Thomas E. Ferrin

30 papers A* 1Misc 5Journal 23Unranked 1
YearRankTypeTitle / Venue / Authors
2017 J jnl
An Atlas of Peroxiredoxins Created Using an Active Site Profile-Based Approach to Functionally Relevant Clustering of Proteins.
PLoS Comput. Biol.
Angela F. Harper, Janelle B. Leuthaeuser, Patricia C. Babbitt, John H. Morris, Thomas E. Ferrin, Leslie B. Poole, Jacquelyn S. Fetrow
2017 J jnl
Biocuration in the structure-function linkage database: the anatomy of a superfamily.
Database J. Biol. Databases Curation
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
2017 J jnl
Biocuration in the structure-function linkage database: the anatomy of a superfamily.
Database J. Biol. Databases Curation
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
2016 J jnl
DASP3: identification of protein sequences belonging to functionally relevant groups.
BMC Bioinform.
Janelle B. Leuthaeuser, John H. Morris, Angela F. Harper, Thomas E. Ferrin, Patricia C. Babbitt, Jacquelyn S. Fetrow
2015 J jnl
CyAnimator: Simple Animations of Cytoscape Networks.
F1000Research
John H. Morris, Vijay Dhameliya, Steven Federowicz, Alexander R. Pico, Thomas E. Ferrin
2015 J jnl
RRDistMaps: a UCSF Chimera tool for viewing and comparing protein distance maps.
Bioinform.
Jonathan E. Chen, Conrad C. Huang, Thomas E. Ferrin
2015 J jnl
cddApp: a Cytoscape app for accessing the NCBI conserved domain database.
Bioinform.
John H. Morris, Allan Wu, Roxanne A. Yamashita, Aron Marchler-Bauer, Thomas E. Ferrin
2014 J jnl
Enhancing UCSF Chimera through web services.
Nucleic Acids Res.
Conrad C. Huang, Elaine C. Meng, John H. Morris, Eric F. Pettersen, Thomas E. Ferrin
2014 J jnl
The Structure-Function Linkage Database.
Nucleic Acids Res.
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
2014 J jnl
enhancedGraphics: a Cytoscape app for enhanced node graphics.
F1000Research
John H. Morris, Allan Kuchinsky, Thomas E. Ferrin, Alexander R. Pico
2014 J jnl
setsApp: Set operations for Cytoscape Nodes and Edges.
F1000Research
John H. Morris, Allan Wu, Nadezhda T. Doncheva, Mario Albrecht, Thomas E. Ferrin
2011 J jnl
Improving the quality of protein similarity network clustering algorithms using the network edge weight distribution.
Bioinform.
Leonard Apeltsin, John H. Morris, Patricia C. Babbitt, Thomas E. Ferrin
2011 J jnl
ModBase, a database of annotated comparative protein structure models, and associated resources.
Nucleic Acids Res.
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
2011 J jnl
clusterMaker: a multi-algorithm clustering plugin for Cytoscape.
BMC Bioinform.
John H. Morris, Leonard Apeltsin, Aaron M. Newman, Jan Baumbach, Tobias Wittkop, Gang Su, Gary D. Bader, Thomas E. Ferrin
2007 J jnl
structureViz: linking Cytoscape and UCSF Chimera.
Bioinform.
John H. Morris, Conrad C. Huang, Patricia C. Babbitt, Thomas E. Ferrin
2006 J jnl
The International Gene Trap Consortium Website: a portal to all publicly available gene trap cell lines in mouse.
Nucleic Acids Res.
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
2006 J jnl
Tools for integrated sequence-structure analysis with UCSF Chimera.
BMC Bioinform.
Elaine C. Meng, Eric F. Pettersen, Gregory S. Couch, Conrad C. Huang, Thomas E. Ferrin
2005 Misc conf
Enhancing Data Sharing in Collaborative Research Projects with DASH.
Pacific Symposium on Biocomputing
Thomas E. Ferrin, Conrad C. Huang, Daniel M. Greenblatt, Doug Stryke, Kathleen M. Giacomini, John H. Morris
2005 Misc conf
Representing Structure-Function Relationships in Mechanistically Diverse Enzyme Superfamilies.
Pacific Symposium on Biocomputing
Scott C.-H. Pegg, Shoshana D. Brown, Sunil Ojha, Conrad C. Huang, Thomas E. Ferrin, Patricia C. Babbitt
2004 J jnl
MODBASE, a database of annotated comparative protein structure models, and associated resources.
Nucleic Acids Res.
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
2004 J jnl
UCSF Chimera - A visualization system for exploratory research and analysis.
J. Comput. Chem.
Eric F. Pettersen, Thomas D. Goddard, Conrad C. Huang, Gregory S. Couch, Daniel M. Greenblatt, Elaine C. Meng, Thomas E. Ferrin
2003 J jnl
BayGenomics: a resource of insertional mutations in mouse embryonic stem cells.
Nucleic Acids Res.
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
2003 J jnl
MINRMS: an efficient algorithm for determining protein structure similarity using root-mean-squared-distance.
Bioinform.
Andrew I. Jewett, Conrad C. Huang, Thomas E. Ferrin
2003 Misc conf
SNP Analysis and Presentation in the Pharmacogenetics of Membrane Transporters Project.
Pacific Symposium on Biocomputing
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
2003 J jnl
The Structure Superposition Database.
Nucleic Acids Res.
Ranyee A. Chiang, Elaine C. Meng, Conrad C. Huang, Thomas E. Ferrin, Patricia C. Babbitt
2001 — conf
Chimera: Affordable Desktop Molecular Modeling on Linux Workstations.
Annual Linux Showcase & Conference
David E. Konerding, Conrad C. Huang, Thomas E. Ferrin
2001 Misc conf
High Performance Computing for Computational Biology - Session Introduction.
Pacific Symposium on Biocomputing
Thomas E. Ferrin, Bruce A. Foster, Richard Hughey
1999 Misc conf
Molecules to Maps: Tools for Visualization & Interaction - Session Introduction.
Pacific Symposium on Biocomputing
Thomas E. Ferrin, Eileen T. Kraemer
1998 J jnl
Molecules to maps: tools for visualization and interaction in support of computational biology.
Bioinform.
Eileen T. Kraemer, Thomas E. Ferrin
1992 A* conf
The MidasPlus molecular modeling system.
CHI
Thomas E. Ferrin, Conrad C. Huang, Gregory S. Couch, Eric F. Pettersen, Robert Langridge