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,
Biomedical Informatics, 1986
- Professor, Departments of
Pharmaceutical Chemistry and
Bioengineering & Therapeutic Sciences, UCSF
- Past Chair, UCSF Biological and Medical Informatics Graduate Program
- Member, California Institute for Quantitative Biosciences (QB3)
- Member, UCSF Biophysics Graduate Program
- Member, UCSF/UCB Bioengineering Graduate Program
- Member, UCSF Pharmaceutical Sciences and Pharmacogenomics Graduate Program
- Member, UCSF Chemistry and Chemical Biology Graduate Program
- Member, UCSF Comprehensive Cancer Center
My research focuses on developing cutting-edge interactive software
tools and advanced web-based computational resources that provide
integrated visualizations and analyses of molecular structures and
related non-structural biological information. Our tools can be applied
to diverse types of biomolecular data, including atomic-resolution
coordinates, 3D density maps and light microscopy data, and protein and
nucleic acid sequences, annotations, and networks. Our primary efforts
are in the interactive visualization and analysis of structures of
molecules and molecular assemblies, protein sequence-structure-function
relationships, and network representations of protein similarity,
binding interactions, and biological pathways. These areas are critical
for addressing important and highly relevant biomedical problems such
as identifying the molecular bases of disease, 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 via our web site
so that other scientists can advance their own research programs effectively.
Also see my UCSF Profiles page.
- Real-time color graphics in studies of molecular interactions. Langridge R, Ferrin TE, Kuntz ID, Connolly ML. Science, 1981 Feb 13, 211(4483):661-6. PMID: 7455704
- A geometric approach to macromolecule-ligand interactions. Kuntz ID, Blaney JM, Oatley SJ, Langridge R, Ferrin TE. J Mol Biol, 1982 Oct 25, 161(2):269-88. PMID: 7154081
- 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
- 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
- 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
- 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
- Biocuration in the structure-function linkage database: the anatomy of a superfamily. Holliday GL, Brown SD, Akiva E, Mischel D, Hicks MA, Morris JH, Huang CC, Meng EC, Pegg SC, Ferrin TE, Babbitt PC. Database (Oxford), 2017 Jan 1, 2017(1). PMID: 28365730 PMCID: PMC5467563
- Actin-based Protrusions
of Migrating Neutrophils are Intrinsically Lamellar and Facilitate Direction Changes.
Lillian K Fritz-Laylin, Megan Riel-Mehan, Bi-Chang Chen, Samuel J Lord, Thomas D Goddard, Thomas E Ferrin, Graham Johnson, Eric Betzig, R. Dyche Mullins,
eLife, Sept 26, 2017.
- UCSF ChimeraX: Meeting modern challenges in visualization and analysis. Goddard TD, Huang CC, Meng EC, Pettersen EF, Couch GS, Morris JH, Ferrin TE. Protein Sci, 2018 Jan, 27(1):14-25. PMID: 28710774 PMCID: PMC5734306
- Molecular Visualization on the Holodeck. Goddard TD, Brilliant AA, Skillman TL, Vergenz S, Tyrwhitt-Drake J, Meng EC, Ferrin TE. J Mol Biol, 2018 Oct 19, 430(21):3982-3996. PMID: 29964044 PMCID: PMC6223615
PubMed search of
all publications authored by T.E. Ferrin,
or view my
Google Scholar Profile.
Some Invited Lectures and Seminars:
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 2012.
"Visualization Tools for Interactive Modeling of Biological Structures at Multiple Scales."
Presented at the VIZBI 2013 conference, March 2013.
"Visualization and Analysis Challenges of Large Biomolecular Complexes"
presented at Molecular Machines:
Integrative Structural and Molecular Biology, Heidelberg, Germany, November 2016.
From Long Long Ago:
- Molecular graphics for visualizing proteins and drugs (1980):
- The Computer Revolution in Biomedical Science
- Interactive Molecular Graphics (video, 13:39 minutes -- no audio track)
- My UNIX kernel-hacking days (late 70's / early 80's) -- Adding interactive graphics to UNIX:
Interactive Computer Graphics and the UNIX Time-Sharing System (1979)
Picture System 2 Graphics Subroutine Package (ps2gsp)
Changing PDP-11/70 hardware instructions
and the Letter reprinted from ;login: that raised a few eyebrows (1978)
Our Unix Version 6 License from Western Electric Co. (1976)
Twenty Years of Berkeley Unix by Marshall Kirk McKusick
The Daemon, the GNU, and the Penguin: A History of Free and Open Source by Dr. Peter H. Salus
BSD and the Computer Systems Research Group (CSRG)
CSRG Members, Supporters, and Contributors
- Young and (maybe a little) Reckless -- My drag racing days (late 60's):
- Ky Michaelson's AA/GD dragsters [picture (1970)]
The Snow Dragster
Hydrogen Peroxide Rocket Dragsters
Other Fun / Interesting Links: