Patricia C. Babbitt

36 papers Misc 5Journal 31
YearRankTypeTitle / Venue / Authors
2020 J jnl
A strategy for large-scale comparison of evolutionary- and reaction-based classifications of enzyme function.
Database J. Biol. Databases Curation
Gemma L. Holliday, Shoshana D. Brown, David Mischel, Benjamin J. Polacco, Patricia C. Babbitt
2019 J jnl
Effusion: prediction of protein function from sequence similarity networks.
Bioinform.
Jeffrey M. Yunes, Patricia C. Babbitt
2019 J jnl
InterPro in 2019: improving coverage, classification and access to protein sequence annotations.
Nucleic Acids Res.
Alex L. Mitchell, Teresa K. Attwood, Patricia C. Babbitt, Matthias Blum, Peer Bork, Alan J. Bridge, Shoshana D. Brown, Hsin-Yu Chang, Sara El-Gebali, Matthew Fraser, Julian Gough, David Haft, Hongzhan Huang, Ivica Letunic, Rodrigo Lopez, Aurelien Luciani, Fábio Madeira, Aron Marchler-Bauer, Huaiyu Mi, Darren A. Natale, Marco Necci, Gift Nuka, Christine A. Orengo, Arun Prasad Pandurangan, Typhaine Paysan-Lafosse, Sebastien Pesseat, Simon C. Potter, Matloob Qureshi, Neil D. Rawlings, Nicole Redaschi, Lorna J. Richardson, Catherine Rivoire, Gustavo A. Salazar, Amaia Sangrador-Vegas, Christian J. A. Sigrist, Ian Sillitoe, Granger G. Sutton, Narmada Thanki, Paul D. Thomas, Silvio C. E. Tosatto, Siew-Yit Yong, Robert D. Finn
2018 J jnl
New computational approaches to understanding molecular protein function.
PLoS Comput. Biol.
Jacquelyn S. Fetrow, Patricia C. Babbitt
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
2017 J jnl
InterPro in 2017 - beyond protein family and domain annotations.
Nucleic Acids Res.
Robert D. Finn, Teresa K. Attwood, Patricia C. Babbitt, Alex Bateman, Peer Bork, Alan J. Bridge, Hsin-Yu Chang, Zsuzsanna Dosztányi, Sara El-Gebali, Matthew Fraser, Julian Gough, David Haft, Gemma L. Holliday, Hongzhan Huang, Xiaosong Huang, Ivica Letunic, Rodrigo Lopez, Shennan Lu, Aron Marchler-Bauer, Huaiyu Mi, Jaina Mistry, Darren A. Natale, Marco Necci, Gift Nuka, Christine A. Orengo, Young Mi Park, Sebastien Pesseat, Damiano Piovesan, Simon C. Potter, Neil D. Rawlings, Nicole Redaschi, Lorna J. Richardson, Catherine Rivoire, Amaia Sangrador-Vegas, Christian J. A. Sigrist, Ian Sillitoe, Ben Smithers, Silvano Squizzato, Granger G. Sutton, Narmada Thanki, Paul D. Thomas, Silvio C. E. Tosatto, Cathy H. Wu, Ioannis Xenarios, Lai-Su L. Yeh, Siew-Yit Yong, Alex L. Mitchell
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
Creating a specialist protein resource network: a meeting report for the protein bioinformatics and community resources retreat.
Database J. Biol. Databases Curation
Patricia C. Babbitt, Pantelis G. Bagos, Amos Bairoch, Alex Bateman, Arnaud Chatonnet, Mark Jinan Chen, David J. Craik, Robert D. Finn, David E. Gloriam, Daniel H. Haft, Bernard Henrissat, Gemma L. Holliday, Vignir Ísberg, Quentin Kaas, David Landsman, Nicolas Lenfant, Gerard Manning, Nozomi Nagano, Narayanaswamy Srinivasan, Claire O'Donovan, Kim D. Pruitt, Ramanathan Sowdhamini, Neil D. Rawlings, Milton H. Saier Jr., Joanna L. Sharman, Michael Spedding, Konstantinos D. Tsirigos, Åke Västermark, Gerrit Vriend
2014 J jnl
Predicting the Functions and Specificity of Triterpenoid Synthases: A Mechanism-Based Multi-intermediate Docking Approach.
PLoS Comput. Biol.
Bo-Xue Tian, Frank H. Wallrapp, Gemma L. Holliday, Jeng-Yeong Chow, Patricia C. Babbitt, C. Dale Poulter, Matthew P. Jacobson
2014 J jnl
Prediction of Substrates for Glutathione Transferases by Covalent Docking.
J. Chem. Inf. Model.
Guang Qiang Dong, Sara Calhoun, Hao Fan, Chakrapani Kalyanaraman, Megan C. Branch, Susan T. Mashiyama, Nir London, Matthew P. Jacobson, Patricia C. Babbitt, Brian K. Shoichet, Richard N. Armstrong, Andrej Sali
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
2013 J jnl
Biases in the Experimental Annotations of Protein Function and Their Effect on Our Understanding of Protein Function Space.
PLoS Comput. Biol.
Alexandra M. Schnoes, David C. Ream, Alexander W. Thorman, Patricia C. Babbitt, Iddo Friedberg
2013 J jnl
Biases in the Experimental Annotations of Protein Function and their Effect on Our Understanding of Protein Function Space
CoRR
Alexandra M. Schnoes, David C. Ream, Alexander W. Thorman, Patricia C. Babbitt, Iddo Friedberg
2013 J jnl
Discovery of new enzymes and metabolic pathways by using structure and genome context.
Nat.
Suwen Zhao, Ritesh Kumar, Ayano Sakai, Matthew W. Vetting, B. McKay Wood, Shoshana D. Brown, Jeffery B. Bonanno, Brandan S. Hillerich, Ronald D. Seidel, Patricia C. Babbitt, Steven C. Almo, Jonathan V. Sweedler, John A. Gerlt, John E. Cronan, Matthew P. Jacobson
2012 J jnl
Pythoscape: a framework for generation of large protein similarity networks.
Bioinform.
Alan E. Barber II, Patricia C. Babbitt
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
2010 J jnl
Quantitative Comparison of Catalytic Mechanisms and Overall Reactions in Convergently Evolved Enzymes: Implications for Classification of Enzyme Function.
PLoS Comput. Biol.
Daniel E. Almonacid, Emmanuel R. Yera, John B. O. Mitchell, Patricia C. Babbitt
2009 J jnl
A Mapping of Drug Space from the Viewpoint of Small Molecule Metabolism.
PLoS Comput. Biol.
James Corey Adams, Michael J. Keiser, Li Basuino, Henry F. Chambers, Deok-Sun Lee, Olaf G. Wiest, Patricia C. Babbitt
2009 J jnl
An Atlas of the Thioredoxin Fold Class Reveals the Complexity of Function-Enabling Adaptations.
PLoS Comput. Biol.
Holly J. Atkinson, Patricia C. Babbitt
2009 J jnl
Annotation Error in Public Databases: Misannotation of Molecular Function in Enzyme Superfamilies.
PLoS Comput. Biol.
Alexandra M. Schnoes, Shoshana D. Brown, Igor Dodevski, Patricia C. Babbitt
2008 J jnl
Evolutionarily Conserved Substrate Substructures for Automated Annotation of Enzyme Superfamilies.
PLoS Comput. Biol.
Ranyee A. Chiang, Andrej Sali, Patricia C. Babbitt
2007 J jnl
Evolution of Function in the "Two Dinucleotide Binding Domains" Flavoproteins.
PLoS Comput. Biol.
Sunil Ojha, Elaine C. Meng, Patricia C. Babbitt
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
Automated discovery of 3D motifs for protein function annotation.
Bioinform.
Benjamin J. Polacco, Patricia C. Babbitt
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
2005 Misc conf
Introduction to Informatics Approaches in Structural Genomics: Modeling and Representation of Function from Macromolecular STructure.
Pacific Symposium on Biocomputing
Patricia C. Babbitt, Philip E. Bourne, Sean D. Mooney
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 Misc conf
Session Introduction.
Pacific Symposium on Biocomputing
Sean D. Mooney, Philip E. Bourne, Patricia C. Babbitt
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 Misc conf
Informatics Approaches in Structural Genomics - Session Introduction.
Pacific Symposium on Biocomputing
Sean D. Mooney, Patricia C. Babbitt
2003 J jnl
Intersect: identification and visualization of overlaps in database search results.
Bioinform.
Scott C.-H. Pegg, Walter R. P. Novak, Patricia C. Babbitt
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 Misc conf
ViewFeature: Integrated Feature Analysis and Visualization.
Pacific Symposium on Biocomputing
D. Rey Banatao, Conrad C. Huang, Patricia C. Babbitt, Russ B. Altman, Teri E. Klein
1999 J jnl
Shotgun: getting more from sequence similarity searches.
Bioinform.
Scott C.-H. Pegg, Patricia C. Babbitt