Literature DB >> 25501940

Using the structure-function linkage database to characterize functional domains in enzymes.

Shoshana Brown1, Patricia Babbitt.   

Abstract

The Structure-Function Linkage Database (SFLD; http://sfld.rbvi.ucsf.edu/) is a Web-accessible database designed to link enzyme sequence, structure, and functional information. This unit describes the protocols by which a user may query the database to predict the function of uncharacterized enzymes and to correct misannotated functional assignments. The information in this unit is especially useful in helping a user discriminate functional capabilities of a sequence that is only distantly related to characterized sequences in publicly available databases.
Copyright © 2014 John Wiley & Sons, Inc.

Entities:  

Keywords:  annotation transfer; protein function prediction; protein sequence analysis; protein superfamily analysis; structure-function relationships

Mesh：

Substances：

Year:  2014        PMID： 25501940      PMCID： PMC4349220          DOI： 10.1002/0471250953.bi0210s48

Source DB:  PubMed          Journal:  Curr Protoc Bioinformatics        ISSN： 1934-3396


  19 in total

1.  Intrinsic errors in genome annotation.

Authors:  D Devos; A Valencia
Journal:  Trends Genet       Date:  2001-08       Impact factor: 11.639

Review 2.  Divergent evolution of enzymatic function: mechanistically diverse superfamilies and functionally distinct suprafamilies.

Authors:  J A Gerlt; P C Babbitt
Journal:  Annu Rev Biochem       Date:  2001       Impact factor: 23.643

3.  On the Evolution of Biochemical Syntheses.

Authors:  N H Horowitz
Journal:  Proc Natl Acad Sci U S A       Date:  1945-06       Impact factor: 11.205

Review 4.  Understanding enzyme superfamilies. Chemistry As the fundamental determinant in the evolution of new catalytic activities.

Authors:  P C Babbitt; J A Gerlt
Journal:  J Biol Chem       Date:  1997-12-05       Impact factor: 5.157

5.  D-Galactonate utilisation by enteric bacteria. The catabolic pathway in Escherichia coli.

Authors:  J Deacon; R A Cooper
Journal:  FEBS Lett       Date:  1977-05-15       Impact factor: 4.124

Review 6.  Enzyme recruitment in evolution of new function.

Authors:  R A Jensen
Journal:  Annu Rev Microbiol       Date:  1976       Impact factor: 15.500

7.  Evolution of structure and function in the o-succinylbenzoate synthase/N-acylamino acid racemase family of the enolase superfamily.

Authors:  Margaret E Glasner; Nima Fayazmanesh; Ranyee A Chiang; Ayano Sakai; Matthew P Jacobson; John A Gerlt; Patricia C Babbitt
Journal:  J Mol Biol       Date:  2006-05-11       Impact factor: 5.469

8.  Modeling the percolation of annotation errors in a database of protein sequences.

Authors:  Walter R Gilks; Benjamin Audit; Daniela De Angelis; Sophia Tsoka; Christos A Ouzounis
Journal:  Bioinformatics       Date:  2002-12       Impact factor: 6.937

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

Authors:  Alexandra M Schnoes; Shoshana D Brown; Igor Dodevski; Patricia C Babbitt
Journal:  PLoS Comput Biol       Date:  2009-12-11       Impact factor: 4.475

10.  The Structure-Function Linkage Database.

Authors:  Eyal Akiva; Shoshana Brown; Daniel E Almonacid; Alan E Barber; 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
Journal:  Nucleic Acids Res       Date:  2013-11-23       Impact factor: 16.971
View more
  4 in total

1.  Biochemical and Spectroscopic Characterization of a Radical S-Adenosyl-L-methionine Enzyme Involved in the Formation of a Peptide Thioether Cross-Link.

Authors:  Nathan A Bruender; Jarett Wilcoxen; R David Britt; Vahe Bandarian
Journal:  Biochemistry       Date:  2016-04-01       Impact factor: 3.162

2.  7-Carboxy-7-deazaguanine Synthase: A Radical S-Adenosyl-l-methionine Enzyme with Polar Tendencies.

Authors:  Nathan A Bruender; Tsehai A J Grell; Daniel P Dowling; Reid M McCarty; Catherine L Drennan; Vahe Bandarian
Journal:  J Am Chem Soc       Date:  2017-01-25       Impact factor: 15.419

3.  Biochemical and Structural Characterization of a Schiff Base in the Radical-Mediated Biosynthesis of 4-Demethylwyosine by TYW1.

Authors:  Tsehai A J Grell; Anthony P Young; Catherine L Drennan; Vahe Bandarian
Journal:  J Am Chem Soc       Date:  2018-05-24       Impact factor: 15.419

4.  Deconvoluting the Reduction Potentials for the Three [4Fe-4S] Clusters in an AdoMet Radical SCIFF Maturase.

Authors:  Lindsey M Walker; William M Kincannon; Vahe Bandarian; Sean J Elliott
Journal:  Biochemistry       Date:  2018-10-10       Impact factor: 3.162
  4 in total

北京卡尤迪生物科技股份有限公司 © 2022-2023.