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We disseminate the technology developed within our Center via the publication of scientific papers and through distribution of documented source code so that others can can use our software for research applications or as a starting point for their own developments. Here are links to a selected list of our publications:

• Jäger S, Cimermancic P, Gulbahce N, Johnson JR, McGovern KE, Clarke SC, Shales M, Mercenne G, Pache L, Li K, Hernandez H, Jang GM, Roth SL, Akiva E, Marlett J, Stephens M, D'Orso I, Fernandes J, Fahey M, Mahon C, O'Donoghue AJ, Todorovic A, Morris JH, Maltby DA, Alber T, Cagney G, Bushman FD, Young JA, Chanda SK, Sundquist WI, Kortemme T, Hernandez RD, Craik CS, Burlingame A, Sali A, Frankel AD, Krogan NJ, Global landscape of HIV-human protein complexes, Nature, 2011 Dec 21, 481(7381):365-70. PMID:22190034 PMCID: PMC3310911
• 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, 2011 Nov 9, 12:436. PMID:22070249 PMCID: PMC3262844
• 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, J Struct Biol, 2012 Sep, 179(3):269-78. PMID:21963794 PMCID: PMC3410985
• Apeltsin L, Morris JH, Babbitt PC, Ferrin TE, Improving the quality of protein similarity network clustering algorithms using the network edge weight distribution, Bioinformatics, 2011 Feb 1, 27(3):326-33. PMID:21118823 PMCID: PMC3031030
• Bromberg S, Chiu W, Ferrin TE, Workshop on molecular animation, Structure, 2010 Oct 13, 18(10):1261-5. PMID:20947014 PMCID: PMC3071847
• Morris JH, Meng EC, Ferrin TE, Computational tools for the interactive exploration of proteomic and structural data, Mol Cell Proteomics, 2010 Aug, 9(8):1703-15. PMID:20525940 PMCID: PMC2938059
• Atkinson HJ, Morris JH, Ferrin TE, Babbitt PC, Using sequence similarity networks for visualization of relationships across diverse protein superfamilies, PLoS One, 2009, 4(2):e4345. PMID:19190775 PMCID: PMC2631154
• Goddard TD, Ferrin TE, Visualization software for molecular assemblies, Curr Opin Struct Biol, 2007 Oct, 17(5):587-95. PMID:17728125 PMCID: PMC2174518
• Morris JH, Huang CC, Babbitt PC, Ferrin TE, structureViz: linking Cytoscape and UCSF Chimera, Bioinformatics, 2007 Sep 1, 23(17):2345-7. PMID:17623706
• Goddard TD, Huang CC, Ferrin TE, Visualizing density maps with UCSF Chimera, J Struct Biol, 2007 Jan, 157(1):281-7. PMID:16963278
• Meng EC, Pettersen EF, Couch GS, Huang CC, Ferrin TE, Tools for integrated sequence-structure analysis with UCSF Chimera, BMC Bioinformatics, 2006 Jul 12, 7:339. PMID:16836757 PMCID: PMC1570152
• 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, 2006 Feb 28, 45(8):2545-55. PMID:16489747
• Couch GS, Hendrix DK, Ferrin TE, Nucleic acid visualization with UCSF Chimera, Nucleic Acids Res, 2006 Feb 14, 34(4):e29. PMID:16478715 PMCID: PMC1368656
• 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, The International Gene Trap Consortium Website: a portal to all publicly available gene trap cell lines in mouse, Nucleic Acids Res, 2006 Jan 1, 34(Database issue):D642-8. PMID:16381950 PMCID: PMC1347459
• Goddard TD, Huang CC, Ferrin TE, Software extensions to UCSF chimera for interactive visualization of large molecular assemblies, Structure, 2005 Mar, 13(3):473-82. PMID:15766548
• Pegg SC, Brown S, Ojha S, Huang CC, Ferrin TE, Babbitt PC, Representing structure-function relationships in mechanistically diverse enzyme superfamilies, Pac Symp Biocomput, 2005, 358-69. PMID:15759641
• Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC, Ferrin TE, UCSF Chimera--a visualization system for exploratory research and analysis, J Comput Chem, 2004 Oct, 25(13):1605-12. PMID:15264254
• Jewett AI, Huang CC, Ferrin TE, MINRMS: an efficient algorithm for determining protein structure similarity using root-mean-squared-distance, Bioinformatics, 2003 Mar 22, 19(5):625-34. PMID:12651721
• 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, Pac Symp Biocomput, 2003, 535-47. PMID:12603056
• Chiang RA, Meng EC, Huang CC, Ferrin TE, Babbitt PC, The Structure Superposition Database, Nucleic Acids Res, 2003 Jan 1, 31(1):505-10. PMID:12520064 PMCID: PMC165574
• Huang CC, Novak WR, Babbitt PC, Jewett AI, Ferrin TE, Klein TE, Integrated tools for structural and sequence alignment and analysis, Pac Symp Biocomput, 2000, 230-41. PMID:10902172
• 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, Pac Symp Biocomput, 1998, 349-61. PMID:9697195
• Couch GS, Pettersen EF, Huang CC, Ferrin TE, Annotating PDB files with scene information, J Mol Graph, 1995 Jun, 13(3):153-8, 193. PMID:7577842
• Huang CC, Pettersen EF, Klein TE, Ferrin TE, Langridge R, Conic: a fast renderer for space-filling molecules with shadows, J Mol Graph, 1991 Dec, 9(4):230-6, 242. PMID:1772848
• Klein TE, Huang CC, Pettersen EF, Couch GS, Ferrin TE, Langridge R, A real-time malleable molecular surface, J Mol Graph, 1990 Mar, 8(1):16-24, 26. PMID:2268622
• Ferrin TE, Huang CC, Jarvis LE, Langridge R, The MIDAS database system, J Mol Graph. 1988 Mar;6(1):2-12. DOI: 10.1016/0263-7855(88)80053-5
• Ferrin TE, Huang CC, Jarvis LE, Langridge R, The MIDAS display system, J Mol Graph. 1988 Mar;6(1):13-27. DOI: 10.1016/0263-7855(88)80054-7
• Bash PA, Pattabiraman N, Huang C, Ferrin TE, Langridge R, Van der waals surfaces in molecular modeling: implementation with real-time computer graphics, Science, 1983 Dec 23, 222(4630):1325-7. PMID:17773334
• Kuntz ID, Blaney JM, Oatley SJ, Langridge R, Ferrin TE, A geometric approach to macromolecule-ligand interactions, J Mol Biol, 1982 Oct 25, 161(2):269-88. PMID:7154081
• Langridge R, Ferrin TE, Kuntz ID, Connolly ML, Real-time color graphics in studies of molecular interactions, Science, 1981 Feb 13, 211(4483):661-6. PMID:7455704

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