Tom Ferrin, PhD
Professor
Pharmaceutical Chemistry
School of Pharmacy

Our tools are applied daily to diverse types of biomolecular data, including atomic-resolution coordinates, 3D cryo-EM and X-ray density maps, light microscopy data sets, and protein and nucleic acid sequences, annotations, and networks. Our primary research efforts are in the interactive visualization and analysis of structures of molecules and molecular assemblies, protein sequence-structure relationships, and network representations of protein similarity, binding interactions, and biological pathways. These areas are critical for addressing important and highly relevant biomedical problems such as identifying the molecular bases of disease, annotating proteins of unknown function, identifying targets for drug development, designing new drugs, and engineering proteins with new functions. For many years we have been disseminating well-documented and robust software tools via our web site so that scientists world-wide can advance their own research programs effectively. Our current software development efforts are focused on ChimeraX, our next-generation desktop app for the interactive visualization and analysis of molecular structures and related data.

• UCSF ChimeraX: Tools for structure building and analysis.
  Protein science : a publication of the Protein Society 2023 Meng EC, Goddard TD, Pettersen EF, Couch GS, Pearson ZJ, Morris JH, Ferrin TE
• Reply to Rockey et al., "Genomics and Chlamydial Persistence In Vivo".
  mBio 2019 Dean D, Ziklo N, Somboonna N, Suh JH, Ferrin T
• Federating Structural Models and Data: Outcomes from A Workshop on Archiving Integrative Structures.
  Structure (London, England : 1993) 2019 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…
• Clinical Persistence of Chlamydia trachomatis Sexually Transmitted Strains Involves Novel Mutations in the Functional αββα Tetramer of the Tryptophan Synthase Operon.
  mBio 2019 Somboonna N, Ziklo N, Ferrin TE, Hyuk Suh J, Dean D
• Actin-based protrusions of migrating neutrophils are intrinsically lamellar and facilitate direction changes.
  eLife 2017 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
• An approach to functionally relevant clustering of the protein universe: Active site profile-based clustering of protein structures and sequences.
  Protein science : a publication of the Protein Society 2017 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
• An Atlas of Peroxiredoxins Created Using an Active Site Profile-Based Approach to Functionally Relevant Clustering of Proteins.
  PLoS computational biology 2017 Harper AF, Leuthaeuser JB, Babbitt PC, Morris JH, Ferrin TE, Poole LB, Fetrow JS
• Biocuration in the structure-function linkage database: the anatomy of a superfamily.
  Database : the journal of biological databases and curation 2017 Holliday GL, Brown SD, Akiva E, Mischel D, Hicks MA, Morris JH, Huang CC, Meng EC, Pegg SC, Ferrin TE, Babbitt PC
• Biocuration in the structure-function linkage database: the anatomy of a superfamily.
  Database : the journal of biological databases and curation 2017 Holliday GL, Brown SD, Akiva E, Mischel D, Hicks MA, Morris JH, Huang CC, Meng EC, Pegg SC, Ferrin TE, Babbitt PC
• DASP3: identification of protein sequences belonging to functionally relevant groups.
  BMC bioinformatics 2016 Leuthaeuser JB, Morris JH, Harper AF, Ferrin TE, Babbitt PC, Fetrow JS
• Transcriptomic variation of pharmacogenes in multiple human tissues and lymphoblastoid cell lines.
  The pharmacogenomics journal 2016 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…
• CyAnimator: Simple Animations of Cytoscape Networks.
  F1000Research 2015 Morris JH, Vijay D, Federowicz S, Pico AR, Ferrin TE
• Outcome of the First wwPDB Hybrid/Integrative Methods Task Force Workshop.
  Structure (London, England : 1993) 2015 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, …
• MDA Generates Models of Large Multidomain Proteins
  Biophysical Journal 2015 Hertig S, Goddard TD, Johnson GT, Ferrin TE
• Multidomain Assembler (MDA) Generates Models of Large Multidomain Proteins.
  Biophysical journal 2015 Hertig S, Goddard TD, Johnson GT, Ferrin TE
• RRDistMaps: a UCSF Chimera tool for viewing and comparing protein distance maps.
  Bioinformatics (Oxford, England) 2014 Chen JE, Huang CC, Ferrin TE
• cddApp: a Cytoscape app for accessing the NCBI conserved domain database.
  Bioinformatics (Oxford, England) 2014 Morris JH, Wu A, Yamashita RA, Marchler-Bauer A, Ferrin TE
• enhancedGraphics: a Cytoscape app for enhanced node graphics.
  F1000Research 2014 Morris JH, Kuchinsky A, Ferrin TE, Pico AR
• setsApp: Set operations for Cytoscape Nodes and Edges.
  F1000Research 2014 Morris JH, Wu A, Doncheva NT, Albrecht M, Ferrin TE
• Enhancing UCSF Chimera through web services.
  Nucleic acids research 2014 Huang CC, Meng EC, Morris JH, Pettersen EF, Ferrin TE
• The Structure-Function Linkage Database.
  Nucleic acids research 2013 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 …
• Genetic and epigenetic regulation of the organic cation transporter 3, SLC22A3.
  The pharmacogenomics journal 2012 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
• Macromolecular assembly structures by comparative modeling and electron microscopy.
  Methods in molecular biology (Clifton, N.J.) 2012 Lasker K, Velázquez-Muriel JA, Webb BM, Yang Z, Ferrin TE, Sali A
• clusterMaker: a multi-algorithm clustering plugin for Cytoscape.
  BMC bioinformatics 2011 Morris JH, Apeltsin L, Newman AM, Baumbach J, Wittkop T, Su G, Bader GD, Ferrin TE
• A common 5'-UTR variant in MATE2-K is associated with poor response to metformin.
  Clinical pharmacology and therapeutics 2011 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 …
• UCSF Chimera, MODELLER, and IMP: an integrated modeling system.
  Journal of structural biology 2011 Yang Z, Lasker K, Schneidman-Duhovny D, Webb B, Huang CC, Pettersen EF, Goddard TD, Meng EC, Sali A, Ferrin TE
• Functional characterization of liver enhancers that regulate drug-associated transporters.
  Clinical pharmacology and therapeutics 2011 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
• Improving the quality of protein similarity network clustering algorithms using the network edge weight distribution.
  Bioinformatics (Oxford, England) 2010 Apeltsin L, Morris JH, Babbitt PC, Ferrin TE
• ModBase, a database of annotated comparative protein structure models, and associated resources.
  Nucleic acids research 2010 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, …
• Role of organic cation transporter 3 (SLC22A3) and its missense variants in the pharmacologic action of metformin.
  Pharmacogenetics and genomics 2010 Chen L, Pawlikowski B, Schlessinger A, More SS, Stryke D, Johns SJ, Portman MA, Chen E, Ferrin TE, Sali A, Giacomini KM
• Workshop on molecular animation.
  Structure (London, England : 1993) 2010 Bromberg S, Chiu W, Ferrin TE
• Genetic variants of human organic anion transporter 4 demonstrate altered transport of endogenous substrates.
  American journal of physiology. Renal physiology 2010 Shima JE, Komori T, Taylor TR, Stryke D, Kawamoto M, Johns SJ, Carlson EJ, Ferrin TE, Giacomini KM
• Computational tools for the interactive exploration of proteomic and structural data.
  Molecular & cellular proteomics : MCP 2010 Morris JH, Meng EC, Ferrin TE
• Comparison of human solute carriers.
  Protein science : a publication of the Protein Society 2010 Schlessinger A, Matsson P, Shima JE, Pieper U, Yee SW, Kelly L, Apeltsin L, Stroud RM, Ferrin TE, Giacomini KM, Sali A
• Identification and characterization of novel polymorphisms in the basal promoter of the human transporter, MATE1.
  Pharmacogenetics and genomics 2009 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
• Genetic variation in the proximal promoter of ABC and SLC superfamilies: liver and kidney specific expression and promoter activity predict variation.
  PloS one 2009 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, …
• Using sequence similarity networks for visualization of relationships across diverse protein superfamilies.
  PloS one 2009 Atkinson HJ, Morris JH, Ferrin TE, Babbitt PC
• Genetic variants in multidrug and toxic compound extrusion-1, hMATE1, alter transport function.
  The pharmacogenomics journal 2009 Chen Y, Teranishi K, Li S, Yee SW, Hesselson S, Stryke D, Johns SJ, Ferrin TE, Kwok P, Giacomini KM
• Functional genetic variation in the basal promoter of the organic cation/carnitine transporters OCTN1 (SLC22A4) and OCTN2 (SLC22A5).
  The Journal of pharmacology and experimental therapeutics 2009 Tahara H, Yee SW, Urban TJ, Hesselson S, Castro RA, Kawamoto M, Stryke D, Johns SJ, Ferrin TE, Kwok PY, Giacomini KM
• Identification and characterization of proximal promoter polymorphisms in the human concentrative nucleoside transporter 2 (SLC28A2).
  The Journal of pharmacology and experimental therapeutics 2008 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
• The human multidrug resistance protein 4 (MRP4, ABCC4): functional analysis of a highly polymorphic gene.
  The Journal of pharmacology and experimental therapeutics 2008 Abla N, Chinn LW, Nakamura T, Liu L, Huang CC, Johns SJ, Kawamoto M, Stryke D, Taylor TR, Ferrin TE, Giacomini KM, Kroetz DL
• Functional effects of protein sequence polymorphisms in the organic cation/ergothioneine transporter OCTN1 (SLC22A4).
  Pharmacogenetics and genomics 2007 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
• Visualization software for molecular assemblies.
  Current opinion in structural biology 2007 Goddard TD, Ferrin TE
• Modeling insertional mutagenesis using gene length and expression in murine embryonic stem cells.
  PloS one 2007 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
• structureViz: linking Cytoscape and UCSF Chimera.
  Bioinformatics (Oxford, England) 2007 Morris JH, Huang CC, Babbitt PC, Ferrin TE
• Comparison of methods for genomic localization of gene trap sequences.
  BMC genomics 2006 Harper CA, Huang CC, Stryke D, Kawamoto M, Ferrin TE, Babbitt PC
• Functional genetic diversity in the high-affinity carnitine transporter OCTN2 (SLC22A5).
  Molecular pharmacology 2006 Urban TJ, Gallagher RC, Brown C, Castro RA, Lagpacan LL, Brett CM, Taylor TR, Carlson EJ, Ferrin TE, Burchard EG, Packman S, Giacomini KM
• Visualizing density maps with UCSF Chimera.
  Journal of structural biology 2006 Goddard TD, Huang CC, Ferrin TE
• Tools for integrated sequence-structure analysis with UCSF Chimera.
  BMC bioinformatics 2006 Meng EC, Pettersen EF, Couch GS, Huang CC, Ferrin TE
• Interaction of methotrexate with organic-anion transporting polypeptide 1A2 and its genetic variants.
  The Journal of pharmacology and experimental therapeutics 2006 Badagnani I, Castro RA, Taylor TR, Brett CM, Huang CC, Stryke D, Kawamoto M, Johns SJ, Ferrin TE, Carlson EJ, Burchard EG, Giacomini KM
• PharmGKB submission update: IV. PMT submissions of genetic variations in ATP-Binding cassette transporters to the PharmGKB network.
  Pharmacological reviews 2006 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
• PharmGKB submission update: V. PMT submissions of genetic variation in SLC22 family transporters.
  Pharmacological reviews 2006 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 …
• PharmGKB submission update: VI. PMT submissions of genetic variations in neurotransmitter transporters (SLC6, SLC17, and SLC18) to the PharmGKB network.
  Pharmacological reviews 2006 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 …
• Leveraging enzyme structure-function relationships for functional inference and experimental design: the structure-function linkage database.
  Biochemistry 2006 Pegg SC, Brown SD, Ojha S, Seffernick J, Meng EC, Morris JH, Chang PJ, Huang CC, Ferrin TE, Babbitt PC
• Designed divergent evolution of enzyme function.
  Nature 2006 Yoshikuni Y, Ferrin TE, Keasling JD
• Nucleic acid visualization with UCSF Chimera.
  Nucleic acids research 2006 Couch GS, Hendrix DK, Ferrin TE
• Engineering cotton (+)-delta-cadinene synthase to an altered function: germacrene D-4-ol synthase.
  Chemistry & biology 2006 Yoshikuni Y, Martin VJ, Ferrin TE, Keasling JD
• The International Gene Trap Consortium Website: a portal to all publicly available gene trap cell lines in mouse.
  Nucleic acids research 2006 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, …
• The human organic anion transporter 3 (OAT3; SLC22A8): genetic variation and functional genomics.
  American journal of physiology. Renal physiology 2005 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
• Functional characterization and haplotype analysis of polymorphisms in the human equilibrative nucleoside transporter, ENT2.
  Drug metabolism and disposition: the biological fate of chemicals 2005 Owen RP, Lagpacan LL, Taylor TR, De La Cruz M, Huang CC, Kawamoto M, Johns SJ, Stryke D, Ferrin TE, Giacomini KM
• Functional analysis of polymorphisms in the organic anion transporter, SLC22A6 (OAT1).
  Pharmacogenetics and genomics 2005 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
• Software extensions to UCSF chimera for interactive visualization of large molecular assemblies.
  Structure (London, England : 1993) 2005 Goddard TD, Huang CC, Ferrin TE
• Genetic analysis and functional characterization of polymorphisms in the human concentrative nucleoside transporter, CNT2.
  Pharmacogenetics and genomics 2005 Owen RP, Gray JH, Taylor TR, Carlson EJ, Huang CC, Kawamoto M, Johns SJ, Stryke D, Ferrin TE, Giacomini KM
• Enhancing data sharing in collaborative research projects with DASH.
  Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 2005 Ferrin TE, Huang CC, Greenblatt DM, Stryke D, Giacomini KM, Morris JH
• Functional analysis of genetic variants in the human concentrative nucleoside transporter 3 (CNT3; SLC28A3).
  The pharmacogenomics journal 2005 Badagnani I, Chan W, Castro RA, Brett CM, Huang CC, Stryke D, Kawamoto M, Johns SJ, Ferrin TE, Carlson EJ, Burchard EG, Giacomini KM
• Representing structure-function relationships in mechanistically diverse enzyme superfamilies.
  Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 2005 Pegg SC, Brown S, Ojha S, Huang CC, Ferrin TE, Babbitt PC
• UCSF Chimera--a visualization system for exploratory research and analysis.
  Journal of computational chemistry 2004 Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC, Ferrin TE
• PharmGKB update: III. Genetic variants of SLC22A1, solute carrier family 22 (organic cation transporter), member 1.
  Pharmacological reviews 2004 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
• Functional and genetic diversity in the concentrative nucleoside transporter, CNT1, in human populations.
  Molecular pharmacology 2004 Gray JH, Mangravite LM, Owen RP, Urban TJ, Chan W, Carlson EJ, Huang CC, Kawamoto M, Johns SJ, Stryke D, Ferrin TE, Giacomini KM
• MODBASE, a database of annotated comparative protein structure models, and associated resources.
  Nucleic acids research 2004 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
• Sequence diversity and haplotype structure in the human ABCB1 (MDR1, multidrug resistance transporter) gene.
  Pharmacogenetics 2003 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 …
• PharmGKB update: I. Genetic variants of the organic cation transporter 2 (OCT2, SLC22A2).
  Pharmacological reviews 2003 Leabman MK, Huang CC, Stryke D, Johns SJ, Kawamoto M, Ferrin TE, DeYoung J, Taylor TR, De La Cruz M, Herskowitz I, Giacomini KM
• Functional characterization in yeast of genetic variants in the human equilibrative nucleoside transporter, ENT1.
  Pharmacogenetics 2003 Osato DH, Huang CC, Kawamoto M, Johns SJ, Stryke D, Wang J, Ferrin TE, Herskowitz I, Giacomini KM
• Evolutionary conservation predicts function of variants of the human organic cation transporter, OCT1.
  Proceedings of the National Academy of Sciences of the United States of America 2003 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
• Natural variation in human membrane transporter genes reveals evolutionary and functional constraints.
  Proceedings of the National Academy of Sciences of the United States of America 2003 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…
• MINRMS: an efficient algorithm for determining protein structure similarity using root-mean-squared-distance.
  Bioinformatics (Oxford, England) 2003 Jewett AI, Huang CC, Ferrin TE
• BayGenomics: a resource of insertional mutations in mouse embryonic stem cells.
  Nucleic acids research 2003 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
• SNP analysis and presentation in the Pharmacogenetics of Membrane Transporters Project.
  Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 2003 Stryke D, Huang CC, Kawamoto M, Johns SJ, Carlson EJ, Deyoung JA, Leabman MK, Herskowitz I, Giacomini KM, Ferrin TE
• The Structure Superposition Database.
  Nucleic acids research 2003 Chiang RA, Meng EC, Huang CC, Ferrin TE, Babbitt PC
• Polymorphisms in a human kidney xenobiotic transporter, OCT2, exhibit altered function.
  Pharmacogenetics 2002 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
• Integrated tools for structural and sequence alignment and analysis.
  Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 2000 Huang CC, Novak WR, Babbitt PC, Jewett AI, Ferrin TE, Klein TE
• Molecules to maps: tools for visualization and interaction in support of computational biology.
  Bioinformatics (Oxford, England) 1998 Kraemer ET, Ferrin TE
• The object technology framework: an object-oriented interface to molecular data and its application to collagen.
  Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 1998 Huang CC, Couch GS, Pettersen EF, Ferrin TE, Howard AE, Klein TE
• Annotating PDB files with scene information.
  Journal of molecular graphics 1995 Couch GS, Pettersen EF, Huang CC, Ferrin TE
• Automated site-directed drug design using molecular lattices.
  Journal of molecular graphics 1992 Lewis RA, Roe DC, Huang C, Ferrin TE, Langridge R, Kuntz ID
• Conic: a fast renderer for space-filling molecules with shadows.
  Journal of molecular graphics 1991 Huang CC, Pettersen EF, Klein TE, Ferrin TE, Langridge R
• Molecular structure and dynamics of tricyclic antidepressant drugs.
  European neuropsychopharmacology : the journal of the European College of Neuropsychopharmacology 1991 Heimstad E, Edvardsen O, Ferrin TE, Dahl SG
• An affordable approach to interactive desktop molecular modeling.
  Journal of molecular graphics 1991 Ferrin TE, Couch GS, Huang CC, Pettersen EF, Langridge R
• A real-time malleable molecular surface.
  Journal of molecular graphics 1990 Klein TE, Huang CC, Pettersen EF, Couch GS, Ferrin TE, Langridge R
• Van der waals surfaces in molecular modeling: implementation with real-time computer graphics.
  Science (New York, N.Y.) 1983 Bash PA, Pattabiraman N, Huang C, Ferrin TE, Langridge R
• A geometric approach to macromolecule-ligand interactions.
  Journal of molecular biology 1982 Kuntz ID, Blaney JM, Oatley SJ, Langridge R, Ferrin TE
• Computer graphics in drug design: molecular modeling of thyroid hormone-prealbumin interactions.
  Journal of medicinal chemistry 1982 Blaney JM, Jorgensen EC, Connolly ML, Ferrin TE, Langridge R, Oatley SJ, Burridge JM, Blake CC