Resource for Biocomputing, Visualization, and Informatics (RBVI)
University of California, M/S 2240
600 16th Street, Rm N472
San Francisco, CA 94158-2517
Email: tef [at] cgl.ucsf.edu
Assistant: JoAnne Williams
Joanne.Williams [at] ucsf.edu
- 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
Bioengineering & Therapeutic Sciences, UCSF
- Past Chair, UCSF Biological and Medical Informatics Graduate Program
- Member, UCSF/UCB Bioengineering Graduate Program
- Member, UCSF Biophysics Graduate Program
- Member, UCSF Chemistry and Chemical Biology Graduate Program
- Member, UCSF Pharmaceutical Sciences and Pharmacogenomics Graduate Program
- Member, California Institute for Quantitative Biosciences (QB3)
- Member, UCSF Comprehensive Cancer Center
- Member, External Scientific Panel, NIH BioAssay Research Database
See my UCSF Profiles link.
My research focuses on developing software tools and advanced web-based
resources for the visualization and analysis of molecular structure
at scales ranging from the atomic to the supramolecular. We create
tools for handling and integrating diverse types of biomolecular data,
including atomic-resolution coordinates, density maps, sequences,
annotations, and networks. Our primary efforts are in the visualization
and analysis of structures of molecules and molecular assemblies, enzyme
sequence-structure-function relationships, and network representations of
protein similarity, binding interactions, and biological pathways. We
provide technologies to enable identifying the molecular bases of
disease and phenotypic variation, annotating proteins of unknown
function, identifying targets for drug development, designing drugs, and
engineering proteins with new functions. We have a strong track record of
creating well-documented robust software tools and disseminating these
in open-source form via our NIH-funded Biomedical Technology Research
Resource web site (www.rbvi.ucsf.edu)
so that other scientists can advance their own research programs effectively.
- UCSF Chimera--a visualization system for exploratory research and analysis. Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC, Ferrin TE. J Comput Chem, 2004 Oct, 25(13):1605-12. PMID: 15264254
(Highly-cited in the literature! See list here)
- Software extensions to UCSF chimera for interactive visualization of large molecular assemblies. Goddard TD, Huang CC, Ferrin TE. Structure, 2005 Mar, 13(3):473-82. PMID: 15766548
- Designed divergent evolution of enzyme function. Yoshikuni Y, Ferrin TE, Keasling JD. Nature, 2006 Apr 20, 440(7087):1078-82. PMID: 16495946
- Tools for integrated sequence-structure analysis with UCSF Chimera. Meng EC, Pettersen EF, Couch GS, Huang CC, Ferrin TE. BMC Bioinformatics, 2006 Jul 12, 7:339. PMID: 16836757 PMCID: PMC1570152
- Visualizing density maps with UCSF Chimera. Goddard TD, Huang CC, Ferrin TE. J Struct Biol, 2007 Jan, 157(1):281-7. PMID: 16963278
- structureViz: linking Cytoscape and UCSF Chimera. Morris JH, Huang CC, Babbitt PC, Ferrin TE. Bioinformatics, 2007 Sep 1, 23(17):2345-7. PMID: 17623706
- Visualization software for molecular assemblies. Goddard TD, Ferrin TE. Curr Opin Struct Biol, 2007 Oct, 17(5):587-95. PMID: 17728125 PMCID: PMC2174518
- Using sequence similarity networks for visualization of relationships across diverse protein superfamilies. Atkinson HJ, Morris JH, Ferrin TE, Babbitt PC. PLoS One, 2009, 4(2):e4345. PMID: 19190775 PMCID: PMC2631154
- Computational tools for the interactive exploration of proteomic and structural data. Morris JH, Meng EC, Ferrin TE. Mol Cell Proteomics, 2010 Aug, 9(8):1703-15. PMID: 20525940 PMCID: PMC2938059
- Improving the quality of protein similarity network clustering algorithms using the network edge weight distribution. Apeltsin L, Morris JH, Babbitt PC, Ferrin TE. Bioinformatics, 2011 Feb 1, 27(3):326-33. PMID: 21118823 PMCID: PMC3031030
- clusterMaker: a multi-algorithm clustering plugin for Cytoscape. Morris JH, Apeltsin L, Newman AM, Baumbach J, Wittkop T, Su G, Bader GD, Ferrin TE. BMC Bioinformatics, 2011 Nov 9, 12:436. PMID: 22070249 PMCID: PMC3262844
- UCSF Chimera, MODELLER, and IMP: an integrated modeling system. Yang Z, Lasker K, Schneidman-Duhovny D, Webb B, Huang CC, Pettersen EF, Goddard TD, Meng EC, Sali A, Ferrin TE. J Struct Biol, 2012 Sep, 179(3):269-78. PMID: 21963794 PMCID: PMC3410985
- The Structure-Function Linkage Database. Akiva E, Brown S, Almonacid DE, Barber AE 2nd, Custer AF, Hicks MA, Huang CC, Lauck F, Mashiyama ST, Meng EC, Mischel D, Morris JH, Ojha S, Schnoes AM, Stryke D, Yunes JM, Ferrin TE, Holliday GL, Babbitt PC. Nucleic Acids Res, 2014 Jan, 42(Database issue):D521-30. PMID: 24271399 PMCID: PMC3965090
- Enhancing UCSF Chimera through web services. Huang CC, Meng EC, Morris JH, Pettersen EF, Ferrin TE. Nucleic Acids Res, 2014 Jul, 42(Web Server issue):W478-84. PMID: 24861624 PMCID: PMC4086125
- RRDistMaps: a UCSF Chimera tool for viewing and comparing protein distance maps. Chen JE, Huang CC, Ferrin TE. Bioinformatics, 2015 May 1, 31(9):1484-6. PMID: 25540183 PMCID: PMC4410660
- Multidomain Assembler (MDA) Generates Models of Large Multidomain Proteins. Hertig S, Goddard TD, Johnson GT, Ferrin TE. Biophys J, 2015 May 5, 108(9):2097-102. PMID: 25954868 PMCID: PMC4423039
PubMed search of
all publications authored by T.E. Ferrin,
or do the
same using Google Scholar.
Some Invited Lectures and Seminars:
"Modeling GroEL" An 'Inside the Image' interview by Apple's Nancy Eaton, February 2007.
A Conversation with Tom Ferrin, PhD" A 'Science Café' interview
by UCSF's Jeff Miller, August 10, 2007.
Also available as a podcast.
"Future Lab: 3D Molecular Visualization" A podcast interview by Deirdre Kennedy, May 31, 2011.
"Using 3D Interactive Graphics to Guide Drug Development."
Presented at the 'Unusual Thinkers' track of the Dreamforce 2012 conference, September 20, 2012.
"Visualization Tools for Interactive Modeling of Biological Structures at Multiple Scales."
Presented at the VIZBI 2013 conference, March 21, 2013.
From Long Ago:
- My UNIX kernel hacking days (circa late 70's and early 80's):
Our Unix Version 6 License from Western Electric Co.
The Daemon, the GNU, and the Penguin: A History of Free and Open Source
BSD and the CSRG
CSRG Members, Supporters, and Contributors
Interactive computer graphics with the UNIX time-sharing system
Modifying the PDP-11/70 mfpi instruction hardware
and the Letter reprinted from ;login:
that raised a few eyebrows
Heuristics for Disk Drive Positioning in 4.3BSD
25th Anniversary UNIX Playing Cards
- The early days of molecular graphics (mid 1970's):
- The first interactive color display of molecules
- My drag racing days (late 60's):
- Ky Michaelson's AA/GD dragsters [picture]
The Snow Dragster
Hydrogen Peroxide Rocket Dragsters
Other Fun or Interesting Links: