Research Summary

My research lab develops 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. We focus on unmet software needs for basic and applied biomedical research using highly trained and talented staff, with excellent interdisciplinary knowledge and specialized, state-of-the-art expertise in software engineering, computer graphics visualization, and data analysis. 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, identifying targets for drug development, designing drugs, and engineering proteins with new functions.

Research Funding

  • July 1, 2018 - June 30, 2022 - ChimeraX -- Next Generation Visualization and Analysis Software for Multiscale Modeling, Principal Investigator. Sponsor: NIH/NIGMS, Sponsor Award ID: R01GM129325
  • July 15, 2015 - June 30, 2020 - PGRN Administrative Coordination Hub, Co-Investigator. Sponsor: NIH/NIGMS, Sponsor Award ID: U24GM115370
  • April 1, 2019 - March 31, 2020 - 3D Projector for Group Visualizations of Cellular and Molecular Structures, Principal Investigator. Sponsor: UCSF Strategic Initiatives, Sponsor Award ID: N/A
  • August 1, 2018 - July 31, 2019 - Interactive 3D Analysis of Molecules and Cells in Virtual Reality, Principal Investigator. Sponsor: Program for Breakthrough Biomedical Research (PBBR), Sponsor Award ID: N/A

Education

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

Honors & Awards

  • Academic Senate University Service Award for outstanding contributions to the UCSF data network, 1998
  • Recognition by UC President David S. Saxon for the accomplishments and research conducted by CGL, 1980

Selected Publications

  1. Pettersen EF, Goddard TD, Huang CC, Meng EC, Couch GS, Croll TI, Morris JH, Ferrin TE. UCSF ChimeraX: Structure visualization for researchers, educators, and developers. Protein Sci. 2021 01; 30(1):70-82.  View on PubMed
  2. Dean D, Ziklo N, Somboonna N, Suh JH, Ferrin T. Reply to Rockey et al., "Genomics and Chlamydial Persistence In Vivo". mBio. 2019 12 17; 10(6).  View on PubMed
  3. Berman HM, Adams PD, Bonvin AA, Burley SK, Carragher B, Chiu W, DiMaio F, Ferrin TE, Gabanyi MJ, Goddard TD, Griffin PR, Haas J, Hanke CA, Hoch JC, Hummer G, Kurisu G, Lawson CL, Leitner A, Markley JL, Meiler J, Montelione GT, Phillips GN, Prisner T, Rappsilber J, Schriemer DC, Schwede T, Seidel CAM, Strutzenberg TS, Svergun DI, Tajkhorshid E, Trewhella J, Vallat B, Velankar S, Vuister GW, Webb B, Westbrook JD, White KL, Sali A. Federating Structural Models and Data: Outcomes from A Workshop on Archiving Integrative Structures. Structure. 2019 12 03; 27(12):1745-1759.  View on PubMed
  4. Somboonna N, Ziklo N, Ferrin TE, Hyuk Suh J, Dean D. Clinical Persistence of Chlamydia trachomatis Sexually Transmitted Strains Involves Novel Mutations in the Functional αββα Tetramer of the Tryptophan Synthase Operon. mBio. 2019 07 16; 10(4).  View on PubMed
  5. Goddard TD, Brilliant AA, Skillman TL, Vergenz S, Tyrwhitt-Drake J, Meng EC, Ferrin TE. Molecular Visualization on the Holodeck. J Mol Biol. 2018 10 19; 430(21):3982-3996.  View on PubMed
  6. 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. Actin-based protrusions of migrating neutrophils are intrinsically lamellar and facilitate direction changes. Elife. 2017 09 26; 6.  View on PubMed
  7. Goddard TD, Huang CC, Meng EC, Pettersen EF, Couch GS, Morris JH, Ferrin TE. UCSF ChimeraX: Meeting modern challenges in visualization and analysis. Protein Sci. 2018 01; 27(1):14-25.  View on PubMed
  8. Knutson ST, Westwood BM, Leuthaeuser JB, Turner BE, Nguyendac D, Shea G, Kumar K, Hayden JD, Harper AF, Brown SD, Morris JH, Ferrin TE, Babbitt PC, Fetrow JS. An approach to functionally relevant clustering of the protein universe: Active site profile-based clustering of protein structures and sequences. Protein Sci. 2017 04; 26(4):677-699.  View on PubMed
  9. Harper AF, Leuthaeuser JB, Babbitt PC, Morris JH, Ferrin TE, Poole LB, Fetrow JS. An Atlas of Peroxiredoxins Created Using an Active Site Profile-Based Approach to Functionally Relevant Clustering of Proteins. PLoS Comput Biol. 2017 02; 13(2):e1005284.  View on PubMed
  10. Holliday GL, Brown SD, Akiva E, Mischel D, Hicks MA, Morris JH, Huang CC, Meng EC, Pegg SC, Ferrin TE, Babbitt PC. Biocuration in the structure-function linkage database: the anatomy of a superfamily. Database (Oxford). 2017 01 01; 2017(1).  View on PubMed
  11. Holliday GL, Brown SD, Akiva E, Mischel D, Hicks MA, Morris JH, Huang CC, Meng EC, Pegg SC, Ferrin TE, Babbitt PC. Biocuration in the structure-function linkage database: the anatomy of a superfamily. Database (Oxford). 2017 Jan 01; 2017.  View on PubMed
  12. Leuthaeuser JB, Morris JH, Harper AF, Ferrin TE, Babbitt PC, Fetrow JS. DASP3: identification of protein sequences belonging to functionally relevant groups. BMC Bioinformatics. 2016 Nov 11; 17(1):458.  View on PubMed
  13. Chhibber A, French CE, Yee SW, Gamazon ER, Theusch E, Qin X, Webb A, Papp AC, Wang A, Simmons CQ, Konkashbaev A, Chaudhry AS, Mitchel K, Stryke D, Ferrin TE, Weiss ST, Kroetz DL, Sadee W, Nickerson DA, Krauss RM, George AL, Schuetz EG, Medina MW, Cox NJ, Scherer SE, Giacomini KM, Brenner SE. Transcriptomic variation of pharmacogenes in multiple human tissues and lymphoblastoid cell lines. Pharmacogenomics J. 2017 03; 17(2):137-145.  View on PubMed
  14. Morris JH, Vijay D, Federowicz S, Pico AR, Ferrin TE. CyAnimator: Simple Animations of Cytoscape Networks. F1000Res. 2015; 4:482.  View on PubMed
  15. Sali A, Berman HM, Schwede T, Trewhella J, Kleywegt G, Burley SK, Markley J, Nakamura H, Adams P, Bonvin AM, Chiu W, Peraro MD, Di Maio F, Ferrin TE, Grünewald K, Gutmanas A, Henderson R, Hummer G, Iwasaki K, Johnson G, Lawson CL, Meiler J, Marti-Renom MA, Montelione GT, Nilges M, Nussinov R, Patwardhan A, Rappsilber J, Read RJ, Saibil H, Schröder GF, Schwieters CD, Seidel CA, Svergun D, Topf M, Ulrich EL, Velankar S, Westbrook JD. Outcome of the First wwPDB Hybrid/Integrative Methods Task Force Workshop. Structure. 2015 Jul 07; 23(7):1156-67.  View on PubMed
  16. Hertig S, Goddard TD, Johnson GT, Ferrin TE. MDA Generates Models of Large Multidomain Proteins. Biophysical Journal. 2015; 108(9):2097-2102.  View on PubMed
  17. Hertig S, Goddard TD, Johnson GT, Ferrin TE. Multidomain Assembler (MDA) Generates Models of Large Multidomain Proteins. Biophys J. 2015 May 05; 108(9):2097-102.  View on PubMed
  18. Chen JE, Huang CC, Ferrin TE. RRDistMaps: a UCSF Chimera tool for viewing and comparing protein distance maps. Bioinformatics. 2015 May 01; 31(9):1484-6.  View on PubMed
  19. Morris JH, Wu A, Yamashita RA, Marchler-Bauer A, Ferrin TE. cddApp: a Cytoscape app for accessing the NCBI conserved domain database. Bioinformatics. 2015 Jan 01; 31(1):134-6.  View on PubMed
  20. Morris JH, Kuchinsky A, Ferrin TE, Pico AR. enhancedGraphics: a Cytoscape app for enhanced node graphics. F1000Res. 2014; 3:147.  View on PubMed

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