Tom Ferrin, PhD

Title(s)Professor, Pharmaceutical Chemistry
SchoolSchool of Pharmacy
Address600 16th St
San Francisco CA 94158
Phone415-476-2299
ORCID ORCID Icon0000-0001-6227-0637 Additional info
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    Collapse Biography 
    Collapse Education and Training
    University of California, San FranciscoPh.D.1987 Graduate Division (Biomedical Informatics)
    University of MinnesotaB.S., Electrical Engineering and Computer Science1971Institute of Technology
    Collapse Awards and Honors
    1980Recognition by UC President David S. Saxon for the accomplishments and research conducted by CGL
    1998Academic Senate University Service Award for outstanding contributions to the UCSF data network

    Collapse Overview 
    Collapse Overview
    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.

    Collapse Research 
    Collapse Research Activities and Funding
    3D Projector for Group Visualizations of Cellular and Molecular Structures
    UCSF Strategic Initiatives N/AApr 1, 2019 - Mar 31, 2020
    Role: Principal Investigator
    Interactive 3D Analysis of Molecules and Cells in Virtual Reality
    Program for Breakthrough Biomedical Research (PBBR) N/AAug 1, 2018 - Jul 31, 2019
    Role: Principal Investigator
    ChimeraX -- Next Generation Visualization and Analysis Software for Multiscale Modeling
    NIH/NIGMS R01GM129325Jul 1, 2018 - Jun 30, 2022
    Role: Principal Investigator
    PGRN Administrative Coordination Hub
    NIH/NIGMS U24GM115370Jul 15, 2015 - Jun 30, 2020
    Role: Co-Investigator
    Pharmacogenomics of Membrane Transporters
    NIH U19GM061390Apr 1, 2000 - Jun 30, 2015
    Role: Co-Investigator
    Resource for Biocomputing Visualization and Informatics
    NIH/NIGMS P41GM103311Jul 15, 1997 - May 31, 2018
    Role: Principal Investigator
    Resource for Biocomputing, Visualization, and Informatics
    NIH/NCRR P41RR001081Jun 1, 1976 - Sep 14, 2012
    Role: Principal Investigator

    Collapse ORNG Applications 
    Collapse Featured Publications
    Collapse Academic Senate

    Collapse Bibliographic 
    Collapse Publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help. to make corrections and additions.
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    Altmetrics Details PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. MDA Generates Models of Large Multidomain Proteins. Biophysical Journal. 2015; 108(9):2097-2102. Hertig S, Goddard TD, Johnson GT, Ferrin TE. . View Publication.
    2. Improving the quality of protein similarity network clustering algorithms using the network edge weight distribution. Bioinformatics. 2011 Feb 01; 27(3):326-33. Apeltsin L, Morris JH, Babbitt PC, Ferrin TE. PMID: 21118823.
      View in: PubMed   Mentions: 13     Fields:    Translation:Cells
    3. ModBase, a database of annotated comparative protein structure models, and associated resources. Nucleic Acids Res. 2011 Jan; 39(Database issue):D465-74. Pieper U, Webb BM, Barkan DT, Schneidman-Duhovny D, Schlessinger A, Braberg H, Yang Z, Meng EC, Pettersen EF, Huang CC, Datta RS, Sampathkumar P, Madhusudhan MS, Sjölander K, Ferrin TE, Burley SK, Sali A. PMID: 21097780.
      View in: PubMed   Mentions: 136     Fields:    Translation:Cells
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