Thomas E. Ferrin

Publication Activity (10 Years)

Years Active: 1992-2017
Publications (10 Years): 7

Top Topics

Protein Sequences

Top Venues

Database J. Biol. Databases Curation

Nucleic Acids Res.

Publications

Angela F. Harper, Janelle B. Leuthaeuser, Patricia C. Babbitt, John H. Morris, Thomas E. Ferrin, Leslie B. Poole, Jacquelyn S. Fetrow
An Atlas of Peroxiredoxins Created Using an Active Site Profile-Based Approach to Functionally Relevant Clustering of Proteins. PLoS Comput. Biol. 13 (2) (2017)
Gemma L. Holliday, Shoshana D. Brown, Eyal Akiva, David Mischel, Michael A. Hicks, John H. Morris, Conrad C. Huang, Elaine C. Meng, Scott C.-H. Pegg, Thomas E. Ferrin, Patricia C. Babbitt
Biocuration in the structure-function linkage database: the anatomy of a superfamily. Database J. Biol. Databases Curation 2017 (2017)
Gemma L. Holliday, Shoshana D. Brown, Eyal Akiva, David Mischel, Michael A. Hicks, John H. Morris, Conrad C. Huang, Elaine C. Meng, Scott C.-H. Pegg, Thomas E. Ferrin, Patricia C. Babbitt
Biocuration in the structure-function linkage database: the anatomy of a superfamily. Database J. Biol. Databases Curation 2017 (2017)
Janelle B. Leuthaeuser, John H. Morris, Angela F. Harper, Thomas E. Ferrin, Patricia C. Babbitt, Jacquelyn S. Fetrow
DASP3: identification of protein sequences belonging to functionally relevant groups. BMC Bioinform. 17 (2016)
John H. Morris, Allan Wu, Roxanne A. Yamashita, Aron Marchler-Bauer, Thomas E. Ferrin
cddApp: a Cytoscape app for accessing the NCBI conserved domain database. Bioinform. 31 (1) (2015)
Jonathan E. Chen, Conrad C. Huang, Thomas E. Ferrin
RRDistMaps: a UCSF Chimera tool for viewing and comparing protein distance maps. Bioinform. 31 (9) (2015)
John H. Morris, Vijay Dhameliya, Steven Federowicz, Alexander R. Pico, Thomas E. Ferrin
CyAnimator: Simple Animations of Cytoscape Networks. F1000Research 4 (2015)
Eyal Akiva, Shoshana D. Brown, Daniel E. Almonacid, Alan E. Barber II, Ashley F. Custer, Michael A. Hicks, Conrad C. Huang, Florian Lauck, Susan T. Mashiyama, Elaine C. Meng, David Mischel, John H. Morris, Sunil Ojha, Alexandra M. Schnoes, Doug Stryke, Jeffrey M. Yunes, Thomas E. Ferrin, Gemma L. Holliday, Patricia C. Babbitt
The Structure-Function Linkage Database. Nucleic Acids Res. 42 (Database-Issue) (2014)
John H. Morris, Allan Wu, Nadezhda T. Doncheva, Mario Albrecht, Thomas E. Ferrin
setsApp: Set operations for Cytoscape Nodes and Edges. F1000Research 3 (2014)
Conrad C. Huang, Elaine C. Meng, John H. Morris, Eric F. Pettersen, Thomas E. Ferrin
Enhancing UCSF Chimera through web services. Nucleic Acids Res. 42 (Webserver-Issue) (2014)
John H. Morris, Allan Kuchinsky, Thomas E. Ferrin, Alexander R. Pico
enhancedGraphics: a Cytoscape app for enhanced node graphics. F1000Research 3 (2014)
Leonard Apeltsin, John H. Morris, Patricia C. Babbitt, Thomas E. Ferrin
Improving the quality of protein similarity network clustering algorithms using the network edge weight distribution. Bioinform. 27 (3) (2011)
John H. Morris, Leonard Apeltsin, Aaron M. Newman, Jan Baumbach, Tobias Wittkop, Gang Su, Gary D. Bader, Thomas E. Ferrin
clusterMaker: a multi-algorithm clustering plugin for Cytoscape. BMC Bioinform. 12 (2011)
Ursula Pieper, Benjamin M. Webb, David T. Barkan, Dina Schneidman-Duhovny, Avner Schlessinger, Hannes Braberg, Zheng Yang, Elaine C. Meng, Eric F. Pettersen, Conrad C. Huang, Ruchira S. Datta, Parthasarathy Sampathkumar, Mallur S. Madhusudhan, Kimmen Sjölander, Thomas E. Ferrin, Stephen K. Burley, Andrej Sali
ModBase, a database of annotated comparative protein structure models, and associated resources. Nucleic Acids Res. 39 (Database-Issue) (2011)
John H. Morris, Conrad C. Huang, Patricia C. Babbitt, Thomas E. Ferrin
structureViz: linking Cytoscape and UCSF Chimera. Bioinform. 23 (17) (2007)
Alex S. Nord, Patricia J. Chang, Bruce R. Conklin, Antony V. Cox, Courtney A. Harper, Geoffrey G. Hicks, Conrad C. Huang, Susan J. Johns, Michiko Kawamoto, Songyan Liu, Elaine C. Meng, John H. Morris, Janet Rossant, Patricia Ruiz, William C. Skarnes, Philippe Soriano, William L. Stanford, Doug Stryke, Harald von Melchner, Wolfgang Wurst, Ken-ichi Yamamura, Stephen G. Young, Patricia C. Babbitt, Thomas E. Ferrin
The International Gene Trap Consortium Website: a portal to all publicly available gene trap cell lines in mouse. Nucleic Acids Res. 34 (Database-Issue) (2006)
Elaine C. Meng, Eric F. Pettersen, Gregory S. Couch, Conrad C. Huang, Thomas E. Ferrin
Tools for integrated sequence-structure analysis with UCSF Chimera. BMC Bioinform. 7 (2006)
Scott C.-H. Pegg, Shoshana D. Brown, Sunil Ojha, Conrad C. Huang, Thomas E. Ferrin, Patricia C. Babbitt
Representing Structure-Function Relationships in Mechanistically Diverse Enzyme Superfamilies. Pacific Symposium on Biocomputing (2005)
Thomas E. Ferrin, Conrad C. Huang, Daniel M. Greenblatt, Doug Stryke, Kathleen M. Giacomini, John H. Morris
Enhancing Data Sharing in Collaborative Research Projects with DASH. Pacific Symposium on Biocomputing (2005)
Ursula Pieper, Narayanan Eswar, Hannes Braberg, Mallur S. Madhusudhan, Fred P. Davis, Ashley C. Stuart, Nebojsa Mirkovic, Andrea Rossi, Marc A. Martí-Renom, András Fiser, Ben M. Webb, Daniel M. Greenblatt, Conrad C. Huang, Thomas E. Ferrin, Andrej Sali
MODBASE, a database of annotated comparative protein structure models, and associated resources. Nucleic Acids Res. 32 (Database-Issue) (2004)
Eric F. Pettersen, Thomas D. Goddard, Conrad C. Huang, Gregory S. Couch, Daniel M. Greenblatt, Elaine C. Meng, Thomas E. Ferrin
UCSF Chimera - A visualization system for exploratory research and analysis. J. Comput. Chem. 25 (13) (2004)
Doug Stryke, Michiko Kawamoto, Conrad C. Huang, Susan J. Johns, Leslie A. King, Courtney A. Harper, Elaine C. Meng, Roy E. Lee, Alice Yee, Larry L'Italien, Pao-Tien Chuang, Stephen G. Young, William C. Skarnes, Patricia C. Babbitt, Thomas E. Ferrin
BayGenomics: a resource of insertional mutations in mouse embryonic stem cells. Nucleic Acids Res. 31 (1) (2003)
Andrew I. Jewett, Conrad C. Huang, Thomas E. Ferrin
MINRMS: an efficient algorithm for determining protein structure similarity using root-mean-squared-distance. Bioinform. 19 (5) (2003)
Ranyee A. Chiang, Elaine C. Meng, Conrad C. Huang, Thomas E. Ferrin, Patricia C. Babbitt
The Structure Superposition Database. Nucleic Acids Res. 31 (1) (2003)
Doug Stryke, Conrad C. Huang, Michiko Kawamoto, Susan J. Johns, Elaine J. Carlson, Joseph A. Deyoung, Maya K. Leabman, Ira Herskowitz, Kathleen M. Giacomini, Thomas E. Ferrin
SNP Analysis and Presentation in the Pharmacogenetics of Membrane Transporters Project. Pacific Symposium on Biocomputing (2003)
Thomas E. Ferrin, Bruce A. Foster, Richard Hughey
High Performance Computing for Computational Biology - Session Introduction. Pacific Symposium on Biocomputing (2001)
David E. Konerding, Conrad C. Huang, Thomas E. Ferrin
Chimera: Affordable Desktop Molecular Modeling on Linux Workstations. Annual Linux Showcase & Conference (2001)
Thomas E. Ferrin, Eileen T. Kraemer
Molecules to Maps: Tools for Visualization & Interaction - Session Introduction. Pacific Symposium on Biocomputing (1999)
Eileen T. Kraemer, Thomas E. Ferrin
Molecules to maps: tools for visualization and interaction in support of computational biology. Bioinform. 14 (9) (1998)
Thomas E. Ferrin, Conrad C. Huang, Gregory S. Couch, Eric F. Pettersen, Robert Langridge
The MidasPlus molecular modeling system. CHI (1992)