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Patricia C. Babbitt
Person information
- affiliation: University of California, San Francisco, CA, USA
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2020 – today
- 2020
- [j30]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)
2010 – 2019
- 2019
- [j29]Jeffrey M. Yunes
, Patricia C. Babbitt
:
Effusion: prediction of protein function from sequence similarity networks. Bioinform. 35(3): 442-451 (2019) - [j28]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
:
InterPro in 2019: improving coverage, classification and access to protein sequence annotations. Nucleic Acids Res. 47(Database-Issue): D351-D360 (2019) - 2018
- [j27]Jacquelyn S. Fetrow
, Patricia C. Babbitt
:
New computational approaches to understanding molecular protein function. PLoS Comput. Biol. 14(4) (2018) - 2017
- [j26]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: bax006 (2017) - [j25]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: bax045 (2017) - [j24]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
:
InterPro in 2017 - beyond protein family and domain annotations. Nucleic Acids Res. 45(Database-Issue): D190-D199 (2017) - [j23]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) - 2016
- [j22]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: 458:1-458:13 (2016) - 2015
- [j21]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) - 2014
- [j20]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): 1687-1699 (2014) - [j19]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): 521-530 (2014) - [j18]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) - 2013
- [j17]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): 698-702 (2013) - [j16]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) - [i1]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 abs/1301.1740 (2013) - 2012
- [j15]Alan E. Barber II, Patricia C. Babbitt:
Pythoscape: a framework for generation of large protein similarity networks. Bioinform. 28(21): 2845-2846 (2012) - 2011
- [j14]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): 326-333 (2011) - 2010
- [j13]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)
2000 – 2009
- 2009
- [j12]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) - [j11]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) - [j10]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) - 2008
- [j9]Ranyee A. Chiang, Andrej Sali, Patricia C. Babbitt:
Evolutionarily Conserved Substrate Substructures for Automated Annotation of Enzyme Superfamilies. PLoS Comput. Biol. 4(8) (2008) - 2007
- [j8]John H. Morris
, Conrad C. Huang, Patricia C. Babbitt, Thomas E. Ferrin:
structureViz: linking Cytoscape and UCSF Chimera. Bioinform. 23(17): 2345-2347 (2007) - [j7]Sunil Ojha, Elaine C. Meng, Patricia C. Babbitt:
Evolution of Function in the "Two Dinucleotide Binding Domains" Flavoproteins. PLoS Comput. Biol. 3(7) (2007) - 2006
- [j6]Benjamin J. Polacco
, Patricia C. Babbitt:
Automated discovery of 3D motifs for protein function annotation. Bioinform. 22(6): 723-730 (2006) - [j5]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): 642-648 (2006) - 2005
- [c5]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 - [c4]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 - 2004
- [c3]Sean D. Mooney, Philip E. Bourne, Patricia C. Babbitt:
Session Introduction. Pacific Symposium on Biocomputing 2004: 372-374 - 2003
- [j4]Scott C.-H. Pegg, Walter R. P. Novak
, Patricia C. Babbitt:
Intersect: identification and visualization of overlaps in database search results. Bioinform. 19(15): 1997-1999 (2003) - [j3]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): 278-281 (2003) - [j2]Ranyee A. Chiang, Elaine C. Meng, Conrad C. Huang, Thomas E. Ferrin, Patricia C. Babbitt:
The Structure Superposition Database. Nucleic Acids Res. 31(1): 505-510 (2003) - [c2]Sean D. Mooney, Patricia C. Babbitt:
Informatics Approaches in Structural Genomics - Session Introduction. Pacific Symposium on Biocomputing 2003: 176-179 - 2001
- [c1]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: 240-250
1990 – 1999
- 1999
- [j1]Scott C.-H. Pegg, Patricia C. Babbitt:
Shotgun: getting more from sequence similarity searches. Bioinform. 15(9): 729-740 (1999)
Coauthor Index
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