2002.

Recommended Web Links:

• Pacfic Symposium on Biocomputing
• In Honor of Seymour Cray
• Biorhythm Charting Service
• The Dilbert Zone
• Live Video Feed of San Francisco
• Tom Ferrin's ``Tools for Windows'' Page
• Handy References for Writing HTML Documents