P. Babbitt

Publications
Influence

InterPro in 2017—beyond protein family and domain annotations

R. Finn, T. Attwood, +44 authors A. Mitchell
Biology, Computer Science
Nucleic Acids Res.
28 November 2016

We report recent developments with InterPro and its associated software, including the addition of two new databases (SFLD and CDD), and the functionality to include residue-level annotation. Expand

A large-scale evaluation of computational protein function prediction

P. Radivojac, W. Clark, +99 authors I. Friedberg
Biology, Medicine
Nature Methods
27 January 2013

Automated annotation of protein function is challenging. As the number of sequenced genomes rapidly grows, the overwhelming majority of protein products can only be annotated computationally. If… Expand

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

A. Mitchell, T. Attwood, +39 authors R. Finn
Biology, Computer Science
Nucleic Acids Res.
6 November 2018

We report recent developments with InterPro (version 70.0) and its associated software, including an 18% growth in the size of the database in terms on new InterPro entries, updates to content, the inclusion of an additional entry type, refined modelling of discontinuous domains, and the development of a new website. Expand

BayGenomics: a resource of insertional mutations in mouse embryonic stem cells

D. Stryke, Michiko Kawamoto, +12 authors T. Ferrin
Biology, Medicine
Nucleic Acids Res.
2003

The BayGenomics gene-trap resource (http://baygenomics.ucsf.edu) provides researchers with access to thousands of mouse embryonic stem (ES) cell lines harboring characterized insertional mutations in both known and novel genes. Expand

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

Alexandra M. Schnoes, S. Brown, Igor Dodevski, P. Babbitt
Biology, Medicine
PLoS Comput. Biol.
1 December 2009

We have investigated the misannotation levels for molecular function in four public protein sequence databases (UniProtKB, GenBank NR, UniProtKB/TrEMBL, and KEGG) for a model set of 37 enzyme families for which extensive experimental information is available. Expand

An expanded evaluation of protein function prediction methods shows an improvement in accuracy

Yuxiang Jiang, Tal Ronnen Oron, +144 authors P. Radivojac
Biology, Medicine
Genome Biology
3 January 2016

We evaluated 126 methods from 56 research groups for their ability to predict biological functions using Gene Ontology and gene-disease associations using Human Phenotype Ontology. Expand

Divergent evolution of enzymatic function: mechanistically diverse superfamilies and functionally distinct suprafamilies.

J. A. Gerlt, P. Babbitt
Biology, Medicine
Annual review of biochemistry
30 July 2001

The protein sequence and structure databases are now sufficiently representative that strategies nature uses to evolve new catalytic functions can be identified. Groups of divergently related enzymes… Expand

Using Sequence Similarity Networks for Visualization of Relationships Across Diverse Protein Superfamilies

H. J. Atkinson, J. Morris, T. Ferrin, P. Babbitt
Biology, Medicine
PloS one
3 February 2009

The dramatic increase in heterogeneous types of biological data—in particular, the abundance of new protein sequences—requires fast and user-friendly methods for organizing this information in a way… Expand

The enolase superfamily: a general strategy for enzyme-catalyzed abstraction of the alpha-protons of carboxylic acids.

P. Babbitt, M. S. Hasson, +7 authors J. Gerlt
Chemistry, Medicine
Biochemistry
24 December 1996

We have discovered a superfamily of enzymes related by their ability to catalyze the abstraction of the alpha-proton of a carboxylic acid to form an enolic intermediate. Although each reaction… Expand

The Structure–Function Linkage Database

Eyal Akiva, S. Brown, +16 authors P. Babbitt
Biology, Computer Science
Nucleic Acids Res.
1 March 2006

The Structure–Function Linkage Database (SFLD, http://sfld.rbvi.ucsf.edu/) is a manually curated classification resource describing structure–function relationships for functionally diverse enzyme superfamilies. Expand

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