Thomas E. Ferrin

According to our database, Thomas E. Ferrin authored at least 29 papers between 1992 and 2017.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of four.

2017

An Atlas of Peroxiredoxins Created Using an Active Site Profile-Based Approach to Functionally Relevant Clustering of Proteins.

Angela F. Harper, Janelle B. Leuthaeuser, Patricia C. Babbitt, John H. Morris, Thomas E. Ferrin, Leslie B. Poole, Jacquelyn S. Fetrow

PLoS Comput. Biol., 2017

Biocuration in the structure-function linkage database: the anatomy of a superfamily.

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

Database J. Biol. Databases Curation, 2017

2016

DASP3: identification of protein sequences belonging to functionally relevant groups.

Janelle B. Leuthaeuser, John H. Morris, Angela F. Harper, Thomas E. Ferrin, Patricia C. Babbitt, Jacquelyn S. Fetrow

BMC Bioinform., 2016

2015

CyAnimator: Simple Animations of Cytoscape Networks.

John H. Morris, Vijay Dhameliya, Steven Federowicz, Alexander R. Pico, Thomas E. Ferrin

F1000Research, 2015

cddApp: a Cytoscape app for accessing the NCBI conserved domain database.

John H. Morris, Allan Wu, Roxanne A. Yamashita, Aron Marchler-Bauer, Thomas E. Ferrin

Bioinform., 2015

RRDistMaps: a UCSF Chimera tool for viewing and comparing protein distance maps.

Jonathan E. Chen, Conrad C. Huang, Thomas E. Ferrin

Bioinform., 2015

2014

Enhancing UCSF Chimera through web services.

Conrad C. Huang, Elaine C. Meng, John H. Morris, Eric F. Pettersen, Thomas E. Ferrin

Nucleic Acids Res., 2014

The Structure-Function Linkage Database.

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

Nucleic Acids Res., 2014

setsApp: Set operations for Cytoscape Nodes and Edges.

John H. Morris, Allan Wu, Nadezhda T. Doncheva, Mario Albrecht, Thomas E. Ferrin

F1000Research, 2014

enhancedGraphics: a Cytoscape app for enhanced node graphics.

John H. Morris, Allan Kuchinsky, Thomas E. Ferrin, Alexander R. Pico

F1000Research, 2014

2011

ModBase, a database of annotated comparative protein structure models, and associated resources.

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

Nucleic Acids Res., 2011

clusterMaker: a multi-algorithm clustering plugin for Cytoscape.

John H. Morris, Leonard Apeltsin, Aaron M. Newman, Jan Baumbach, Tobias Wittkop, Gang Su, Gary D. Bader, Thomas E. Ferrin

BMC Bioinform., 2011

Improving the quality of protein similarity network clustering algorithms using the network edge weight distribution.

Leonard Apeltsin, John H. Morris, Patricia C. Babbitt, Thomas E. Ferrin

Bioinform., 2011

2007

structureViz: linking Cytoscape and UCSF Chimera.

John H. Morris, Conrad C. Huang, Patricia C. Babbitt, Thomas E. Ferrin

Bioinform., 2007

2006

The International Gene Trap Consortium Website: a portal to all publicly available gene trap cell lines in mouse.

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

Nucleic Acids Res., 2006

Tools for integrated sequence-structure analysis with UCSF Chimera.

Elaine C. Meng, Eric F. Pettersen, Gregory S. Couch, Conrad C. Huang, Thomas E. Ferrin

BMC Bioinform., 2006

2005

Representing Structure-Function Relationships in Mechanistically Diverse Enzyme Superfamilies.

Scott C.-H. Pegg, Shoshana D. Brown, Sunil Ojha, Conrad C. Huang, Thomas E. Ferrin, Patricia C. Babbitt

Proceedings of the Biocomputing 2005, 2005

Enhancing Data Sharing in Collaborative Research Projects with DASH.

Thomas E. Ferrin, Conrad C. Huang, Daniel M. Greenblatt, Doug Stryke, Kathleen M. Giacomini, John H. Morris

Proceedings of the Biocomputing 2005, 2005

2004

MODBASE, a database of annotated comparative protein structure models, and associated resources.

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

Nucleic Acids Res., 2004

UCSF Chimera - A visualization system for exploratory research and analysis.

Eric F. Pettersen, Thomas D. Goddard, Conrad C. Huang, Gregory S. Couch, Daniel M. Greenblatt, Elaine C. Meng, Thomas E. Ferrin

J. Comput. Chem., 2004

2003

BayGenomics: a resource of insertional mutations in mouse embryonic stem cells.

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

Nucleic Acids Res., 2003

The Structure Superposition Database.

Ranyee A. Chiang, Elaine C. Meng, Conrad C. Huang, Thomas E. Ferrin, Patricia C. Babbitt

Nucleic Acids Res., 2003

MINRMS: an efficient algorithm for determining protein structure similarity using root-mean-squared-distance.

Andrew I. Jewett, Conrad C. Huang, Thomas E. Ferrin

Bioinform., 2003

SNP Analysis and Presentation in the Pharmacogenetics of Membrane Transporters Project.

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

Proceedings of the 8th Pacific Symposium on Biocomputing, 2003

2001

High Performance Computing for Computational Biology - Session Introduction.

Thomas E. Ferrin, Bruce A. Foster, Richard Hughey

Proceedings of the 6th Pacific Symposium on Biocomputing, 2001

Chimera: Affordable Desktop Molecular Modeling on Linux Workstations.

David E. Konerding, Conrad C. Huang, Thomas E. Ferrin

Proceedings of the 5th Annual Linux Showcase & Conference 2001, 2001

1999

Molecules to Maps: Tools for Visualization & Interaction - Session Introduction.

Thomas E. Ferrin, Eileen T. Kraemer

Proceedings of the 4th Pacific Symposium on Biocomputing, 1999

1998

Molecules to maps: tools for visualization and interaction in support of computational biology.

Eileen T. Kraemer, Thomas E. Ferrin

Bioinform., 1998

1992

The MidasPlus molecular modeling system.

Thomas E. Ferrin, Conrad C. Huang, Gregory S. Couch, Eric F. Pettersen, Robert Langridge

Proceedings of the Conference on Human Factors in Computing Systems, 1992