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IHMCIF: An Extension of the PDBx/mmCIF Data Standard for Integrative Structure Determination Methods. J Mol Biol. 2024 Sep 01; 436(17):168546.
Vallat B, Webb BM, Westbrook JD, Goddard TD, Hanke CA, Graziadei A, Peisach E, Zalevsky A, Sagendorf J, Tangmunarunkit H, Voinea S, Sekharan M, Yu J, Bonvin AAMJJ, DiMaio F, Hummer G, Meiler J, Tajkhorshid E, Ferrin TE, Lawson CL, Leitner A, Rappsilber J, Seidel CAM, Jeffries CM, Burley SK, Hoch JC, Kurisu G, Morris K, Patwardhan A, Velankar S, Schwede T, Trewhella J, Kesselman C, Berman HM, Sali A. PMID: 38508301; PMCID: PMC11377171.
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PubMed Mentions:
1 Fields:
Translation:
Cells
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UCSF ChimeraX: Tools for structure building and analysis. Protein Sci. 2023 11; 32(11):e4792.
Meng EC, Goddard TD, Pettersen EF, Couch GS, Pearson ZJ, Morris JH, Ferrin TE. PMID: 37774136; PMCID: PMC10588335.
View in:
PubMed Mentions:
373 Fields:
Translation:
Cells
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UCSF ChimeraX: Structure visualization for researchers, educators, and developers. Protein Sci. 2021 01; 30(1):70-82.
Pettersen EF, Goddard TD, Huang CC, Meng EC, Couch GS, Croll TI, Morris JH, Ferrin TE. PMID: 32881101; PMCID: PMC7737788.
View in:
PubMed Mentions:
3092 Fields:
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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; PMCID: PMC6918091.
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PubMed Mentions: Fields:
Translation:
Cells
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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; PMCID: PMC7108332.
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PubMed Mentions:
19 Fields:
Translation:
Cells
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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).
Somboonna N, Ziklo N, Ferrin TE, Hyuk Suh J, Dean D. PMID: 31311884; PMCID: PMC6635532.
View in:
PubMed Mentions:
15 Fields:
Translation:
HumansCells
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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; PMCID: PMC6223615.
View in:
PubMed Mentions:
24 Fields:
Translation:
HumansAnimalsCells
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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; PMCID: PMC5614560.
View in:
PubMed Mentions:
60 Fields:
Translation:
HumansCells
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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; PMCID: PMC5734306.
View in:
PubMed Mentions:
2176 Fields:
Translation:
Cells
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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; PMCID: PMC5368075.
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PubMed Mentions:
5 Fields:
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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; PMCID: PMC5302317.
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PubMed Mentions:
11 Fields:
Translation:
Cells
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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; PMCID: PMC5467563.
View in:
PubMed Mentions:
2 Fields:
Translation:
Cells
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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; PMCID: PMC5467548.
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PubMed Mentions:
2 Fields:
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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; PMCID: PMC5106842.
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PubMed Mentions:
2 Fields:
Translation:
Cells
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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; PMCID: PMC4980276.
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PubMed Mentions:
15 Fields:
Translation:
HumansCells
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CyAnimator: Simple Animations of Cytoscape Networks. F1000Res. 2015; 4:482.
Morris JH, Vijay D, Federowicz S, Pico AR, Ferrin TE. PMID: 26937268; PMCID: PMC4752027.
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PubMed Mentions:
8 Fields:
-
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; PMCID: PMC4933300.
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PubMed Mentions:
96 Fields:
Translation:
HumansCells
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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; PMCID: PMC4423039.
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PubMed Mentions:
8 Fields:
Translation:
Cells
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MDA Generates Models of Large Multidomain Proteins. Biophysical Journal. 2015; 108(9):2097-2102.
Hertig S, Goddard TD, Johnson GT, Ferrin TE. View Publication.
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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; PMCID: PMC4410660.
View in:
PubMed Mentions:
27 Fields:
Translation:
Cells
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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; PMCID: PMC4271147.
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PubMed Mentions:
3 Fields:
Translation:
HumansCells
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enhancedGraphics: a Cytoscape app for enhanced node graphics. F1000Res. 2014; 3:147.
Morris JH, Kuchinsky A, Ferrin TE, Pico AR. PMID: 25285206; PMCID: PMC4176421.
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PubMed Mentions:
26 Fields:
-
setsApp: Set operations for Cytoscape Nodes and Edges. F1000Res. 2014; 3:149.
Morris JH, Wu A, Doncheva NT, Albrecht M, Ferrin TE. PMID: 25352980; PMCID: PMC4207244.
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PubMed Mentions:
5 Fields:
-
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; PMCID: PMC4086125.
View in:
PubMed Mentions:
69 Fields:
Translation:
Cells
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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; PMCID: PMC3965090.
View in:
PubMed Mentions:
132 Fields:
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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; PMCID: PMC3396779.
View in:
PubMed Mentions:
39 Fields:
Translation:
HumansCells
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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
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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; PMCID: PMC3262844.
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PubMed Mentions:
302 Fields:
Translation:
Animals
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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; PMCID: PMC3329222.
View in:
PubMed Mentions:
61 Fields:
Translation:
HumansAnimalsCells
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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; PMCID: PMC3410985.
View in:
PubMed Mentions:
282 Fields:
Translation:
AnimalsCells
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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; PMCID: PMC3227682.
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PubMed Mentions:
16 Fields:
Translation:
HumansAnimalsCells
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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; PMCID: PMC3031030.
View in:
PubMed Mentions:
19 Fields:
Translation:
Cells
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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; PMCID: PMC3013688.
View in:
PubMed Mentions:
143 Fields:
Translation:
Cells
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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; PMCID: PMC2976715.
View in:
PubMed Mentions:
104 Fields:
Translation:
Cells
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Workshop on molecular animation. Structure. 2010 Oct 13; 18(10):1261-5.
Bromberg S, Chiu W, Ferrin TE. PMID: 20947014; PMCID: PMC3071847.
View in:
PubMed Mentions:
1 Fields:
Translation:
HumansCells
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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; PMCID: PMC2957254.
View in:
PubMed Mentions:
9 Fields:
Translation:
HumansCells
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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; PMCID: PMC2938059.
View in:
PubMed Mentions:
6 Fields:
Translation:
HumansAnimalsCells
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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; PMCID: PMC2866268.
View in:
PubMed Mentions:
52 Fields:
Translation:
HumansCells
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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; PMCID: PMC2976711.
View in:
PubMed Mentions:
22 Fields:
Translation:
HumansCells
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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; PMCID: PMC2735003.
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PubMed Mentions:
15 Fields:
Translation:
HumansCells
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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; PMCID: PMC2631154.
View in:
PubMed Mentions:
254 Fields:
Translation:
HumansCells
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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; PMCID: PMC2949062.
View in:
PubMed Mentions:
41 Fields:
Translation:
HumansCells
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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; PMCID: PMC2670604.
View in:
PubMed Mentions:
20 Fields:
Translation:
HumansCells
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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; PMCID: PMC2682268.
View in:
PubMed Mentions:
14 Fields:
Translation:
HumansAnimalsCells
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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; PMCID: PMC2612728.
View in:
PubMed Mentions:
48 Fields:
Translation:
HumansCells
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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:
22 Fields:
Translation:
HumansCells
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Visualization software for molecular assemblies. Curr Opin Struct Biol. 2007 Oct; 17(5):587-95.
Goddard TD, Ferrin TE. PMID: 17728125; PMCID: PMC2174518.
View in:
PubMed Mentions:
15 Fields:
Translation:
Cells
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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; PMCID: PMC1910612.
View in:
PubMed Mentions:
8 Fields:
Translation:
AnimalsCells
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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:
38 Fields:
Translation:
Cells
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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; PMCID: PMC1617135.
View in:
PubMed Mentions: Fields:
Translation:
Animals
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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:
20 Fields:
Translation:
HumansCells
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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:
497 Fields:
Translation:
Cells
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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; PMCID: PMC1570152.
View in:
PubMed Mentions:
285 Fields:
Translation:
Cells
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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:
61 Fields:
Translation:
HumansAnimalsCells
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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:
1 Fields:
Translation:
Humans
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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
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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:
1 Fields:
Translation:
Humans
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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:
88 Fields:
Translation:
HumansAnimals
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Designed divergent evolution of enzyme function. Nature. 2006 Apr 20; 440(7087):1078-82.
Yoshikuni Y, Ferrin TE, Keasling JD. PMID: 16495946.
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PubMed Mentions:
134 Fields:
Translation:
Cells
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Nucleic acid visualization with UCSF Chimera. Nucleic Acids Res. 2006 Feb 14; 34(4):e29.
Couch GS, Hendrix DK, Ferrin TE. PMID: 16478715; PMCID: PMC1368656.
View in:
PubMed Mentions:
33 Fields:
Translation:
Cells
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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; PMCID: PMC1347459.
View in:
PubMed Mentions:
61 Fields:
Translation:
AnimalsCells
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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:
37 Fields:
Translation:
AnimalsCells
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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:
37 Fields:
Translation:
Humans
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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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PubMed Mentions:
11 Fields:
Translation:
HumansAnimalsCells
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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.
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PubMed Mentions:
34 Fields:
Translation:
HumansAnimalsCells
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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.
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PubMed Mentions:
113 Fields:
Translation:
Cells
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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.
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PubMed Mentions:
9 Fields:
Translation:
HumansAnimalsCells
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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.
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PubMed Mentions:
18 Fields:
Translation:
HumansAnimalsCells
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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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PubMed Mentions: Fields:
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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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PubMed Mentions:
14 Fields:
Translation:
Cells
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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.
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PubMed Mentions:
19459 Fields:
Translation:
Cells
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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.
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PubMed Mentions:
3 Fields:
Translation:
Humans
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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.
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PubMed Mentions:
17 Fields:
Translation:
HumansCells
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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; PMCID: PMC308829.
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PubMed Mentions:
88 Fields:
Translation:
HumansAnimalsCells
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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, Pharmacogenetics of Membrane Transporters Investigators. PMID: 12893986.
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PubMed Mentions:
108 Fields:
Translation:
HumansCells
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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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PubMed Mentions:
4 Fields:
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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.
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PubMed Mentions:
23 Fields:
Translation:
HumansAnimalsCells
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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, Pharmacogenetics Of Membrane Transporters Investigators. PMID: 12719534; PMCID: PMC156299.
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PubMed Mentions:
83 Fields:
Translation:
HumansAnimalsCells
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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, Pharmacogenetics Of Membrane Transporters Investigators. PMID: 12719533; PMCID: PMC156298.
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PubMed Mentions:
82 Fields:
Translation:
Humans
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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.
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PubMed Mentions:
15 Fields:
Translation:
Cells
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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.
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PubMed Mentions:
1 Fields:
Translation:
HumansAnimalsCells
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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; PMCID: PMC165511.
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PubMed Mentions:
147 Fields:
Translation:
AnimalsCells
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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; PMCID: PMC165574.
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PubMed Mentions:
5 Fields:
Translation:
AnimalsCells
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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, Pharmacogenetics of Membrane Transporters Investigators. PMID: 12142729.
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PubMed Mentions:
49 Fields:
Translation:
HumansAnimalsCells
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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.
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PubMed Mentions:
8 Fields:
Translation:
Cells
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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.
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PubMed Mentions:
11 Fields:
Translation:
Cells
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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.
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PubMed Mentions:
1 Fields:
Translation:
Humans
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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.
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PubMed Mentions:
3 Fields:
Translation:
Cells
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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.
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PubMed Mentions:
23 Fields:
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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.
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PubMed Mentions:
21 Fields:
Translation:
Cells
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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.
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PubMed Mentions:
2 Fields:
Translation:
Cells
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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.
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PubMed Mentions:
1 Fields:
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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.
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PubMed Mentions:
2 Fields:
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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.
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PubMed Mentions:
10 Fields:
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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.
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PubMed Mentions:
450 Fields:
Translation:
Cells
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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.
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PubMed Mentions:
8 Fields:
Translation:
HumansCells
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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.
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PubMed Mentions:
18 Fields:
Translation:
Cells