Patricia C. Babbitt

According to our database, Patricia C. Babbitt authored at least 34 papers between 1999 and 2020.

Collaborative distances:

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

2020

A strategy for large-scale comparison of evolutionary- and reaction-based classifications of enzyme function.

Gemma L. Holliday, Shoshana D. Brown, David Mischel, Benjamin J. Polacco, Patricia C. Babbitt

Database J. Biol. Databases Curation, 2020

2019

InterPro in 2019: improving coverage, classification and access to protein sequence annotations.

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

Nucleic Acids Res., 2019

Effusion: prediction of protein function from sequence similarity networks.

Jeffrey M. Yunes, Patricia C. Babbitt

Bioinform., 2019

2018

New computational approaches to understanding molecular protein function.

Jacquelyn S. Fetrow, Patricia C. Babbitt

PLoS Comput. Biol., 2018

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

InterPro in 2017 - beyond protein family and domain annotations.

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

Nucleic Acids Res., 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

Creating a specialist protein resource network: a meeting report for the protein bioinformatics and community resources retreat.

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

Database J. Biol. Databases Curation, 2015

2014

Predicting the Functions and Specificity of Triterpenoid Synthases: A Mechanism-Based Multi-intermediate Docking Approach.

Bo-Xue Tian, Frank H. Wallrapp, Gemma L. Holliday, Jeng-Yeong Chow, Patricia C. Babbitt, C. Dale Poulter, Matthew P. Jacobson

PLoS Comput. Biol., 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

Prediction of Substrates for Glutathione Transferases by Covalent Docking.

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

J. Chem. Inf. Model., 2014

2013

Biases in the Experimental Annotations of Protein Function and Their Effect on Our Understanding of Protein Function Space.

Alexandra M. Schnoes, David C. Ream, Alexander W. Thorman, Patricia C. Babbitt, Iddo Friedberg

PLoS Comput. Biol., 2013

Discovery of new enzymes and metabolic pathways by using structure and genome context.

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

Nat., 2013

2012

Pythoscape: a framework for generation of large protein similarity networks.

Alan E. Barber II, Patricia C. Babbitt

Bioinform., 2012

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

2010

Quantitative Comparison of Catalytic Mechanisms and Overall Reactions in Convergently Evolved Enzymes: Implications for Classification of Enzyme Function.

Daniel E. Almonacid, Emmanuel R. Yera, John B. O. Mitchell, Patricia C. Babbitt

PLoS Comput. Biol., 2010

2009

Annotation Error in Public Databases: Misannotation of Molecular Function in Enzyme Superfamilies.

Alexandra M. Schnoes, Shoshana D. Brown, Igor Dodevski, Patricia C. Babbitt

PLoS Comput. Biol., 2009

An Atlas of the Thioredoxin Fold Class Reveals the Complexity of Function-Enabling Adaptations.

Holly J. Atkinson, Patricia C. Babbitt

PLoS Comput. Biol., 2009

A Mapping of Drug Space from the Viewpoint of Small Molecule Metabolism.

James Corey Adams, Michael J. Keiser, Li Basuino, Henry F. Chambers, Deok-Sun Lee, Olaf G. Wiest, Patricia C. Babbitt

PLoS Comput. Biol., 2009

2008

Evolutionarily Conserved Substrate Substructures for Automated Annotation of Enzyme Superfamilies.

Ranyee A. Chiang, Andrej Sali, Patricia C. Babbitt

PLoS Comput. Biol., 2008

2007

Evolution of Function in the "Two Dinucleotide Binding Domains" Flavoproteins.

Sunil Ojha, Elaine C. Meng, Patricia C. Babbitt

PLoS Comput. Biol., 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

Automated discovery of 3D motifs for protein function annotation.

Benjamin J. Polacco, Patricia C. Babbitt

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

Introduction to Informatics Approaches in Structural Genomics: Modeling and Representation of Function from Macromolecular STructure.

Patricia C. Babbitt, Philip E. Bourne, Sean D. Mooney

Proceedings of the Biocomputing 2005, 2005

2004

Session Introduction.

Sean D. Mooney, Philip E. Bourne, Patricia C. Babbitt

Proceedings of the Biocomputing 2004, 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

Intersect: identification and visualization of overlaps in database search results.

Scott C.-H. Pegg, Walter R. P. Novak, Patricia C. Babbitt

Bioinform., 2003

Informatics Approaches in Structural Genomics - Session Introduction.

Sean D. Mooney, Patricia C. Babbitt

Proceedings of the 8th Pacific Symposium on Biocomputing, 2003

2001

ViewFeature: Integrated Feature Analysis and Visualization.

D. Rey Banatao, Conrad C. Huang, Patricia C. Babbitt, Russ B. Altman, Teri E. Klein

Proceedings of the 6th Pacific Symposium on Biocomputing, 2001

1999

Shotgun: getting more from sequence similarity searches.

Scott C.-H. Pegg, Patricia C. Babbitt

Bioinform., 1999