Patricia C. Babbitt

Publication Activity (10 Years)

Years Active: 1999-2020
Publications (10 Years): 9

Top Topics

Protein Function

Computational Approaches

Protein Function Prediction

Top Venues

Database J. Biol. Databases Curation

PLoS Comput. Biol.

Nucleic Acids Res.

Publications

Gemma L. Holliday, Shoshana D. Brown, David Mischel, Benjamin J. Polacco, Patricia C. Babbitt
A strategy for large-scale comparison of evolutionary- and reaction-based classifications of enzyme function. Database J. Biol. Databases Curation 2020 (2020)
Alex L. Mitchell, Teresa K. Attwood, Patricia C. Babbitt, Matthias Blum, Peer Bork, Alan 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
InterPro in 2019: improving coverage, classification and access to protein sequence annotations. Nucleic Acids Res. 47 (Database-Issue) (2019)
Jeffrey M. Yunes, Patricia C. Babbitt
Effusion: prediction of protein function from sequence similarity networks. Bioinform. 35 (3) (2019)
Jacquelyn S. Fetrow, Patricia C. Babbitt
New computational approaches to understanding molecular protein function. PLoS Comput. Biol. 14 (4) (2018)
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)
Robert D. Finn, Teresa K. Attwood, Patricia C. Babbitt, Alex Bateman, Peer Bork, Alan 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, Youngmi 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
InterPro in 2017 - beyond protein family and domain annotations. Nucleic Acids Res. 45 (Database-Issue) (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)
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
Creating a specialist protein resource network: a meeting report for the protein bioinformatics and community resources retreat. Database J. Biol. Databases Curation 2015 (2015)
Bo-Xue Tian, Frank H. Wallrapp, Gemma L. Holliday, Jeng-Yeong Chow, Patricia C. Babbitt, C. Dale Poulter, Matthew P. Jacobson
Predicting the Functions and Specificity of Triterpenoid Synthases: A Mechanism-Based Multi-intermediate Docking Approach. PLoS Comput. Biol. 10 (10) (2014)
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)
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
Prediction of Substrates for Glutathione Transferases by Covalent Docking. J. Chem. Inf. Model. 54 (6) (2014)
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
Discovery of new enzymes and metabolic pathways by using structure and genome context. Nat. 502 (7473) (2013)
Alexandra M. Schnoes, David C. Ream, Alexander W. Thorman, Patricia C. Babbitt, Iddo Friedberg
Biases in the Experimental Annotations of Protein Function and their Effect on Our Understanding of Protein Function Space CoRR (2013)
Alexandra M. Schnoes, David C. Ream, Alexander W. Thorman, Patricia C. Babbitt, Iddo Friedberg
Biases in the Experimental Annotations of Protein Function and Their Effect on Our Understanding of Protein Function Space. PLoS Comput. Biol. 9 (5) (2013)
Alan E. Barber II, Patricia C. Babbitt
Pythoscape: a framework for generation of large protein similarity networks. Bioinform. 28 (21) (2012)
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)
Daniel E. Almonacid, Emmanuel R. Yera, John B. O. Mitchell, Patricia C. Babbitt
Quantitative Comparison of Catalytic Mechanisms and Overall Reactions in Convergently Evolved Enzymes: Implications for Classification of Enzyme Function. PLoS Comput. Biol. 6 (3) (2010)
Holly J. Atkinson, Patricia C. Babbitt
An Atlas of the Thioredoxin Fold Class Reveals the Complexity of Function-Enabling Adaptations. PLoS Comput. Biol. 5 (10) (2009)
Alexandra M. Schnoes, Shoshana D. Brown, Igor Dodevski, Patricia C. Babbitt
Annotation Error in Public Databases: Misannotation of Molecular Function in Enzyme Superfamilies. PLoS Comput. Biol. 5 (12) (2009)
James Corey Adams, Michael J. Keiser, Li Basuino, Henry F. Chambers, Deok-Sun Lee, Olaf G. Wiest, Patricia C. Babbitt
A Mapping of Drug Space from the Viewpoint of Small Molecule Metabolism. PLoS Comput. Biol. 5 (8) (2009)
Ranyee A. Chiang, Andrej Sali, Patricia C. Babbitt
Evolutionarily Conserved Substrate Substructures for Automated Annotation of Enzyme Superfamilies. PLoS Comput. Biol. 4 (8) (2008)
John H. Morris, Conrad C. Huang, Patricia C. Babbitt, Thomas E. Ferrin
structureViz: linking Cytoscape and UCSF Chimera. Bioinform. 23 (17) (2007)
Sunil Ojha, Elaine C. Meng, Patricia C. Babbitt
Evolution of Function in the "Two Dinucleotide Binding Domains" Flavoproteins. PLoS Comput. Biol. 3 (7) (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)
Benjamin J. Polacco, Patricia C. Babbitt
Automated discovery of 3D motifs for protein function annotation. Bioinform. 22 (6) (2006)
Patricia C. Babbitt, Philip E. Bourne, Sean D. Mooney
Introduction to Informatics Approaches in Structural Genomics: Modeling and Representation of Function from Macromolecular STructure. Pacific Symposium on Biocomputing (2005)
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)
Sean D. Mooney, Philip E. Bourne, Patricia C. Babbitt
Session Introduction. Pacific Symposium on Biocomputing (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)
Scott C.-H. Pegg, Walter R. P. Novak, Patricia C. Babbitt
Intersect: identification and visualization of overlaps in database search results. Bioinform. 19 (15) (2003)
Sean D. Mooney, Patricia C. Babbitt
Informatics Approaches in Structural Genomics - Session Introduction. Pacific Symposium on Biocomputing (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)
D. Rey Banatao, Conrad C. Huang, Patricia C. Babbitt, Russ B. Altman, Teri E. Klein
ViewFeature: Integrated Feature Analysis and Visualization. Pacific Symposium on Biocomputing (2001)
Scott C.-H. Pegg, Patricia C. Babbitt
Shotgun: getting more from sequence similarity searches. Bioinform. 15 (9) (1999)