Shotgun: getting more from sequence similarity searches. - Scott C.-H. Pegg; Patricia C. Babbitt (Bioinform., 1999)

ViewFeature: Integrated Feature Analysis and Visualization. - D. Rey Banatao; Conrad C. Huang; Patricia C. Babbitt; Russ B. Altman; Teri E. Klein (Pacific Symposium on Biocomputing, 2001)

Informatics Approaches in Structural Genomics - Session Introduction. - Sean D. Mooney; Patricia C. Babbitt (Pacific Symposium on Biocomputing, 2003)

Intersect: identification and visualization of overlaps in database search results. - Scott C.-H. Pegg; Walter R. P. Novak; Patricia C. Babbitt (Bioinform., 2003)

The Structure Superposition Database. - Ranyee A. Chiang; Elaine C. Meng; Conrad C. Huang; Thomas E. Ferrin; Patricia C. Babbitt (Nucleic Acids Res., 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; et al. (Nucleic Acids Res., 2003)

Session Introduction. - Sean D. Mooney; Philip E. Bourne; Patricia C. Babbitt (Pacific Symposium on Biocomputing, 2004)

Introduction to Informatics Approaches in Structural Genomics: Modeling and Representation of Function from Macromolecular STructure. - Patricia C. Babbitt; Philip E. Bourne; Sean D. Mooney (Pacific Symposium on Biocomputing, 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 (Pacific Symposium on Biocomputing, 2005)

Automated discovery of 3D motifs for protein function annotation. - Benjamin J. Polacco; Patricia C. Babbitt (Bioinform., 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; et al. (Nucleic Acids Res., 2006)

structureViz: linking Cytoscape and UCSF Chimera. - John H. Morris; Conrad C. Huang; Patricia C. Babbitt; Thomas E. Ferrin (Bioinform., 2007)

Evolution of Function in the "Two Dinucleotide Binding Domains" Flavoproteins. - Sunil Ojha; Elaine C. Meng; Patricia C. Babbitt (PLoS Comput. Biol., 2007)

Evolutionarily Conserved Substrate Substructures for Automated Annotation of Enzyme Superfamilies. - Ranyee A. Chiang; Andrej Sali; Patricia C. Babbitt (PLoS Comput. Biol., 2008)

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)

An Atlas of the Thioredoxin Fold Class Reveals the Complexity of Function-Enabling Adaptations. - Holly J. Atkinson; Patricia C. Babbitt (PLoS Comput. Biol., 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)

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)

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)

Pythoscape: a framework for generation of large protein similarity networks. - Alan E. Barber II; Patricia C. Babbitt (Bioinform., 2012)

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; et al. (Nat., 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)

Prediction of Substrates for Glutathione Transferases by Covalent Docking. - Guang Qiang Dong; Sara Calhoun; Hao Fan 002; 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)

The Structure-Function Linkage Database. - Eyal Akiva; Shoshana D. Brown; Daniel E. Almonacid; Alan E. Barber II; Ashley F. Custer; Michael A. Hicks 002; Conrad C. Huang; Florian Lauck; Susan T. Mashiyama; Elaine C. Meng; David Mischel; John H. Morris; et al. (Nucleic Acids Res., 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)

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; et al. (Database J. Biol. Databases Curation, 2015)

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)

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 002; 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)

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; et al. (Nucleic Acids Res., 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)

New computational approaches to understanding molecular protein function. - Jacquelyn S. Fetrow; Patricia C. Babbitt (PLoS Comput. Biol., 2018)

Effusion: prediction of protein function from sequence similarity networks. - Jeffrey M. Yunes; Patricia C. Babbitt (Bioinform., 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; et al. (Nucleic Acids Res., 2019)

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)