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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, annotating proteins of unknown function, identifying targets for drug development, designing drugs, and engineering proteins with new functions.

    I'm also the director of the Resource for Biocomputing, Visualization, and Informatics, an NIH Biomedical Technology Research Resource.

    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 Websites
    Collapse In The News
    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.
    Newest   |   Oldest   |   Most Cited   |   Most Discussed   |   Timeline   |   Field Summary   |   Plain Text
    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. UCSF ChimeraX: Structure Visualization for Researchers, Educators, and Developers. Protein Sci. 2020 Sep 03. Pettersen EF, Goddard TD, Huang CC, Meng EC, Couch GS, Croll TI, Morris JH, Ferrin TE. PMID: 32881101.
      View in: PubMed   Mentions:    Fields:    
    2. Reply to Rockey et al., "Genomics and Chlamydial Persistence In Vivo". mBio. 2019 12 17; 10(6). Dean D, Ziklo N, Somboonna N, Suh JH, Ferrin T. PMID: 31848290.
      View in: PubMed   Mentions:    Fields:    Translation:Cells
    3. Federating Structural Models and Data: Outcomes from A Workshop on Archiving Integrative Structures. Structure. 2019 12 03; 27(12):1745-1759. 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. PMID: 31780431.
      View in: PubMed   Mentions: 3     Fields:    Translation:Cells
    4. Clinical Persistence of Chlamydia trachomatis Sexually Transmitted Strains Involves Novel Mutations in the Functional aßßa Tetramer of the Tryptophan Synthase Operon. mBio. 2019 07 16; 10(4). Somboonna N, Ziklo N, Ferrin TE, Hyuk Suh J, Dean D. PMID: 31311884.
      View in: PubMed   Mentions:    Fields:    Translation:HumansCells
    5. Molecular Visualization on the Holodeck. J Mol Biol. 2018 10 19; 430(21):3982-3996. Goddard TD, Brilliant AA, Skillman TL, Vergenz S, Tyrwhitt-Drake J, Meng EC, Ferrin TE. PMID: 29964044.
      View in: PubMed   Mentions: 4     Fields:    Translation:HumansAnimalsCells
    6. Actin-based protrusions of migrating neutrophils are intrinsically lamellar and facilitate direction changes. Elife. 2017 09 26; 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. PMID: 28948912.
      View in: PubMed   Mentions: 12     Fields:    Translation:HumansCells
    7. UCSF ChimeraX: Meeting modern challenges in visualization and analysis. Protein Sci. 2018 01; 27(1):14-25. Goddard TD, Huang CC, Meng EC, Pettersen EF, Couch GS, Morris JH, Ferrin TE. PMID: 28710774.
      View in: PubMed   Mentions: 158     Fields:    Translation:Cells
    8. 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. 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. PMID: 28054422.
      View in: PubMed   Mentions: 3     Fields:    
    9. 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. Harper AF, Leuthaeuser JB, Babbitt PC, Morris JH, Ferrin TE, Poole LB, Fetrow JS. PMID: 28187133.
      View in: PubMed   Mentions: 4     Fields:    Translation:Cells
    10. Biocuration in the structure-function linkage database: the anatomy of a superfamily. Database (Oxford). 2017 01 01; 2017(1). Holliday GL, Brown SD, Akiva E, Mischel D, Hicks MA, Morris JH, Huang CC, Meng EC, Pegg SC, Ferrin TE, Babbitt PC. PMID: 28365730.
      View in: PubMed   Mentions: 1     Fields:    Translation:Cells
    11. Biocuration in the structure-function linkage database: the anatomy of a superfamily. Database (Oxford). 2017 Jan 01; 2017. Holliday GL, Brown SD, Akiva E, Mischel D, Hicks MA, Morris JH, Huang CC, Meng EC, Pegg SC, Ferrin TE, Babbitt PC. PMID: 28605775.
      View in: PubMed   Mentions: 1     Fields:    
    12. DASP3: identification of protein sequences belonging to functionally relevant groups. BMC Bioinformatics. 2016 Nov 11; 17(1):458. Leuthaeuser JB, Morris JH, Harper AF, Ferrin TE, Babbitt PC, Fetrow JS. PMID: 27835946.
      View in: PubMed   Mentions: 2     Fields:    Translation:Cells
    13. Transcriptomic variation of pharmacogenes in multiple human tissues and lymphoblastoid cell lines. Pharmacogenomics J. 2017 03; 17(2):137-145. 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. PMID: 26856248.
      View in: PubMed   Mentions: 10     Fields:    Translation:HumansCells
    14. CyAnimator: Simple Animations of Cytoscape Networks. F1000Res. 2015; 4:482. Morris JH, Vijay D, Federowicz S, Pico AR, Ferrin TE. PMID: 26937268.
      View in: PubMed   Mentions:    Fields:    
    15. Outcome of the First wwPDB Hybrid/Integrative Methods Task Force Workshop. Structure. 2015 Jul 07; 23(7):1156-67. 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. PMID: 26095030.
      View in: PubMed   Mentions: 55     Fields:    Translation:HumansCells
    16. Multidomain Assembler (MDA) Generates Models of Large Multidomain Proteins. Biophys J. 2015 May 05; 108(9):2097-102. Hertig S, Goddard TD, Johnson GT, Ferrin TE. PMID: 25954868.
      View in: PubMed   Mentions: 3     Fields:    Translation:Cells
    17. MDA Generates Models of Large Multidomain Proteins. Biophysical Journal. 2015; 108(9):2097-2102. Hertig S, Goddard TD, Johnson GT, Ferrin TE.. View Publication.
    18. RRDistMaps: a UCSF Chimera tool for viewing and comparing protein distance maps. Bioinformatics. 2015 May 01; 31(9):1484-6. Chen JE, Huang CC, Ferrin TE. PMID: 25540183.
      View in: PubMed   Mentions: 6     Fields:    Translation:Cells
    19. cddApp: a Cytoscape app for accessing the NCBI conserved domain database. Bioinformatics. 2015 Jan 01; 31(1):134-6. Morris JH, Wu A, Yamashita RA, Marchler-Bauer A, Ferrin TE. PMID: 25212755.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansCells
    20. enhancedGraphics: a Cytoscape app for enhanced node graphics. F1000Res. 2014; 3:147. Morris JH, Kuchinsky A, Ferrin TE, Pico AR. PMID: 25285206.
      View in: PubMed   Mentions: 12     Fields:    
    21. setsApp: Set operations for Cytoscape Nodes and Edges. F1000Res. 2014; 3:149. Morris JH, Wu A, Doncheva NT, Albrecht M, Ferrin TE. PMID: 25352980.
      View in: PubMed   Mentions:    Fields:    
    22. Enhancing UCSF Chimera through web services. Nucleic Acids Res. 2014 Jul; 42(Web Server issue):W478-84. Huang CC, Meng EC, Morris JH, Pettersen EF, Ferrin TE. PMID: 24861624.
      View in: PubMed   Mentions: 27     Fields:    Translation:Cells
    23. The Structure-Function Linkage Database. Nucleic Acids Res. 2014 Jan; 42(Database issue):D521-30. 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. PMID: 24271399.
      View in: PubMed   Mentions: 77     Fields:    
    24. Genetic and epigenetic regulation of the organic cation transporter 3, SLC22A3. Pharmacogenomics J. 2013 Apr; 13(2):110-20. Chen L, Hong C, Chen EC, Yee SW, Xu L, Almof EU, Wen C, Fujii K, Johns SJ, Stryke D, Ferrin TE, Simko J, Chen X, Costello JF, Giacomini KM. PMID: 22231567.
      View in: PubMed   Mentions: 19     Fields:    Translation:HumansCells
    25. Macromolecular assembly structures by comparative modeling and electron microscopy. Methods Mol Biol. 2012; 857:331-50. Lasker K, Velázquez-Muriel JA, Webb BM, Yang Z, Ferrin TE, Sali A. PMID: 22323229.
      View in: PubMed   Mentions: 3     Fields:    Translation:Cells
    26. clusterMaker: a multi-algorithm clustering plugin for Cytoscape. BMC Bioinformatics. 2011 Nov 09; 12:436. Morris JH, Apeltsin L, Newman AM, Baumbach J, Wittkop T, Su G, Bader GD, Ferrin TE. PMID: 22070249.
      View in: PubMed   Mentions: 111     Fields:    Translation:Animals
    27. A common 5'-UTR variant in MATE2-K is associated with poor response to metformin. Clin Pharmacol Ther. 2011 Nov; 90(5):674-84. Choi JH, Yee SW, Ramirez AH, Morrissey KM, Jang GH, Joski PJ, Mefford JA, Hesselson SE, Schlessinger A, Jenkins G, Castro RA, Johns SJ, Stryke D, Sali A, Ferrin TE, Witte JS, Kwok PY, Roden DM, Wilke RA, McCarty CA, Davis RL, Giacomini KM. PMID: 21956618.
      View in: PubMed   Mentions: 36     Fields:    Translation:HumansAnimalsCells
    28. UCSF Chimera, MODELLER, and IMP: an integrated modeling system. J Struct Biol. 2012 Sep; 179(3):269-78. Yang Z, Lasker K, Schneidman-Duhovny D, Webb B, Huang CC, Pettersen EF, Goddard TD, Meng EC, Sali A, Ferrin TE. PMID: 21963794.
      View in: PubMed   Mentions: 124     Fields:    Translation:AnimalsCells
    29. Functional characterization of liver enhancers that regulate drug-associated transporters. Clin Pharmacol Ther. 2011 Apr; 89(4):571-8. Kim MJ, Skewes-Cox P, Fukushima H, Hesselson S, Yee SW, Ramsey LB, Nguyen L, Eshragh JL, Castro RA, Wen CC, Stryke D, Johns SJ, Ferrin TE, Kwok PY, Relling MV, Giacomini KM, Kroetz DL, Ahituv N. PMID: 21368754.
      View in: PubMed   Mentions: 15     Fields:    Translation:HumansAnimalsCells
    30. 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
    31. 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: 128     Fields:    Translation:Cells
    32. Role of organic cation transporter 3 (SLC22A3) and its missense variants in the pharmacologic action of metformin. Pharmacogenet Genomics. 2010 Nov; 20(11):687-99. Chen L, Pawlikowski B, Schlessinger A, More SS, Stryke D, Johns SJ, Portman MA, Chen E, Ferrin TE, Sali A, Giacomini KM. PMID: 20859243.
      View in: PubMed   Mentions: 61     Fields:    Translation:Cells
    33. Workshop on molecular animation. Structure. 2010 Oct 13; 18(10):1261-5. Bromberg S, Chiu W, Ferrin TE. PMID: 20947014.
      View in: PubMed   Mentions:    Fields:    Translation:HumansCells
    34. Genetic variants of human organic anion transporter 4 demonstrate altered transport of endogenous substrates. Am J Physiol Renal Physiol. 2010 Oct; 299(4):F767-75. Shima JE, Komori T, Taylor TR, Stryke D, Kawamoto M, Johns SJ, Carlson EJ, Ferrin TE, Giacomini KM. PMID: 20668102.
      View in: PubMed   Mentions: 6     Fields:    Translation:HumansCells
    35. Computational tools for the interactive exploration of proteomic and structural data. Mol Cell Proteomics. 2010 Aug; 9(8):1703-15. Morris JH, Meng EC, Ferrin TE. PMID: 20525940.
      View in: PubMed   Mentions: 5     Fields:    Translation:HumansAnimalsCells
    36. Comparison of human solute carriers. Protein Sci. 2010 Mar; 19(3):412-28. Schlessinger A, Matsson P, Shima JE, Pieper U, Yee SW, Kelly L, Apeltsin L, Stroud RM, Ferrin TE, Giacomini KM, Sali A. PMID: 20052679.
      View in: PubMed   Mentions: 38     Fields:    Translation:HumansCells
    37. Identification and characterization of novel polymorphisms in the basal promoter of the human transporter, MATE1. Pharmacogenet Genomics. 2009 Oct; 19(10):770-80. Ha Choi J, Wah Yee S, Kim MJ, Nguyen L, Ho Lee J, Kang JO, Hesselson S, Castro RA, Stryke D, Johns SJ, Kwok PY, Ferrin TE, Goo Lee M, Black BL, Ahituv N, Giacomini KM. PMID: 19745787.
      View in: PubMed   Mentions: 18     Fields:    Translation:HumansCells
    38. Genetic variation in the proximal promoter of ABC and SLC superfamilies: liver and kidney specific expression and promoter activity predict variation. PLoS One. 2009 Sep 09; 4(9):e6942. Hesselson SE, Matsson P, Shima JE, Fukushima H, Yee SW, Kobayashi Y, Gow JM, Ha C, Ma B, Poon A, Johns SJ, Stryke D, Castro RA, Tahara H, Choi JH, Chen L, Picard N, Sjödin E, Roelofs MJ, Ferrin TE, Myers R, Kroetz DL, Kwok PY, Giacomini KM. PMID: 19742321.
      View in: PubMed   Mentions: 14     Fields:    Translation:HumansCells
    39. Using sequence similarity networks for visualization of relationships across diverse protein superfamilies. PLoS One. 2009; 4(2):e4345. Atkinson HJ, Morris JH, Ferrin TE, Babbitt PC. PMID: 19190775.
      View in: PubMed   Mentions: 142     Fields:    Translation:HumansCells
    40. Genetic variants in multidrug and toxic compound extrusion-1, hMATE1, alter transport function. Pharmacogenomics J. 2009 Apr; 9(2):127-36. Chen Y, Teranishi K, Li S, Yee SW, Hesselson S, Stryke D, Johns SJ, Ferrin TE, Kwok P, Giacomini KM. PMID: 19172157.
      View in: PubMed   Mentions: 32     Fields:    Translation:HumansCells
    41. Functional genetic variation in the basal promoter of the organic cation/carnitine transporters OCTN1 (SLC22A4) and OCTN2 (SLC22A5). J Pharmacol Exp Ther. 2009 Apr; 329(1):262-71. Tahara H, Yee SW, Urban TJ, Hesselson S, Castro RA, Kawamoto M, Stryke D, Johns SJ, Ferrin TE, Kwok PY, Giacomini KM. PMID: 19141711.
      View in: PubMed   Mentions: 15     Fields:    Translation:HumansCells
    42. Identification and characterization of proximal promoter polymorphisms in the human concentrative nucleoside transporter 2 (SLC28A2). J Pharmacol Exp Ther. 2009 Mar; 328(3):699-707. Yee SW, Shima JE, Hesselson S, Nguyen L, De Val S, Lafond RJ, Kawamoto M, Johns SJ, Stryke D, Kwok PY, Ferrin TE, Black BL, Gurwitz D, Ahituv N, Giacomini KM. PMID: 19098160.
      View in: PubMed   Mentions: 13     Fields:    Translation:HumansAnimalsCells
    43. The human multidrug resistance protein 4 (MRP4, ABCC4): functional analysis of a highly polymorphic gene. J Pharmacol Exp Ther. 2008 Jun; 325(3):859-68. Abla N, Chinn LW, Nakamura T, Liu L, Huang CC, Johns SJ, Kawamoto M, Stryke D, Taylor TR, Ferrin TE, Giacomini KM, Kroetz DL. PMID: 18364470.
      View in: PubMed   Mentions: 39     Fields:    Translation:HumansCells
    44. Functional effects of protein sequence polymorphisms in the organic cation/ergothioneine transporter OCTN1 (SLC22A4). Pharmacogenet Genomics. 2007 Sep; 17(9):773-82. Urban TJ, Yang C, Lagpacan LL, Brown C, Castro RA, Taylor TR, Huang CC, Stryke D, Johns SJ, Kawamoto M, Carlson EJ, Ferrin TE, Burchard EG, Giacomini KM. PMID: 17700366.
      View in: PubMed   Mentions: 17     Fields:    Translation:HumansCells
    45. Visualization software for molecular assemblies. Curr Opin Struct Biol. 2007 Oct; 17(5):587-95. Goddard TD, Ferrin TE. PMID: 17728125.
      View in: PubMed   Mentions: 10     Fields:    Translation:Cells
    46. Modeling insertional mutagenesis using gene length and expression in murine embryonic stem cells. PLoS One. 2007 Jul 18; 2(7):e617. Nord AS, Vranizan K, Tingley W, Zambon AC, Hanspers K, Fong LG, Hu Y, Bacchetti P, Ferrin TE, Babbitt PC, Doniger SW, Skarnes WC, Young SG, Conklin BR. PMID: 17637833.
      View in: PubMed   Mentions: 7     Fields:    Translation:AnimalsCells
    47. structureViz: linking Cytoscape and UCSF Chimera. Bioinformatics. 2007 Sep 01; 23(17):2345-7. Morris JH, Huang CC, Babbitt PC, Ferrin TE. PMID: 17623706.
      View in: PubMed   Mentions: 19     Fields:    Translation:Cells
    48. Comparison of methods for genomic localization of gene trap sequences. BMC Genomics. 2006 Sep 18; 7:236. Harper CA, Huang CC, Stryke D, Kawamoto M, Ferrin TE, Babbitt PC. PMID: 16982004.
      View in: PubMed   Mentions: 1     Fields:    Translation:Animals
    49. Functional genetic diversity in the high-affinity carnitine transporter OCTN2 (SLC22A5). Mol Pharmacol. 2006 Nov; 70(5):1602-11. Urban TJ, Gallagher RC, Brown C, Castro RA, Lagpacan LL, Brett CM, Taylor TR, Carlson EJ, Ferrin TE, Burchard EG, Packman S, Giacomini KM. PMID: 16931768.
      View in: PubMed   Mentions: 14     Fields:    Translation:HumansCells
    50. Visualizing density maps with UCSF Chimera. J Struct Biol. 2007 Jan; 157(1):281-7. Goddard TD, Huang CC, Ferrin TE. PMID: 16963278.
      View in: PubMed   Mentions: 311     Fields:    Translation:Cells
    51. Tools for integrated sequence-structure analysis with UCSF Chimera. BMC Bioinformatics. 2006 Jul 12; 7:339. Meng EC, Pettersen EF, Couch GS, Huang CC, Ferrin TE. PMID: 16836757.
      View in: PubMed   Mentions: 121     Fields:    Translation:Cells
    52. Interaction of methotrexate with organic-anion transporting polypeptide 1A2 and its genetic variants. J Pharmacol Exp Ther. 2006 Aug; 318(2):521-9. Badagnani I, Castro RA, Taylor TR, Brett CM, Huang CC, Stryke D, Kawamoto M, Johns SJ, Ferrin TE, Carlson EJ, Burchard EG, Giacomini KM. PMID: 16702441.
      View in: PubMed   Mentions: 48     Fields:    Translation:HumansAnimalsCells
    53. PharmGKB submission update: V. PMT submissions of genetic variation in SLC22 family transporters. Pharmacol Rev. 2006 Mar; 58(1):3-4. Shu Y, Urban TJ, Leabman MK, Fujita T, Erdman AR, Lagpacan LL, Brown C, Castro RA, Huang CC, Stryke D, Kawamoto M, Johns SJ, Taylor TR, Chan W, De La Cruz M, Carlson EJ, Ferrin TE, Brett CM, Burchard EG, Herskowitz I, Kroetz DL, Giacomini KM. PMID: 16507878.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    54. PharmGKB submission update: IV. PMT submissions of genetic variations in ATP-Binding cassette transporters to the PharmGKB network. Pharmacol Rev. 2006 Mar; 58(1):1-2. Nguyen TD, Gow JM, Chinn LW, Kelly L, Jeong H, Huang CC, Stryke D, Kawamoto M, Johns SJ, Carlson E, Taylor T, Ferrin TE, Sali A, Giacomini KM, Kroetz DL. PMID: 16507877.
      View in: PubMed   Mentions: 2     Fields:    Translation:Humans
    55. PharmGKB submission update: VI. PMT submissions of genetic variations in neurotransmitter transporters (SLC6, SLC17, and SLC18) to the PharmGKB network. Pharmacol Rev. 2006 Mar; 58(1):5-6. Badagnani I, Sorani M, Edwards RH, Brown C, Castro RA, Huang CC, Stryke D, Kawamoto M, Johns SJ, Carlson EJ, Taylor T, Chan W, De La Cruz M, Ferrin TE, Burchard EG, Herskowitz I, Kroetz DL, Giacomini KM. PMID: 16507879.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    56. Leveraging enzyme structure-function relationships for functional inference and experimental design: the structure-function linkage database. Biochemistry. 2006 Feb 28; 45(8):2545-55. Pegg SC, Brown SD, Ojha S, Seffernick J, Meng EC, Morris JH, Chang PJ, Huang CC, Ferrin TE, Babbitt PC. PMID: 16489747.
      View in: PubMed   Mentions: 81     Fields:    Translation:HumansAnimals
    57. Designed divergent evolution of enzyme function. Nature. 2006 Apr 20; 440(7087):1078-82. Yoshikuni Y, Ferrin TE, Keasling JD. PMID: 16495946.
      View in: PubMed   Mentions: 102     Fields:    Translation:Cells
    58. Nucleic acid visualization with UCSF Chimera. Nucleic Acids Res. 2006 Feb 14; 34(4):e29. Couch GS, Hendrix DK, Ferrin TE. PMID: 16478715.
      View in: PubMed   Mentions: 19     Fields:    Translation:Cells
    59. The International Gene Trap Consortium Website: a portal to all publicly available gene trap cell lines in mouse. Nucleic Acids Res. 2006 Jan 01; 34(Database issue):D642-8. Nord AS, Chang PJ, Conklin BR, Cox AV, Harper CA, Hicks GG, Huang CC, Johns SJ, Kawamoto M, Liu S, Meng EC, Morris JH, Rossant J, Ruiz P, Skarnes WC, Soriano P, Stanford WL, Stryke D, von Melchner H, Wurst W, Yamamura K, Young SG, Babbitt PC, Ferrin TE. PMID: 16381950.
      View in: PubMed   Mentions: 58     Fields:    Translation:AnimalsCells
    60. Engineering cotton (+)-delta-cadinene synthase to an altered function: germacrene D-4-ol synthase. Chem Biol. 2006 Jan; 13(1):91-8. Yoshikuni Y, Martin VJ, Ferrin TE, Keasling JD. PMID: 16426975.
      View in: PubMed   Mentions: 21     Fields:    Translation:AnimalsCells
    61. The human organic anion transporter 3 (OAT3; SLC22A8): genetic variation and functional genomics. Am J Physiol Renal Physiol. 2006 Apr; 290(4):F905-12. Erdman AR, Mangravite LM, Urban TJ, Lagpacan LL, Castro RA, de la Cruz M, Chan W, Huang CC, Johns SJ, Kawamoto M, Stryke D, Taylor TR, Carlson EJ, Ferrin TE, Brett CM, Burchard EG, Giacomini KM. PMID: 16291576.
      View in: PubMed   Mentions: 27     Fields:    Translation:Humans
    62. Functional characterization and haplotype analysis of polymorphisms in the human equilibrative nucleoside transporter, ENT2. Drug Metab Dispos. 2006 Jan; 34(1):12-5. Owen RP, Lagpacan LL, Taylor TR, De La Cruz M, Huang CC, Kawamoto M, Johns SJ, Stryke D, Ferrin TE, Giacomini KM. PMID: 16214850.
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    63. Functional analysis of polymorphisms in the organic anion transporter, SLC22A6 (OAT1). Pharmacogenet Genomics. 2005 Apr; 15(4):201-9. Fujita T, Brown C, Carlson EJ, Taylor T, de la Cruz M, Johns SJ, Stryke D, Kawamoto M, Fujita K, Castro R, Chen CW, Lin ET, Brett CM, Burchard EG, Ferrin TE, Huang CC, Leabman MK, Giacomini KM. PMID: 15864112.
      View in: PubMed   Mentions: 25     Fields:    Translation:HumansAnimalsCells
    64. Software extensions to UCSF chimera for interactive visualization of large molecular assemblies. Structure. 2005 Mar; 13(3):473-82. Goddard TD, Huang CC, Ferrin TE. PMID: 15766548.
      View in: PubMed   Mentions: 67     Fields:    Translation:Cells
    65. Genetic analysis and functional characterization of polymorphisms in the human concentrative nucleoside transporter, CNT2. Pharmacogenet Genomics. 2005 Feb; 15(2):83-90. Owen RP, Gray JH, Taylor TR, Carlson EJ, Huang CC, Kawamoto M, Johns SJ, Stryke D, Ferrin TE, Giacomini KM. PMID: 15861032.
      View in: PubMed   Mentions: 8     Fields:    Translation:HumansAnimalsCells
    66. Functional analysis of genetic variants in the human concentrative nucleoside transporter 3 (CNT3; SLC28A3). Pharmacogenomics J. 2005; 5(3):157-65. Badagnani I, Chan W, Castro RA, Brett CM, Huang CC, Stryke D, Kawamoto M, Johns SJ, Ferrin TE, Carlson EJ, Burchard EG, Giacomini KM. PMID: 15738947.
      View in: PubMed   Mentions: 15     Fields:    Translation:HumansAnimalsCells
    67. Enhancing data sharing in collaborative research projects with DASH. Pac Symp Biocomput. 2005; 260-71. Ferrin TE, Huang CC, Greenblatt DM, Stryke D, Giacomini KM, Morris JH. PMID: 15759632.
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    68. Representing structure-function relationships in mechanistically diverse enzyme superfamilies. Pac Symp Biocomput. 2005; 358-69. Pegg SC, Brown S, Ojha S, Huang CC, Ferrin TE, Babbitt PC. PMID: 15759641.
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    69. UCSF Chimera--a visualization system for exploratory research and analysis. J Comput Chem. 2004 Oct; 25(13):1605-12. Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC, Ferrin TE. PMID: 15264254.
      View in: PubMed   Mentions: 8575     Fields:    Translation:Cells
    70. PharmGKB update: III. Genetic variants of SLC22A1, solute carrier family 22 (organic cation transporter), member 1. Pharmacol Rev. 2004 Jun; 56(2):161. Shu Y, Leabman MK, Feng B, Mangravite LM, Huang CC, Stryke D, Kawamoto M, Johns SJ, DeYoung J, Carlson E, Ferrin TE, Herskowitz I, Giacomini KM. PMID: 15169925.
      View in: PubMed   Mentions: 2     Fields:    Translation:Humans
    71. Functional and genetic diversity in the concentrative nucleoside transporter, CNT1, in human populations. Mol Pharmacol. 2004 Mar; 65(3):512-9. Gray JH, Mangravite LM, Owen RP, Urban TJ, Chan W, Carlson EJ, Huang CC, Kawamoto M, Johns SJ, Stryke D, Ferrin TE, Giacomini KM. PMID: 14978229.
      View in: PubMed   Mentions: 14     Fields:    Translation:HumansCells
    72. MODBASE, a database of annotated comparative protein structure models, and associated resources. Nucleic Acids Res. 2004 Jan 01; 32(Database issue):D217-22. Pieper U, Eswar N, Braberg H, Madhusudhan MS, Davis FP, Stuart AC, Mirkovic N, Rossi A, Marti-Renom MA, Fiser A, Webb B, Greenblatt D, Huang CC, Ferrin TE, Sali A. PMID: 14681398.
      View in: PubMed   Mentions: 82     Fields:    Translation:HumansAnimalsCells
    73. Sequence diversity and haplotype structure in the human ABCB1 (MDR1, multidrug resistance transporter) gene. Pharmacogenetics. 2003 Aug; 13(8):481-94. Kroetz DL, Pauli-Magnus C, Hodges LM, Huang CC, Kawamoto M, Johns SJ, Stryke D, Ferrin TE, DeYoung J, Taylor T, Carlson EJ, Herskowitz I, Giacomini KM, Clark AG. PMID: 12893986.
      View in: PubMed   Mentions: 87     Fields:    Translation:HumansCells
    74. PharmGKB update: I. Genetic variants of the organic cation transporter 2 (OCT2, SLC22A2). Pharmacol Rev. 2003 Sep; 55(3):399. Leabman MK, Huang CC, Stryke D, Johns SJ, Kawamoto M, Ferrin TE, DeYoung J, Taylor TR, De La Cruz M, Herskowitz I, Giacomini KM. PMID: 12869664.
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    75. Functional characterization in yeast of genetic variants in the human equilibrative nucleoside transporter, ENT1. Pharmacogenetics. 2003 May; 13(5):297-301. Osato DH, Huang CC, Kawamoto M, Johns SJ, Stryke D, Wang J, Ferrin TE, Herskowitz I, Giacomini KM. PMID: 12724623.
      View in: PubMed   Mentions: 17     Fields:    Translation:HumansAnimalsCells
    76. Natural variation in human membrane transporter genes reveals evolutionary and functional constraints. Proc Natl Acad Sci U S A. 2003 May 13; 100(10):5896-901. Leabman MK, Huang CC, DeYoung J, Carlson EJ, Taylor TR, de la Cruz M, Johns SJ, Stryke D, Kawamoto M, Urban TJ, Kroetz DL, Ferrin TE, Clark AG, Risch N, Herskowitz I, Giacomini KM. PMID: 12719533.
      View in: PubMed   Mentions: 71     Fields:    Translation:Humans
    77. Evolutionary conservation predicts function of variants of the human organic cation transporter, OCT1. Proc Natl Acad Sci U S A. 2003 May 13; 100(10):5902-7. Shu Y, Leabman MK, Feng B, Mangravite LM, Huang CC, Stryke D, Kawamoto M, Johns SJ, DeYoung J, Carlson E, Ferrin TE, Herskowitz I, Giacomini KM. PMID: 12719534.
      View in: PubMed   Mentions: 58     Fields:    Translation:HumansAnimalsCells
    78. MINRMS: an efficient algorithm for determining protein structure similarity using root-mean-squared-distance. Bioinformatics. 2003 Mar 22; 19(5):625-34. Jewett AI, Huang CC, Ferrin TE. PMID: 12651721.
      View in: PubMed   Mentions: 11     Fields:    Translation:Cells
    79. BayGenomics: a resource of insertional mutations in mouse embryonic stem cells. Nucleic Acids Res. 2003 Jan 01; 31(1):278-81. Stryke D, Kawamoto M, Huang CC, Johns SJ, King LA, Harper CA, Meng EC, Lee RE, Yee A, L'Italien L, Chuang PT, Young SG, Skarnes WC, Babbitt PC, Ferrin TE. PMID: 12520002.
      View in: PubMed   Mentions: 130     Fields:    Translation:AnimalsCells
    80. SNP analysis and presentation in the Pharmacogenetics of Membrane Transporters Project. Pac Symp Biocomput. 2003; 535-47. Stryke D, Huang CC, Kawamoto M, Johns SJ, Carlson EJ, Deyoung JA, Leabman MK, Herskowitz I, Giacomini KM, Ferrin TE. PMID: 12603056.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansAnimalsCells
    81. The Structure Superposition Database. Nucleic Acids Res. 2003 Jan 01; 31(1):505-10. Chiang RA, Meng EC, Huang CC, Ferrin TE, Babbitt PC. PMID: 12520064.
      View in: PubMed   Mentions: 5     Fields:    Translation:AnimalsCells
    82. Polymorphisms in a human kidney xenobiotic transporter, OCT2, exhibit altered function. Pharmacogenetics. 2002 Jul; 12(5):395-405. Leabman MK, Huang CC, Kawamoto M, Johns SJ, Stryke D, Ferrin TE, DeYoung J, Taylor T, Clark AG, Herskowitz I, Giacomini KM. PMID: 12142729.
      View in: PubMed   Mentions: 36     Fields:    Translation:HumansAnimalsCells
    83. Integrated tools for structural and sequence alignment and analysis. Pac Symp Biocomput. 2000; 230-41. Huang CC, Novak WR, Babbitt PC, Jewett AI, Ferrin TE, Klein TE. PMID: 10902172.
      View in: PubMed   Mentions: 5     Fields:    Translation:Cells
    84. The object technology framework: an object-oriented interface to molecular data and its application to collagen. Pac Symp Biocomput. 1998; 349-61. Huang CC, Couch GS, Pettersen EF, Ferrin TE, Howard AE, Klein TE. PMID: 9697195.
      View in: PubMed   Mentions: 5     Fields:    Translation:Cells
    85. Molecules to maps: tools for visualization and interaction in support of computational biology. Bioinformatics. 1998; 14(9):764-71. Kraemer ET, Ferrin TE. PMID: 9918946.
      View in: PubMed   Mentions: 1     Fields:    Translation:Humans
    86. Annotating PDB files with scene information. J Mol Graph. 1995 Jun; 13(3):153-8, 193. Couch GS, Pettersen EF, Huang CC, Ferrin TE. PMID: 7577842.
      View in: PubMed   Mentions: 3     Fields:    Translation:Cells
    87. Automated site-directed drug design using molecular lattices. J Mol Graph. 1992 Jun; 10(2):66-78, 106. Lewis RA, Roe DC, Huang C, Ferrin TE, Langridge R, Kuntz ID. PMID: 1637751.
      View in: PubMed   Mentions: 21     Fields:    
    88. Conic: a fast renderer for space-filling molecules with shadows. J Mol Graph. 1991 Dec; 9(4):230-6, 242. Huang CC, Pettersen EF, Klein TE, Ferrin TE, Langridge R. PMID: 1772848.
      View in: PubMed   Mentions: 21     Fields:    Translation:Cells
    89. Molecular structure and dynamics of tricyclic antidepressant drugs. Eur Neuropsychopharmacol. 1991 May; 1(2):127-37. Heimstad E, Edvardsen O, Ferrin TE, Dahl SG. PMID: 1821702.
      View in: PubMed   Mentions:    Fields:    Translation:Cells
    90. An affordable approach to interactive desktop molecular modeling. J Mol Graph. 1991 Mar; 9(1):27-32, 37-8. Ferrin TE, Couch GS, Huang CC, Pettersen EF, Langridge R. PMID: 1902113.
      View in: PubMed   Mentions:    Fields:    
    91. A real-time malleable molecular surface. J Mol Graph. 1990 Mar; 8(1):16-24, 26. Klein TE, Huang CC, Pettersen EF, Couch GS, Ferrin TE, Langridge R. PMID: 2268622.
      View in: PubMed   Mentions: 2     Fields:    
    92. Van der waals surfaces in molecular modeling: implementation with real-time computer graphics. Science. 1983 Dec 23; 222(4630):1325-7. Bash PA, Pattabiraman N, Huang C, Ferrin TE, Langridge R. PMID: 17773334.
      View in: PubMed   Mentions: 10     Fields:    
    93. A geometric approach to macromolecule-ligand interactions. J Mol Biol. 1982 Oct 25; 161(2):269-88. Kuntz ID, Blaney JM, Oatley SJ, Langridge R, Ferrin TE. PMID: 7154081.
      View in: PubMed   Mentions: 321     Fields:    Translation:Cells
    94. Computer graphics in drug design: molecular modeling of thyroid hormone-prealbumin interactions. J Med Chem. 1982 Jul; 25(7):785-90. Blaney JM, Jorgensen EC, Connolly ML, Ferrin TE, Langridge R, Oatley SJ, Burridge JM, Blake CC. PMID: 7108895.
      View in: PubMed   Mentions: 7     Fields:    Translation:HumansCells
    95. Real-time color graphics in studies of molecular interactions. Science. 1981 Feb 13; 211(4483):661-6. Langridge R, Ferrin TE, Kuntz ID, Connolly ML. PMID: 7455704.
      View in: PubMed   Mentions: 16     Fields:    Translation:Cells
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