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Thomas E. Ferrin - Publications

Affiliations: 
University of California, San Francisco, San Francisco, CA 
Area:
Biomedical Engineering
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57 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2020 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 Science : a Publication of the Protein Society. PMID 32881101 DOI: 10.1002/Pro.3943  0.317
2018 Goddard TD, Brilliant AA, Skillman TL, Vergenz S, Tyrwhitt-Drake J, Meng EC, Ferrin TE. Molecular Visualization on the Holodeck. Journal of Molecular Biology. PMID 29964044 DOI: 10.1016/J.Jmb.2018.06.040  0.319
2017 Goddard TD, Huang CC, Meng EC, Pettersen EF, Couch GS, Morris JH, Ferrin TE. UCSF ChimeraX: Meeting Modern Challenges in Visualization and Analysis. Protein Science : a Publication of the Protein Society. PMID 28710774 DOI: 10.1002/Pro.3235  0.334
2017 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 : the Journal of Biological Databases and Curation. 2017. PMID 28365730 DOI: 10.1093/Database/Bax006  0.348
2017 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 Computational Biology. 13: e1005284. PMID 28187133 DOI: 10.1371/Journal.Pcbi.1005284  0.407
2017 Knutson ST, Westwood BM, Leuthaeuser JB, Turner B, Nguyendac D, Shea G, Kumar K, Hayden J, Harper A, 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 Science : a Publication of the Protein Society. PMID 28054422 DOI: 10.1002/Pro.3112  0.404
2016 Leuthaeuser JB, Morris JH, Harper AF, Ferrin TE, Babbitt PC, Fetrow JS. DASP3: identification of protein sequences belonging to functionally relevant groups. Bmc Bioinformatics. 17: 458. PMID 27835946 DOI: 10.1186/S12859-016-1295-Z  0.391
2015 Hertig S, Goddard TD, Johnson GT, Ferrin TE. Multidomain Assembler (MDA) Generates Models of Large Multidomain Proteins. Biophysical Journal. 108: 2097-102. PMID 25954868 DOI: 10.1016/J.Bpj.2015.03.051  0.344
2015 Chen JE, Huang CC, Ferrin TE. RRDistMaps: a UCSF Chimera tool for viewing and comparing protein distance maps. Bioinformatics (Oxford, England). 31: 1484-6. PMID 25540183 DOI: 10.1093/Bioinformatics/Btu841  0.313
2015 Morris JH, Wu A, Yamashita RA, Marchler-Bauer A, Ferrin TE. cddApp: a Cytoscape app for accessing the NCBI conserved domain database. Bioinformatics (Oxford, England). 31: 134-6. PMID 25212755 DOI: 10.7490/F1000Research.1111825.1  0.31
2014 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, ... ... Ferrin TE, et al. The Structure-Function Linkage Database. Nucleic Acids Research. 42: D521-30. PMID 24271399 DOI: 10.1093/Nar/Gkt1130  0.371
2011 Morris JH, Apeltsin L, Newman AM, Baumbach J, Wittkop T, Su G, Bader GD, Ferrin TE. clusterMaker: a multi-algorithm clustering plugin for Cytoscape. Bmc Bioinformatics. 12: 436. PMID 22070249 DOI: 10.1186/1471-2105-12-436  0.717
2011 Apeltsin L, Morris JH, Babbitt PC, Ferrin TE. Improving the quality of protein similarity network clustering algorithms using the network edge weight distribution. Bioinformatics (Oxford, England). 27: 326-33. PMID 21118823 DOI: 10.1093/Bioinformatics/Btq655  0.707
2010 Chen L, Pawlikowski B, Schlessinger A, More SS, Stryke D, Johns SJ, Portman MA, Chen E, Ferrin TE, Sali A, Giacomini KM. Role of organic cation transporter 3 (SLC22A3) and its missense variants in the pharmacologic action of metformin. Pharmacogenetics and Genomics. 20: 687-99. PMID 20859243 DOI: 10.1097/Fpc.0B013E32833Fe789  0.309
2010 Shima JE, Komori T, Taylor TR, Stryke D, Kawamoto M, Johns SJ, Carlson EJ, Ferrin TE, Giacomini KM. Genetic variants of human organic anion transporter 4 demonstrate altered transport of endogenous substrates. American Journal of Physiology. Renal Physiology. 299: F767-75. PMID 20668102 DOI: 10.1152/Ajprenal.00312.2010  0.356
2010 Morris JH, Meng EC, Ferrin TE. Computational tools for the interactive exploration of proteomic and structural data. Molecular & Cellular Proteomics : McP. 9: 1703-15. PMID 20525940 DOI: 10.1074/Mcp.R000007-Mcp201  0.337
2010 Schlessinger A, Matsson P, Shima JE, Pieper U, Yee SW, Kelly L, Apeltsin L, Stroud RM, Ferrin TE, Giacomini KM, Sali A. Comparison of human solute carriers. Protein Science : a Publication of the Protein Society. 19: 412-28. PMID 20052679 DOI: 10.1002/Pro.320  0.708
2009 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, ... ... Ferrin TE, et al. Genetic variation in the proximal promoter of ABC and SLC superfamilies: liver and kidney specific expression and promoter activity predict variation. Plos One. 4: e6942. PMID 19742321 DOI: 10.1371/Journal.Pone.0006942  0.312
2009 Atkinson HJ, Morris JH, Ferrin TE, Babbitt PC. Using sequence similarity networks for visualization of relationships across diverse protein superfamilies. Plos One. 4: e4345. PMID 19190775 DOI: 10.1371/Journal.Pone.0004345  0.414
2009 Chen Y, Teranishi K, Li S, Yee SW, Hesselson S, Stryke D, Johns SJ, Ferrin TE, Kwok P, Giacomini KM. Genetic variants in multidrug and toxic compound extrusion-1, hMATE1, alter transport function. The Pharmacogenomics Journal. 9: 127-36. PMID 19172157 DOI: 10.1038/Tpj.2008.19  0.331
2009 Tahara H, Yee SW, Urban TJ, Hesselson S, Castro RA, Kawamoto M, Stryke D, Johns SJ, Ferrin TE, Kwok PY, Giacomini KM. Functional genetic variation in the basal promoter of the organic cation/carnitine transporters OCTN1 (SLC22A4) and OCTN2 (SLC22A5). The Journal of Pharmacology and Experimental Therapeutics. 329: 262-71. PMID 19141711 DOI: 10.1124/Jpet.108.146449  0.305
2008 Abla N, Chinn LW, Nakamura T, Liu L, Huang CC, Johns SJ, Kawamoto M, Stryke D, Taylor TR, Ferrin TE, Giacomini KM, Kroetz DL. The human multidrug resistance protein 4 (MRP4, ABCC4): functional analysis of a highly polymorphic gene. The Journal of Pharmacology and Experimental Therapeutics. 325: 859-68. PMID 18364470 DOI: 10.1124/Jpet.108.136523  0.347
2007 Goddard TD, Ferrin TE. Visualization software for molecular assemblies. Current Opinion in Structural Biology. 17: 587-95. PMID 17728125 DOI: 10.1016/J.Sbi.2007.06.008  0.32
2007 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. Functional effects of protein sequence polymorphisms in the organic cation/ergothioneine transporter OCTN1 (SLC22A4). Pharmacogenetics and Genomics. 17: 773-82. PMID 17700366 DOI: 10.1097/Fpc.0B013E3281C6D08E  0.324
2007 Morris JH, Huang CC, Babbitt PC, Ferrin TE. structureViz: linking Cytoscape and UCSF Chimera. Bioinformatics (Oxford, England). 23: 2345-7. PMID 17623706 DOI: 10.1093/Bioinformatics/Btm329  0.38
2007 Goddard TD, Huang CC, Ferrin TE. Visualizing density maps with UCSF Chimera. Journal of Structural Biology. 157: 281-7. PMID 16963278 DOI: 10.1016/J.Jsb.2006.06.010  0.301
2006 Harper CA, Huang CC, Stryke D, Kawamoto M, Ferrin TE, Babbitt PC. Comparison of methods for genomic localization of gene trap sequences. Bmc Genomics. 7: 236. PMID 16982004 DOI: 10.1186/1471-2164-7-236  0.306
2006 Urban TJ, Gallagher RC, Brown C, Castro RA, Lagpacan LL, Brett CM, Taylor TR, Carlson EJ, Ferrin TE, Burchard EG, Packman S, Giacomini KM. Functional genetic diversity in the high-affinity carnitine transporter OCTN2 (SLC22A5). Molecular Pharmacology. 70: 1602-11. PMID 16931768 DOI: 10.1124/Mol.106.028126  0.338
2006 Meng EC, Pettersen EF, Couch GS, Huang CC, Ferrin TE. Tools for integrated sequence-structure analysis with UCSF Chimera. Bmc Bioinformatics. 7: 339. PMID 16836757 DOI: 10.1186/1471-2105-7-339  0.365
2006 Badagnani I, Castro RA, Taylor TR, Brett CM, Huang CC, Stryke D, Kawamoto M, Johns SJ, Ferrin TE, Carlson EJ, Burchard EG, Giacomini KM. Interaction of methotrexate with organic-anion transporting polypeptide 1A2 and its genetic variants. The Journal of Pharmacology and Experimental Therapeutics. 318: 521-9. PMID 16702441 DOI: 10.1124/Jpet.106.104364  0.327
2006 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, et al. PharmGKB submission update: VI. PMT submissions of genetic variations in neurotransmitter transporters (SLC6, SLC17, and SLC18) to the PharmGKB network. Pharmacological Reviews. 58: 5-6. PMID 16507879 DOI: 10.1124/Pr.58.1.3  0.33
2006 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, ... ... Ferrin TE, et al. PharmGKB submission update: V. PMT submissions of genetic variation in SLC22 family transporters. Pharmacological Reviews. 58: 3-4. PMID 16507878 DOI: 10.1124/Pr.58.1.2  0.318
2006 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. PharmGKB submission update: IV. PMT submissions of genetic variations in ATP-Binding cassette transporters to the PharmGKB network. Pharmacological Reviews. 58: 1-2. PMID 16507877 DOI: 10.1124/Pr.58.1.1  0.328
2006 Yoshikuni Y, Ferrin TE, Keasling JD. Designed divergent evolution of enzyme function. Nature. 440: 1078-82. PMID 16495946 DOI: 10.1038/Nature04607  0.306
2006 Pegg SC, Brown SD, Ojha S, Seffernick J, Meng EC, Morris JH, Chang PJ, Huang CC, Ferrin TE, Babbitt PC. Leveraging enzyme structure-function relationships for functional inference and experimental design: the structure-function linkage database. Biochemistry. 45: 2545-55. PMID 16489747 DOI: 10.1021/Bi052101L  0.334
2006 Couch GS, Hendrix DK, Ferrin TE. Nucleic acid visualization with UCSF Chimera Nucleic Acids Research. 34. PMID 16478715 DOI: 10.1093/Nar/Gnj031  0.317
2006 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, et al. The human organic anion transporter 3 (OAT3; SLC22A8): genetic variation and functional genomics. American Journal of Physiology. Renal Physiology. 290: F905-12. PMID 16291576 DOI: 10.1152/Ajprenal.00272.2005  0.352
2006 Owen RP, Lagpacan LL, Taylor TR, De La Cruz M, Huang CC, Kawamoto M, Johns SJ, Stryke D, Ferrin TE, Giacomini KM. Functional characterization and haplotype analysis of polymorphisms in the human equilibrative nucleoside transporter, ENT2. Drug Metabolism and Disposition: the Biological Fate of Chemicals. 34: 12-5. PMID 16214850 DOI: 10.1124/Dmd.105.006270  0.35
2005 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, et al. Functional analysis of polymorphisms in the organic anion transporter, SLC22A6 (OAT1). Pharmacogenetics and Genomics. 15: 201-9. PMID 15864112 DOI: 10.1097/01213011-200504000-00003  0.308
2005 Owen RP, Gray JH, Taylor TR, Carlson EJ, Huang CC, Kawamoto M, Johns SJ, Stryke D, Ferrin TE, Giacomini KM. Genetic analysis and functional characterization of polymorphisms in the human concentrative nucleoside transporter, CNT2. Pharmacogenetics and Genomics. 15: 83-90. PMID 15861032 DOI: 10.1097/01213011-200502000-00004  0.302
2005 Goddard TD, Huang CC, Ferrin TE. Software extensions to UCSF chimera for interactive visualization of large molecular assemblies. Structure (London, England : 1993). 13: 473-82. PMID 15766548 DOI: 10.1016/J.Str.2005.01.006  0.34
2005 Badagnani I, Chan W, Castro RA, Brett CM, Huang CC, Stryke D, Kawamoto M, Johns SJ, Ferrin TE, Carlson EJ, Burchard EG, Giacomini KM. Functional analysis of genetic variants in the human concentrative nucleoside transporter 3 (CNT3; SLC28A3). The Pharmacogenomics Journal. 5: 157-65. PMID 15738947 DOI: 10.1038/Sj.Tpj.6500303  0.342
2004 Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC, Ferrin TE. UCSF Chimera--a visualization system for exploratory research and analysis. Journal of Computational Chemistry. 25: 1605-12. PMID 15264254 DOI: 10.1002/Jcc.20084  0.355
2004 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. PharmGKB update: III. Genetic variants of SLC22A1, solute carrier family 22 (organic cation transporter), member 1. Pharmacological Reviews. 56: 161. PMID 15169925 DOI: 10.1124/Pr.56.2.2  0.324
2004 Gray JH, Mangravite LM, Owen RP, Urban TJ, Chan W, Carlson EJ, Huang CC, Kawamoto M, Johns SJ, Stryke D, Ferrin TE, Giacomini KM. Functional and genetic diversity in the concentrative nucleoside transporter, CNT1, in human populations. Molecular Pharmacology. 65: 512-9. PMID 14978229 DOI: 10.1124/Mol.65.3.512  0.308
2003 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. Sequence diversity and haplotype structure in the human ABCB1 (MDR1, multidrug resistance transporter) gene. Pharmacogenetics. 13: 481-94. PMID 12893986 DOI: 10.1097/00008571-200308000-00006  0.326
2003 Leabman MK, Huang CC, Stryke D, Johns SJ, Kawamoto M, Ferrin TE, DeYoung J, Taylor TR, De La Cruz M, Herskowitz I, Giacomini KM. PharmGKB update: I. Genetic variants of the organic cation transporter 2 (OCT2, SLC22A2). Pharmacological Reviews. 55: 399. PMID 12869664 DOI: 10.1124/Pr.55.3.6  0.325
2003 Osato DH, Huang CC, Kawamoto M, Johns SJ, Stryke D, Wang J, Ferrin TE, Herskowitz I, Giacomini KM. Functional characterization in yeast of genetic variants in the human equilibrative nucleoside transporter, ENT1. Pharmacogenetics. 13: 297-301. PMID 12724623 DOI: 10.1097/00008571-200305000-00010  0.333
2003 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. Evolutionary conservation predicts function of variants of the human organic cation transporter, OCT1. Proceedings of the National Academy of Sciences of the United States of America. 100: 5902-7. PMID 12719534 DOI: 10.1073/Pnas.0730858100  0.335
2003 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, et al. Natural variation in human membrane transporter genes reveals evolutionary and functional constraints. Proceedings of the National Academy of Sciences of the United States of America. 100: 5896-901. PMID 12719533 DOI: 10.1073/Pnas.0730857100  0.318
2003 Jewett AI, Huang CC, Ferrin TE. MINRMS: an efficient algorithm for determining protein structure similarity using root-mean-squared-distance. Bioinformatics (Oxford, England). 19: 625-34. PMID 12651721 DOI: 10.1093/Bioinformatics/Btg035  0.341
2003 Chiang RA, Meng EC, Huang CC, Ferrin TE, Babbitt PC. The Structure Superposition Database. Nucleic Acids Research. 31: 505-10. PMID 12520064 DOI: 10.1093/Nar/Gkg127  0.352
2002 Leabman MK, Huang CC, Kawamoto M, Johns SJ, Stryke D, Ferrin TE, DeYoung J, Taylor T, Clark AG, Herskowitz I, Giacomini KM. Polymorphisms in a human kidney xenobiotic transporter, OCT2, exhibit altered function. Pharmacogenetics. 12: 395-405. PMID 12142729 DOI: 10.1097/00008571-200207000-00007  0.348
1998 Kraemer ET, Ferrin TE. Molecules to maps: tools for visualization and interaction in support of computational biology. Bioinformatics (Oxford, England). 14: 764-71. PMID 9918946 DOI: 10.1093/Bioinformatics/14.9.764  0.325
1992 Lewis RA, Roe DC, Huang C, Ferrin TE, Langridge R, Kuntz ID. Automated site-directed drug design using molecular lattices. Journal of Molecular Graphics. 10: 66-78, 106. PMID 1637751 DOI: 10.1016/0263-7855(92)80059-M  0.303
1988 Ferrin TE, Huang CC, Jarvis LE, Langridge R. The MIDAS database system Journal of Molecular Graphics. 6: 2-12. DOI: 10.1016/0263-7855(88)80053-5  0.305
1981 Langridge R, Ferrin TE, Kuntz ID, Connolly ML. Real-time color graphics in studies of molecular interactions. Science (New York, N.Y.). 211: 661-6. PMID 7455704 DOI: 10.1126/Science.7455704  0.333
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