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UCSF ChimeraX: Structure visualization for researchers, educators, and developers. Pettersen EF, Goddard TD, Huang CC, Meng EC, Couch GS, Croll TI, Morris JH, Ferrin TE. Protein Sci, 2021, 30(1):70-82. PMID: 32881101 PMCID: 7737788

Federating Structural Models and Data: Outcomes from A Workshop on Archiving Integrative Structures. 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. Structure, 2019, 27(12):1745-1759. PMID: 31780431 PMCID: 7108332

Cytoscape StringApp: Network Analysis and Visualization of Proteomics Data. Doncheva NT, Morris JH, Gorodkin J, Jensen LJ. J Proteome Res, 2019, 18(2):623-632. PMID: 30450911 PMCID: 6800166

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 PMCID: 6445391

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: 6013757

Molecular Visualization on the Holodeck. Goddard TD, Brilliant AA, Skillman TL, Vergenz S, Tyrwhitt-Drake J, Meng EC, Ferrin TE. J Mol Biol, 2018, 430(21):3982-3996. PMID: 29964044 PMCID: 6223615

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, 7None. PMID: 29377793 PMCID: 5788505

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, 27(1):14-25. PMID: 28710774 PMCID: 5734306

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, 2017(1)None. PMID: 28365730 PMCID: 5467563

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, 45(D1):D362-D368. PMID: 27924014 PMCID: 5210637

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, 17(1):458. PMID: 27835946 PMCID: 5106842

RRDistMaps: a UCSF Chimera tool for viewing and comparing protein distance maps. Chen JE, Huang CC, Ferrin TE. Bioinformatics, 2015, 31(9):1484-6. PMID: 25540183 PMCID: 4410660

Enhancing UCSF Chimera through web services. Huang CC, Meng EC, Morris JH, Pettersen EF, Ferrin TE. Nucleic Acids Res, 2014, 42(Web Server issue):W478-84. PMID: 24861624 PMCID: 4086125

The Structure-Function Linkage Database. 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. Nucleic Acids Res, 2014, 42(Database issue):D521-30. PMID: 24271399 PMCID: 3965090

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, 481(7381):365-70. PMID: 22190034 PMCID: 3310911

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, 12:436. PMID: 22070249 PMCID: 3262844

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, 179(3):269-78. PMID: 21963794 PMCID: 3410985

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, 27(3):326-33. PMID: 21118823 PMCID: 3031030

Workshop on molecular animation. Bromberg S, Chiu W, Ferrin TE. Structure, 2010, 18(10):1261-5. PMID: 20947014 PMCID: 3071847

Computational tools for the interactive exploration of proteomic and structural data. Morris JH, Meng EC, Ferrin TE. Mol Cell Proteomics, 2010, 9(8):1703-15. PMID: 20525940 PMCID: 2938059

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: 2631154

Visualization software for molecular assemblies. Goddard TD, Ferrin TE. Curr Opin Struct Biol, 2007, 17(5):587-95. PMID: 17728125 PMCID: 2174518

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

Visualizing density maps with UCSF Chimera. Goddard TD, Huang CC, Ferrin TE. J Struct Biol, 2007, 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, 7:339. PMID: 16836757 PMCID: 1570152

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, 45(8):2545-55. PMID: 16489747

Nucleic acid visualization with UCSF Chimera. Couch GS, Hendrix DK, Ferrin TE. Nucleic Acids Res, 2006, 34(4):e29. PMID: 16478715 PMCID: 1368656

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, 34(Database issue):D642-8. PMID: 16381950 PMCID: 1347459

Software extensions to UCSF chimera for interactive visualization of large molecular assemblies. Goddard TD, Huang CC, Ferrin TE. Structure, 2005, 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, 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, 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, 31(1):505-10. PMID: 12520064 PMCID: 165574

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, 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, 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, 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, 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, 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, 211(4483):661-6. PMID: 7455704