Thomas E. Ferrin - Publications

Affiliations: 
University of California, San Francisco, San Francisco, CA 
Area:
Biomedical Engineering

89 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  0.48
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  0.48
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 28605775 DOI: 10.1093/database/bax045  0.48
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  0.48
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  0.48
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  0.48
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  0.48
2015 Morris JH, Vijay D, Federowicz S, Pico AR, Ferrin TE. CyAnimator: Simple Animations of Cytoscape Networks. F1000research. 4: 482. PMID 26937268 DOI: 10.12688/f1000research.6852.2  0.48
2015 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, et al. Outcome of the First wwPDB Hybrid/Integrative Methods Task Force Workshop. Structure (London, England : 1993). PMID 26095030 DOI: 10.1016/j.str.2015.05.013  0.48
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  0.48
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: 10.1093/bioinformatics/btu605  0.48
2014 Morris JH, Wu A, Doncheva NT, Albrecht M, Ferrin TE. setsApp: Set operations for Cytoscape Nodes and Edges. F1000research. 3: 149. PMID 25352980 DOI: 10.12688/f1000research.4392.2  0.48
2014 Morris JH, Kuchinsky A, Ferrin TE, Pico AR. enhancedGraphics: a Cytoscape app for enhanced node graphics. F1000research. 3: 147. PMID 25285206 DOI: 10.12688/f1000research.4460.1  0.48
2014 Huang CC, Meng EC, Morris JH, Pettersen EF, Ferrin TE. Enhancing UCSF Chimera through web services. Nucleic Acids Research. 42: W478-84. PMID 24861624 DOI: 10.1093/nar/gku377  0.48
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  0.48
2013 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. Genetic and epigenetic regulation of the organic cation transporter 3, SLC22A3 Pharmacogenomics Journal. 13: 110-120. PMID 22231567 DOI: 10.1038/tpj.2011.60  0.48
2012 Lasker K, Velázquez-Muriel JA, Webb BM, Yang Z, Ferrin TE, Sali A. Macromolecular assembly structures by comparative modeling and electron microscopy. Methods in Molecular Biology (Clifton, N.J.). 857: 331-50. PMID 22323229 DOI: 10.1007/978-1-61779-588-6_15  0.48
2012 Yang Z, Lasker K, Schneidman-Duhovny D, Webb B, Huang CC, Pettersen EF, Goddard TD, Meng EC, Sali A, Ferrin TE. UCSF Chimera, MODELLER, and IMP: an integrated modeling system. Journal of Structural Biology. 179: 269-78. PMID 21963794 DOI: 10.1016/j.jsb.2011.09.006  0.48
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  0.48
2011 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, et al. A common 5'-UTR variant in MATE2-K is associated with poor response to metformin. Clinical Pharmacology and Therapeutics. 90: 674-84. PMID 21956618 DOI: 10.1038/clpt.2011.165  0.48
2011 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, et al. Functional characterization of liver enhancers that regulate drug-associated transporters. Clinical Pharmacology and Therapeutics. 89: 571-8. PMID 21368754 DOI: 10.1038/clpt.2010.353  0.48
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  0.48
2011 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, et al. ModBase, a database of annotated comparative protein structure models, and associated resources. Nucleic Acids Research. 39: D465-74. PMID 21097780 DOI: 10.1093/nar/gkq1091  0.48
2010 Bromberg S, Chiu W, Ferrin TE. Workshop on molecular animation. Structure (London, England : 1993). 18: 1261-5. PMID 20947014 DOI: 10.1016/j.str.2010.09.001  0.48
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  0.48
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  0.48
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  0.48
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  0.48
2009 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, et al. Identification and characterization of novel polymorphisms in the basal promoter of the human transporter, MATE1 Pharmacogenetics and Genomics. 19: 770-780. PMID 19745787 DOI: 10.1097/FPC.0b013e328330eeca  0.48
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  0.48
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  0.48
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  0.48
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  0.48
2009 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. Identification and characterization of proximal promoter polymorphisms in the human concentrative nucleoside transporter 2 (SLC28A2). The Journal of Pharmacology and Experimental Therapeutics. 328: 699-707. PMID 19098160 DOI: 10.1124/jpet.108.147207  0.48
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  0.48
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  0.48
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.  0.48
2007 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. Modeling insertional mutagenesis using gene length and expression in murine embryonic stem cells. Plos One. 2: e617. PMID 17637833 DOI: 10.1371/journal.pone.0000617  0.48
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  0.48
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  0.48
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  0.48
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  0.48
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  0.48
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  0.48
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  0.48
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  0.48
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  0.48
2006 Yoshikuni Y, Ferrin TE, Keasling JD. Designed divergent evolution of enzyme function. Nature. 440: 1078-82. PMID 16495946 DOI: 10.1038/nature04607  0.48
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  0.48
2006 Couch GS, Hendrix DK, Ferrin TE. Nucleic acid visualization with UCSF Chimera Nucleic Acids Research. 34. PMID 16478715 DOI: 10.1093/nar/gnj031  0.48
2006 Yoshikuni Y, Martin VJ, Ferrin TE, Keasling JD. Engineering cotton (+)-delta-cadinene synthase to an altered function: germacrene D-4-ol synthase. Chemistry & Biology. 13: 91-8. PMID 16426975 DOI: 10.1016/j.chembiol.2005.10.016  0.48
2006 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, ... ... Ferrin TE, et al. The International Gene Trap Consortium Website: a portal to all publicly available gene trap cell lines in mouse. Nucleic Acids Research. 34: D642-8. PMID 16381950 DOI: 10.1093/nar/gkj097  0.48
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  0.48
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  0.48
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  0.48
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  0.48
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  0.48
2005 Pegg SC, Brown S, Ojha S, Huang CC, Ferrin TE, Babbitt PC. Representing structure-function relationships in mechanistically diverse enzyme superfamilies. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 358-69. PMID 15759641  0.48
2005 Ferrin TE, Huang CC, Greenblatt DM, Stryke D, Giacomini KM, Morris JH. Enhancing data sharing in collaborative research projects with DASH. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 260-71. PMID 15759632  0.48
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  0.48
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  0.48
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  0.48
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  0.48
2004 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. MODBASE, a database of annotated comparative protein structure models, and associated resources. Nucleic Acids Research. 32: D217-22. PMID 14681398 DOI: 10.1093/nar/gkh095  0.48
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: 10.1097/01.fpc.0000054113.14659.b9  0.48
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  0.48
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: 10.1097/01.fpc.0000054083.64000.2a  0.48
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  0.48
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  0.48
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  0.48
2003 Stryke D, Huang CC, Kawamoto M, Johns SJ, Carlson EJ, Deyoung JA, Leabman MK, Herskowitz I, Giacomini KM, Ferrin TE. SNP analysis and presentation in the Pharmacogenetics of Membrane Transporters Project. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 535-47. PMID 12603056  0.48
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  0.48
2003 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. BayGenomics: a resource of insertional mutations in mouse embryonic stem cells. Nucleic Acids Research. 31: 278-81. PMID 12520002 DOI: 10.1093/nar/gkg064  0.48
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  0.48
2000 Huang CC, Novak WR, Babbitt PC, Jewett AI, Ferrin TE, Klein TE. Integrated tools for structural and sequence alignment and analysis. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 230-41. PMID 10902172  0.48
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  0.48
1998 Huang CC, Couch GS, Pettersen EF, Ferrin TE, Howard AE, Klein TE. The object technology framework: an object-oriented interface to molecular data and its application to collagen Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 349-361. PMID 9697195  0.48
1995 Couch GS, Pettersen EF, Huang CC, Ferrin TE. Annotating PDB files with scene information Journal of Molecular Graphics. 13: 153-158. PMID 7577842 DOI: 10.1016/0263-7855(95)00003-O  0.48
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  0.48
1991 Ferrin TE, Couch GS, Huang CC, Pettersen EF, Langridge R. An affordable approach to interactive desktop molecular modeling. Journal of Molecular Graphics. 9: 27-32, 37-8. PMID 1902113 DOI: 10.1016/0263-7855(91)80030-4  0.48
1991 Heimstad E, Edvardsen, Ferrin TE, Dahl SG. Molecular structure and dynamics of tricyclic antidepressant drugs European Neuropsychopharmacology. 1: 127-136. PMID 1821702 DOI: 10.1016/0924-977X(91)90714-6  0.48
1991 Huang CC, Pettersen EF, Klein TE, Ferrin TE, Langridge R. Conic: a fast renderer for space-filling molecules with shadows. Journal of Molecular Graphics. 9: 230-6, 242. PMID 1772848 DOI: 10.1016/0263-7855(91)80016-S  0.48
1990 Klein TE, Huang CC, Pettersen EF, Couch GS, Ferrin TE, Langridge R. A real-time malleable molecular surface. Journal of Molecular Graphics. 8: 16-24, 26. PMID 2268622 DOI: 10.1016/0263-7855(90)80064-M  0.48
1988 Ferrin TE, Huang CC, Jarvis LE, Langridge R. The MIDAS display system Journal of Molecular Graphics. 6: 13-27. DOI: 10.1016/0263-7855(88)80054-7  0.48
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  0.48
1983 Bash PA, Pattabiraman N, Huang C, Ferrin TE, Langridge R. Van der Waals surfaces in molecular modeling: Implementation with real-time computer graphics Science. 222: 1325-1327.  0.48
1982 Kuntz ID, Blaney JM, Oatley SJ, Langridge R, Ferrin TE. A geometric approach to macromolecule-ligand interactions. Journal of Molecular Biology. 161: 269-88. PMID 7154081 DOI: 10.1016/0022-2836(82)90153-X  0.48
1982 Blaney JM, Jorgensen EC, Connolly ML, Ferrin TE, Langridge R, Oatley SJ, Burridge JM, Blake CC. Computer graphics in drug design: molecular modeling of thyroid hormone-prealbumin interactions. Journal of Medicinal Chemistry. 25: 785-90. PMID 7108895  0.48
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  0.48
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