Thomas E. Ferrin, PhD

University of Minnesota, B.S., 1971
University of California San Francisco, Ph.D., 1986, Med. Info. Science

• 1970-71
  Engineering Assistant, Biophysics Group, University of Minnesota
• 1972-76
  Development Engineer, Cardiovascular Research Institute, UCSF
• 1976-86
  Computer Facilities Manager, Computer Graphics Laboratory, UCSF
• 1977-87
  Lecturer, School of Pharmacy, UCSF
• 1986-93
  Director of Computing, Computer Graphics Laboratory, UCSF
• 1987-89
  Adjunct Associate Professor, School of Pharmacy, UCSF
• 1989-93
  Adjunct Professor, School of Pharmacy, UCSF
• 1993-present
  Professor In-Residence, School of Pharmacy, and Director, Computer Graphics Laboratory, UCSF

• R. Langridge, E. C. Jorgensen, T. E. Ferrin, M. J. Pensak, and R. Anderson, "Interactive Three Dimensional Computer Graphics in Drug Design," ACS Symposium on Computer Assisted Drug Design, Am. Chem. Soc., 1979.
• T. E. Ferrin and R. Langridge, "Interactive Computer Graphics in Molecular Modeling and Drug Design," Computer Graphics Techniques (SIGGRAPH), (Science Film Exposition), Assoc. Comput. Machinery, 1979.
• T. E. Ferrin and R. Langridge, "Interactive Computer Graphics with the UNIX Time-Sharing System," Computer Graphics, 13(4):320-331, 1980.
• T. E. Ferrin and R. Langridge, "Interactive Molecular Graphics," Computer Graphics (SIGGRAPH), (Science Film Exposition), Assoc. Comput. Machinery, 1980.
• R. Langridge, T. E. Ferrin, I. D. Kuntz, and M. L. Connolly, "Real Time Color Graphics in Studies of Molecular Interactions," Science, 211:661-666, 1981.
• J. M. Blaney, E. C. Jorgensen, M. L. Connolly, T. E. Ferrin, R. Langridge, S. J. Oatley, J. M. Burridge, and C. F. Blake, "Computer Graphics in Drug Design: Molecular Modeling of Thyroid Hormone-Prealbumin Interactions," J. Med. Chem., 25:785-790, 1982.
• I. D. Kuntz, J. M. Blaney, S. J. Oatley, R. Langridge, and T. E. Ferrin, "A geometric approach to macromolecular-ligand interactions," J. Mol. Biol., 161:269-288, 1982.
• P. A. Bash, N. Pattabiraman, C. C. Huang, T. E. Ferrin, and R. Langridge, "Van der Walls Surfaces in Molecular Modeling: Implementation with Real-Time Computer Graphics," Science, 222:1325-1327, 1983.
• T. E. Klein, D. Kneller, C. C. Huang, T. E. Ferrin, and R. Langridge, "Computer Graphics and Artificial Intelligence in Drug Design," J. Mol. Graphics, 3(3):111-113, 1985.
• N. Pattabiraman, M. Levitt, T. E. Ferrin, and R. Langridge, "Computer Graphics in Real-Time Docking with Energy Calculation and Minimization," J. Comp. Chem., 6:432-436, 1985.
• T. E. Klein, C. C. Huang, T. E. Ferrin, R. Langridge, and C. Hansch, "Computer Assisted Drug Receptor Mapping Analysis," in: Artificial Intelligence in Chemistry, B. Hohne and T. Pierce, eds., vol. 306. p. 147-158, Am. Chem. Soc., 1986.
• T. E. Klein, C. C. Huang, T. E. Ferrin, C. Hansch, and R. Langridge, "KARMA: A Knowledge-Based System for Receptor Mapping," J. Mol. Graphics, 4(4):229, 1986.
• T. E. Ferrin and R. Langridge, "The UCSF Computer Graphics Laboratory," in: Current Communications in Molecular Biology: Computer Graphics and Molecular Modeling, R. Fletterick and M. Zoller, eds., p. 21-26, Cold Spring Harbor Laboratory, 1986.
• T. E. Ferrin, C. C. Huang, L. E. Jarvis, and R. Langridge, "The MIDAS Database System," J. Mol. Graphics, 6(1):2-12, 1988.
• T. E. Ferrin, C. C. Huang, L. E. Jarvis, and R. Langridge, "The MIDAS Display System," J. Mol. Graphics, 6(1):13-27, 36-37, 1988. The MidasPlus software package is licensed by the Regents of the University of California. For additional information see http://www.cgl.ucsf.edu/midasplus.html.
• 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, 26- 27, 1990.
• C. C. Huang, T. E. Klein, J. H. Morris, T. E. Ferrin, and R. Langridge, "The Macromolecular Workbench and its Applications to the Study of Collagen," in: Proc. 24th Hawaii International Conference on System Sciences, V. Milutinovic and B. Shriver, eds., vol. 1. (Architecture and Emerging Technologies Track), p. 636-643, IEEE Computer Society Press, Los Alamitos, CA, 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):27-32,37-38, 1991.
• E. Heimstad, O. Edvardsen, T. E. Ferrin, and S. F. Dahl, "Molecular Structure and Dynamics of Tricyclic Antidepressant Drugs," J. European Neuropsychopharmacology, 1:127-137, 1991.
• 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, 242, 1991.
• R. A. Lewis, D. C. 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.
• 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. W. Chu, A. F. Cardenas, and R. K. Taira, eds., p. 29- 33, National Science Foundation, 1993.
• G. S. Couch, E. F. Pettersen, C. C. Huang, and T. E. Ferrin, "Annotating PDB Files with Scene Information," J. Mol. Graphics, 13(3):153-158, 1995.
• C. C. Huang, G. S. Couch, E. F. Pettersen, and T. E. Ferrin, "Chimera: An Extensible Molecular Modeling Application Constructed Using Standard Components," in: Pacific Symposium on Biocomputing '96, L. Hunter and T. E. Klein, eds., p. 724, World Scientific Publishing, Singapore, 1996.
• T. E. Ferrin and T. E. Klein, "Computer graphics and molecular modelling," in: Encyclopedia of Computational Chemistry, P. V. R. Schleyer, ed., John Wiley & Sons, (in press).
• C. C. Huang, G. S. Couch, E. F. Pettersen, T. E. Ferrin, A. E. Howard, and T. E. Klein, "The object technology framework: An object-oriented interface to molecular data and its application to collagen," in: Pacific Symposium on Biocomputing '98, L. Hunter and T. E. Klein, eds., World Scientific Publishing, Singapore, 1998. The source code and documentation for the software described in this paper is available via the World-Wide Web at http://www.cgl.ucsf.edu/home/otf/.