Contact Information:
Resource for Biocomputing, Visualization, and Informatics (RBVI)
University of California, Box 2240
600 16th Street, Rm N472E
San Francisco, CA 94143
Email: tef [at] cgl.ucsf.edu
RBVI Executive Director: Scooter Morris
scooter [at] cgl.ucsf.edu
Education/Affiliations:
- B.Sc. University of Minnesota,
Electrical Engineering and Computer Science, 1971
- Ph.D. University of California, San Francisco,
Biomedical Informatics, 1986
- Professor Emeritus, Departments of
Pharmaceutical Chemistry and
Bioengineering & Therapeutic Sciences, UCSF
- Member, UCSF Quantitative Biosciences Institute (QBI)
- Member, Advisory Committee, RCSB Protein Data Bank
- Past Chair, UCSF Biological and Medical Informatics Graduate Program
Research Interests:
My research focuses on developing cutting-edge interactive software
tools and advanced web-based computational resources that provide
integrated visualization and analyses of molecular structures and
related non-structural biological information. Our tools are applied daily
to diverse types of biomolecular data, including atomic-resolution
coordinates, 3D cryo-EM and X-ray density maps, light microscopy data sets,
and protein and nucleic acid sequences, annotations, and networks.
Our primary research efforts are in the interactive visualization and analysis
of structures of molecules and molecular assemblies, protein sequence-structure
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
new drugs, and engineering proteins with new functions. For many years
we have been disseminating well-documented and robust software tools
via our web site, https://www.rbvi.ucsf.edu,
so that scientists world-wide can advance their own research programs effectively.
Our current software development efforts are focused on
ChimeraX,
our next-generation desktop app for the interactive visualization
and analysis of molecular structures and related data.
Potential students and postdocs please note: I moved to emertius status
in July 2019 and am no longer taking any new students or postdocs into my lab.
Our still very-active research program is now exclusively built around
a team of dedicated full-time professional research scientists.
We welcome creative contributions to our projects,
which you can do through the addition of new "plug-in" tools
to our ChimeraX visualization application; please see
ChimeraX Toolshed.
Also note that all the software we develop is available in our GitHub source code repository at
https://github.com/RBVI.
Also see my UCSF Profiles page.
Awards:
I've received several awards over the years, but because of the broad and significant
impact my work has had on my many UCSF colleagues, feel most honored by this 1998
Academic Senate University Service Award
that acknowledges the contributions I made to the early development and implementation
of the UCSF data network, including implementing a 56 kbps link to the ARPAnet in 1982
and the founding (together with colleagues from other local Bay Area universities) of
BARRNet
in 1986 that linked UCSF to NSFnet, the precursor to today's Internet.
Selected Publications:
- Real-time color graphics in studies of molecular interactions. Langridge R, Ferrin TE, Kuntz ID, Connolly ML. Science, 1981, 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, 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, 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, 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, 7:339. PMID: 16836757 PMCID: 1570152
- Visualizing density maps with UCSF Chimera. Goddard TD, Huang CC, Ferrin TE. J Struct Biol, 2007, 157(1):281-7. PMID: 16963278
- structureViz: linking Cytoscape and UCSF Chimera. Morris JH, Huang CC, Babbitt PC, Ferrin TE. Bioinformatics, 2007, 23(17):2345-7. PMID: 17623706
- Visualization software for molecular assemblies. Goddard TD, Ferrin TE. Curr Opin Struct Biol, 2007, 17(5):587-95. PMID: 17728125 PMCID: 2174518
- 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, 12:436. PMID: 22070249 PMCID: 3262844
- 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, 179(3):269-78. PMID: 21963794 PMCID: 3410985
- The Structure-Function Linkage Database. Akiva E, Brown S, Almonacid DE, Barber AE, 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, 42(Database issue):D521-30. PMID: 24271399 PMCID: 3965090
- Enhancing UCSF Chimera through web services. Huang CC, Meng EC, Morris JH, Pettersen EF, Ferrin TE. Nucleic Acids Res, 2014, 42(Web Server issue):W478-84. PMID: 24861624 PMCID: 4086125
- Multidomain Assembler (MDA) Generates Models of Large Multidomain Proteins. Hertig S, Goddard TD, Johnson GT, Ferrin TE. Biophys J, 2015, 108(9):2097-102. PMID: 25954868 PMCID: 4423039
- 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, 2017(1)None. PMID: 28365730 PMCID: 5467563
- Actin-based protrusions of migrating neutrophils are intrinsically lamellar and facilitate direction changes. Fritz-Laylin LK, Riel-Mehan M, Chen BC, Lord SJ, Goddard TD, Ferrin TE, Nicholson-Dykstra SM, Higgs H, Johnson GT, Betzig E, Mullins RD. Elife, 2017, 6None. PMID: 28948912 PMCID: 5614560
- 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, 27(1):14-25. PMID: 28710774 PMCID: 5734306
- Molecular Visualization on the Holodeck. Goddard TD, Brilliant AA, Skillman TL, Vergenz S, Tyrwhitt-Drake J, Meng EC, Ferrin TE. J Mol Biol, 2018, 430(21):3982-3996. PMID: 29964044 PMCID: 6223615
- UCSF ChimeraX: Structure visualization for researchers, educators, and developers. Pettersen EF, Goddard TD, Huang CC, Meng EC, Couch GS, Croll TI, Morris JH, Ferrin TE. Protein Sci, 2021, 30(1):70-82. PMID: 32881101 PMCID: 7737788
(A top cited article in Protein Science. See list here.)
- UCSF ChimeraX: Tools for structure building and analysis. Meng EC, Goddard TD, Pettersen EF, Couch GS, Pearson ZJ, Morris JH, Ferrin TE. Protein Sci, 2023, 32(11):e4792. PMID: 37774136 PMCID: 10588335
- IHMCIF: An Extension of the PDBx/mmCIF Data Standard for Integrative Structure Determination Methods. Vallat B, Webb BM, Westbrook JD, Goddard TD, Hanke CA, Graziadei A, Peisach E, Zalevsky A, Sagendorf J, Tangmunarunkit H, Voinea S, Sekharan M, Yu J, Bonvin AAMJJ, DiMaio F, Hummer G, Meiler J, Tajkhorshid E, Ferrin TE, Lawson CL, Leitner A, Rappsilber J, Seidel CAM, Jeffries CM, Burley SK, Hoch JC, Kurisu G, Morris K, Patwardhan A, Velankar S, Schwede T, Trewhella J, Kesselman C, Berman HM, Sali A. J Mol Biol, 2024, 168546. PMID: 38508301
PubMed search of
all publications authored by T.E. Ferrin,
or view my
Google Scholar
or
Web of Science profiles.
Some Invited Lectures and Seminars:
From Long, Long Ago:
- Molecular graphics for visualizing proteins and drugs (1980):
- The Computer Revolution in Biomedical Science
- Interactive Molecular Graphics (archival video, 13:39 minutes -- no audio track)
- My UNIX kernel-hacking days (late 70's / early 80's) --
Adding interactive graphics capabilities to Bell Lab's UNIX:
-
Interactive Computer Graphics and the UNIX Time-Sharing System (1979)
Picture System 2 Graphics Subroutine Package (ps2gsp)
Modifying PDP-11/70 hardware instructions
and the Letter reprinted from ;login: that raised a few eyebrows (1978)
CGL's Version 6 Unix
License from Western Electric (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)]
Snow Dragsters
Hydrogen Peroxide Rocket Dragsters