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D-Index & Metrics

Biology and Biochemistry

D-Index
71
Citations
19149
World Ranking
6600
National Ranking
3073

Research.com Recognitions

  • 2020 - Fellow of the American Association for the Advancement of Science (AAAS)
  • 2018 - Fellow of the International Society for Computational Biology

Overview

Patricia C. Babbitt is affiliated with the University of California, San Francisco in the United States. Their research primarily focuses on biochemistry, genetics, and molecular biology, with specific interests spanning molecular biology, immunology, organic chemistry, materials chemistry, and computational theory and mathematics.

The scientist's recent published work includes the following papers:

  • Parallel molecular mechanisms for enzyme temperature adaptation (2021), published in Science
  • A strategy for large-scale comparison of evolutionary- and reaction-based classifications of enzyme function (2020), published in Database
  • Structural Basis for the Asymmetry of a 4-Oxalocrotonate Tautomerase Trimer (2020), published in Biochemistry
  • Kinetic and Structural Analysis of Two Linkers in the Tautomerase Superfamily: Analysis and Implications (2021), published in Biochemistry

Babbitt's work extensively addresses topics such as protein structure and dynamics, macrophage migration inhibitory factor, enzyme structure and function, microbial metabolic engineering and bioproduction, computational drug discovery methods, and microbial natural products and biosynthesis, as well as carbohydrate chemistry and synthesis.

Frequent co-authors in their research include:

  • Shoshana Brown
  • Brenda P. Medellin
  • Emily B. Lancaster
  • Yan Zhang
  • Christian P. Whitman

Publication venues where Babbitt has contributed multiple works include Biochemistry, Science, and Database. The dominant fields of study are biochemistry, genetics, and molecular biology, reflecting the interdisciplinary nature of their research.

Among distinctions awarded, Babbitt was recognized as a Fellow of the American Association for the Advancement of Science (AAAS) in 2020 and a Fellow of the International Society for Computational Biology in 2018.

Best Publications

  • InterPro in 2017-beyond protein family and domain annotations

    Robert D. Finn;Teresa K. Attwood;Patricia C. Babbitt;Alex Bateman

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

    Alex L. Mitchell;Teresa K. Attwood;Patricia C. Babbitt;Matthias Blum

  • A large-scale evaluation of computational protein function prediction

    Predrag Radivojac;Wyatt T Clark;Tal Ronnen Oron;Alexandra M Schnoes

  • Annotation error in public databases: misannotation of molecular function in enzyme superfamilies.

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

  • Divergent Evolution of Enzymatic Function: Mechanistically Diverse Superfamilies and Functionally Distinct Suprafamilies

    John A. Gerlt;Patricia C. Babbitt

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

    Holly J. Atkinson;John H. Morris;Thomas E. Ferrin;Patricia C. Babbitt

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

    Yuxiang Jiang;Tal Ronnen Oron;Wyatt T. Clark;Asma R. Bankapur

  • The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens

    Naihui Zhou;Yuxiang Jiang;Timothy R. Bergquist;Alexandra J. Lee

  • The Enolase Superfamily: A General Strategy for Enzyme-Catalyzed Abstraction of the α-Protons of Carboxylic Acids†

    Patricia C. Babbitt;Miriam S. Hasson;Miriam S. Hasson;Joseph E. Wedekind;Joseph E. Wedekind;David R.J. Palmer

  • Understanding Enzyme Superfamilies CHEMISTRY AS THE FUNDAMENTAL DETERMINANT IN THE EVOLUTION OF NEW CATALYTIC ACTIVITIES

    Patricia C. Babbitt;John A. Gerlt

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

    Yuxiang Jiang;Tal Ronnen Oron;Wyatt T Clark;Asma R Bankapur

  • Evolution of enzyme superfamilies

    Margaret E Glasner;John A Gerlt;Patricia C Babbitt

  • Ancestry of the 4-chlorobenzoate dehalogenase: analysis of amino acid sequence identities among families of acyl:adenyl ligases, enoyl-CoA hydratases/isomerases, and acyl-CoA thioesterases.

    Patricia C. Babbitt;George L. Kenyon;Brian M. Martin;Hugues Charest

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

    Doug Stryke;Michiko Kawamoto;Conrad C. Huang;Susan J. Johns

  • The Structure–Function Linkage Database

    Eyal Akiva;Shoshana D. Brown;Daniel E. Almonacid;Alan E. Barber

  • Divergent evolution in the enolase superfamily: The interplay of mechanism and specificity

    John A. Gerlt;Patricia C. Babbitt;Ivan Rayment

  • Evolutionary Potential of (β/α)8-Barrels: Functional Promiscuity Produced by Single Substitutions in the Enolase Superfamily†

    Dawn M Z Schmidt;Emily C. Mundorff;Michael Dojka;Ericka Bermudez

  • Can sequence determine function

    John A Gerlt;Patricia C Babbitt

  • Leveraging enzyme structure-function relationships for functional inference and experimental design: the structure-function linkage database.

    Scott C.H. Pegg;Shoshana D. Brown;Sunil Ojha;Jennifer L Seffernick

  • Additional file 1 of An expanded evaluation of protein function prediction methods shows an improvement in accuracy

    Yuxiang Jiang;Tal Ronnen Oron;Wyatt T. Clark;Asma R. Bankapur

Frequent Co-Authors

John A. Gerlt
John A. Gerlt University of Illinois at Urbana-Champaign
Thomas E. Ferrin
Thomas E. Ferrin University of California, San Francisco
George L. Kenyon
George L. Kenyon University of California, San Francisco
Matthew P. Jacobson
Matthew P. Jacobson University of California, San Francisco
Steven C. Almo
Steven C. Almo Albert Einstein College of Medicine
Christophe Dessimoz
Christophe Dessimoz University College London
Sean D. Mooney
Sean D. Mooney University of Washington
Andrej Sali
Andrej Sali University of California, San Francisco
Julian Gough
Julian Gough University of Bristol
David T. Jones
David T. Jones University College London

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