RBVI Publications

about projects people publications resources resources visit us visit us search search

Atlas of the Radical SAM Superfamily: Divergent Evolution of Function Using a "Plug and Play" Domain. Holliday GL, Akiva E, Meng EC, Brown SD, Calhoun S, Pieper U, Sali A, Booker SJ, Babbitt PC. Methods Enzymol, 2018, 606:1-71. PMID: 30097089

The Cytoscape Automation app article collection. Demchak B, Otasek D, Pico AR, Bader GD, Ono K, Settle B, Sage E, Morris JH, Longabaugh W, Lopes C, Kucera M, Treister A, Schwikowski B, Molenaar P, Ideker T. F1000Res, 2018, 7:800. PMID: 29983926 PMCID: PMC6013757

Molecular Visualization on the Holodeck. Goddard TD, Brilliant AA, Skillman TL, Vergenz S, Tyrwhitt-Drake J, Meng EC, Ferrin TE. J Mol Biol, 2018 Oct 19, 430(21):3982-3996. PMID: 29964044

Prediction of enzymatic pathways by integrative pathway mapping. Calhoun S, Korczynska M, Wichelecki DJ, San Francisco B, Zhao S, Rodionov DA, Vetting MW, Al-Obaidi NF, Lin H, O'Meara MJ, Scott DA, Morris JH, Russel D, Almo SC, Osterman AL, Gerlt JA, Jacobson MP, Shoichet BK, Sali A. Elife, 2018 Jan 29, 7. PMID: 29377793 PMCID: PMC5788505

UCSF ChimeraX: Meeting modern challenges in visualization and analysis. Goddard TD, Huang CC, Meng EC, Pettersen EF, Couch GS, Morris JH, Ferrin TE. Protein Sci, 2018 Jan, 27(1):14-25. PMID: 28710774 PMCID: PMC5734306

Biocuration in the structure-function linkage database: the anatomy of a superfamily. Holliday GL, Brown SD, Akiva E, Mischel D, Hicks MA, Morris JH, Huang CC, Meng EC, Pegg SC, Ferrin TE, Babbitt PC. Database (Oxford), 2017 Jan 1, 2017(1). PMID: 28365730 PMCID: PMC5467563

The STRING database in 2017: quality-controlled protein-protein association networks, made broadly accessible. Szklarczyk D, Morris JH, Cook H, Kuhn M, Wyder S, Simonovic M, Santos A, Doncheva NT, Roth A, Bork P, Jensen LJ, von Mering C. Nucleic Acids Res, 2017 Jan 4, 45(D1):D362-D368. PMID: 27924014 PMCID: PMC5210637

DASP3: identification of protein sequences belonging to functionally relevant groups. Leuthaeuser JB, Morris JH, Harper AF, Ferrin TE, Babbitt PC, Fetrow JS. BMC Bioinformatics, 2016 Nov 11, 17(1):458. PMID: 27835946 PMCID: PMC5106842

RRDistMaps: a UCSF Chimera tool for viewing and comparing protein distance maps. Chen JE, Huang CC, Ferrin TE. Bioinformatics, 2015 May 1, 31(9):1484-6. PMID: 25540183 PMCID: PMC4410660

Enhancing UCSF Chimera through web services. Huang CC, Meng EC, Morris JH, Pettersen EF, Ferrin TE. Nucleic Acids Res, 2014 Jul, 42(Web Server issue):W478-84. PMID: 24861624 PMCID: PMC4086125

The Structure-Function Linkage Database. Akiva E, Brown S, Almonacid DE, Barber AE 2nd, 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. Nucleic Acids Res, 2014 Jan, 42(Database issue):D521-30. PMID: 24271399 PMCID: PMC3965090

Macromolecular assembly structures by comparative modeling and electron microscopy. Lasker K, Velázquez-Muriel JA, Webb BM, Yang Z, Ferrin TE, Sali A. Methods Mol Biol, 2012, 857:331-50. PMID: 22323229

Global landscape of HIV-human protein complexes. 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. Nature, 2011 Dec 21, 481(7381):365-70. PMID: 22190034 PMCID: PMC3310911

clusterMaker: a multi-algorithm clustering plugin for Cytoscape. Morris JH, Apeltsin L, Newman AM, Baumbach J, Wittkop T, Su G, Bader GD, Ferrin TE. BMC Bioinformatics, 2011 Nov 9, 12:436. PMID: 22070249 PMCID: PMC3262844

UCSF Chimera, MODELLER, and IMP: an integrated modeling system. Yang Z, Lasker K, Schneidman-Duhovny D, Webb B, Huang CC, Pettersen EF, Goddard TD, Meng EC, Sali A, Ferrin TE. J Struct Biol, 2012 Sep, 179(3):269-78. PMID: 21963794 PMCID: PMC3410985

Improving the quality of protein similarity network clustering algorithms using the network edge weight distribution. Apeltsin L, Morris JH, Babbitt PC, Ferrin TE. Bioinformatics, 2011 Feb 1, 27(3):326-33. PMID: 21118823 PMCID: PMC3031030

Workshop on molecular animation. Bromberg S, Chiu W, Ferrin TE. Structure, 2010 Oct 13, 18(10):1261-5. PMID: 20947014 PMCID: PMC3071847

Computational tools for the interactive exploration of proteomic and structural data. Morris JH, Meng EC, Ferrin TE. Mol Cell Proteomics, 2010 Aug, 9(8):1703-15. PMID: 20525940 PMCID: PMC2938059

Using sequence similarity networks for visualization of relationships across diverse protein superfamilies. Atkinson HJ, Morris JH, Ferrin TE, Babbitt PC. PLoS One, 2009, 4(2):e4345. PMID: 19190775 PMCID: PMC2631154

Visualization software for molecular assemblies. Goddard TD, Ferrin TE. Curr Opin Struct Biol, 2007 Oct, 17(5):587-95. PMID: 17728125 PMCID: PMC2174518

structureViz: linking Cytoscape and UCSF Chimera. Morris JH, Huang CC, Babbitt PC, Ferrin TE. Bioinformatics, 2007 Sep 1, 23(17):2345-7. PMID: 17623706

Visualizing density maps with UCSF Chimera. Goddard TD, Huang CC, Ferrin TE. J Struct Biol, 2007 Jan, 157(1):281-7. PMID: 16963278

Tools for integrated sequence-structure analysis with UCSF Chimera. Meng EC, Pettersen EF, Couch GS, Huang CC, Ferrin TE. BMC Bioinformatics, 2006 Jul 12, 7:339. PMID: 16836757 PMCID: PMC1570152

Leveraging enzyme structure-function relationships for functional inference and experimental design: the structure-function linkage database. Pegg SC, Brown SD, Ojha S, Seffernick J, Meng EC, Morris JH, Chang PJ, Huang CC, Ferrin TE, Babbitt PC. Biochemistry, 2006 Feb 28, 45(8):2545-55. PMID: 16489747

Nucleic acid visualization with UCSF Chimera. Couch GS, Hendrix DK, Ferrin TE. Nucleic Acids Res, 2006 Feb 14, 34(4):e29. PMID: 16478715 PMCID: PMC1368656

The International Gene Trap Consortium Website: a portal to all publicly available gene trap cell lines in mouse. 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. Nucleic Acids Res, 2006 Jan 1, 34(Database issue):D642-8. PMID: 16381950 PMCID: PMC1347459

Software extensions to UCSF chimera for interactive visualization of large molecular assemblies. Goddard TD, Huang CC, Ferrin TE. Structure, 2005 Mar, 13(3):473-82. PMID: 15766548

Representing structure-function relationships in mechanistically diverse enzyme superfamilies. Pegg SC, Brown S, Ojha S, Huang CC, Ferrin TE, Babbitt PC. Pac Symp Biocomput, 2005, 358-69. PMID: 15759641

UCSF Chimera--a visualization system for exploratory research and analysis. Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC, Ferrin TE. J Comput Chem, 2004 Oct, 25(13):1605-12. PMID: 15264254

MINRMS: an efficient algorithm for determining protein structure similarity using root-mean-squared-distance. Jewett AI, Huang CC, Ferrin TE. Bioinformatics, 2003 Mar 22, 19(5):625-34. PMID: 12651721

SNP analysis and presentation in the Pharmacogenetics of Membrane Transporters Project. Stryke D, Huang CC, Kawamoto M, Johns SJ, Carlson EJ, Deyoung JA, Leabman MK, Herskowitz I, Giacomini KM, Ferrin TE. Pac Symp Biocomput, 2003, 535-47. PMID: 12603056

The Structure Superposition Database. Chiang RA, Meng EC, Huang CC, Ferrin TE, Babbitt PC. Nucleic Acids Res, 2003 Jan 1, 31(1):505-10. PMID: 12520064 PMCID: PMC165574

Integrated tools for structural and sequence alignment and analysis. Huang CC, Novak WR, Babbitt PC, Jewett AI, Ferrin TE, Klein TE. Pac Symp Biocomput, 2000, 230-41. PMID: 10902172

The object technology framework: an object-oriented interface to molecular data and its application to collagen. Huang CC, Couch GS, Pettersen EF, Ferrin TE, Howard AE, Klein TE. Pac Symp Biocomput, 1998, 349-61. PMID: 9697195

Annotating PDB files with scene information. Couch GS, Pettersen EF, Huang CC, Ferrin TE. J Mol Graph, 1995 Jun, 13(3):153-8, 193. PMID: 7577842

Conic: a fast renderer for space-filling molecules with shadows. Huang CC, Pettersen EF, Klein TE, Ferrin TE, Langridge R. J Mol Graph, 1991 Dec, 9(4):230-6, 242. PMID: 1772848

A real-time malleable molecular surface. Klein TE, Huang CC, Pettersen EF, Couch GS, Ferrin TE, Langridge R. 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

Van der waals surfaces in molecular modeling: implementation with real-time computer graphics. Bash PA, Pattabiraman N, Huang C, Ferrin TE, Langridge R. Science, 1983 Dec 23, 222(4630):1325-7. PMID: 17773334

A geometric approach to macromolecule-ligand interactions. Kuntz ID, Blaney JM, Oatley SJ, Langridge R, Ferrin TE. J Mol Biol, 1982 Oct 25, 161(2):269-88. PMID: 7154081

Real-time color graphics in studies of molecular interactions. Langridge R, Ferrin TE, Kuntz ID, Connolly ML. Science, 1981 Feb 13, 211(4483):661-6. PMID: 7455704