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We dissimenate 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:

  1. 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
  2. Goddard TD, Ferrin TE. Visualization software for molecular assemblies. Curr Opin Struct Biol. 2007 Oct;17(5):587-95. PMID: 17728125
  3. Morris JH, Huang CC, Babbitt PC, Ferrin TE. structureViz: linking Cytoscape and UCSF Chimera. Bioinformatics. 2007 Sep 1;23(17):2345-7. PMID: 17623706
  4. Goddard TD, Huang CC, Ferrin TE. Visualizing density maps with UCSF Chimera. J Struct Biol. 2007 Jan;157(1):281-7. PMID: 16963278
  5. 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
  6. 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
  7. Couch GS, Hendrix DK, Ferrin TE. Nucleic acid visualization with UCSF Chimera. Nucleic Acids Res. 2006 Feb 14;34(4):e29. PMID: 16478715
  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. 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
  9. 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
  10. 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
  11. 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
  12. 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
  13. 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
  14. 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
  15. 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
  16. 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
  17. 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
  18. 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
  19. 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
  20. 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
  21. 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
  22. 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):1325-1327. PMID: 17773334
  23. 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
  24. 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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