Literature DB >> 16188925

MACiE: a database of enzyme reaction mechanisms.

Gemma L Holliday1, Gail J Bartlett, Daniel E Almonacid, Noel M O'Boyle, Peter Murray-Rust, Janet M Thornton, John B O Mitchell.   

Abstract

SUMMARY: MACiE (mechanism, annotation and classification in enzymes) is a publicly available web-based database, held in CMLReact (an XML application), that aims to help our understanding of the evolution of enzyme catalytic mechanisms and also to create a classification system which reflects the actual chemical mechanism (catalytic steps) of an enzyme reaction, not only the overall reaction. AVAILABILITY: http://www-mitchell.ch.cam.ac.uk/macie/.

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Year:  2005        PMID： 16188925      PMCID： PMC2748267          DOI： 10.1093/bioinformatics/bti693

Source DB:  PubMed          Journal:  Bioinformatics        ISSN： 1367-4803            Impact factor:   6.937


  9 in total

1.  The Protein Data Bank.

Authors:  H M Berman; J Westbrook; Z Feng; G Gilliland; T N Bhat; H Weissig; I N Shindyalov; P E Bourne
Journal:  Nucleic Acids Res       Date:  2000-01-01       Impact factor: 16.971

2.  Analysis of catalytic residues in enzyme active sites.

Authors:  Gail J Bartlett; Craig T Porter; Neera Borkakoti; Janet M Thornton
Journal:  J Mol Biol       Date:  2002-11-15       Impact factor: 5.469

3.  BRENDA, the enzyme database: updates and major new developments.

Authors:  Ida Schomburg; Antje Chang; Christian Ebeling; Marion Gremse; Christian Heldt; Gregor Huhn; Dietmar Schomburg
Journal:  Nucleic Acids Res       Date:  2004-01-01       Impact factor: 16.971

4.  The Catalytic Site Atlas: a resource of catalytic sites and residues identified in enzymes using structural data.

Authors:  Craig T Porter; Gail J Bartlett; Janet M Thornton
Journal:  Nucleic Acids Res       Date:  2004-01-01       Impact factor: 16.971

5.  The KEGG resource for deciphering the genome.

Authors:  Minoru Kanehisa; Susumu Goto; Shuichi Kawashima; Yasushi Okuno; Masahiro Hattori
Journal:  Nucleic Acids Res       Date:  2004-01-01       Impact factor: 16.971

6.  Representing structure-function relationships in mechanistically diverse enzyme superfamilies.

Authors:  Scott C H Pegg; Shoshana Brown; Sunil Ojha; Conrad C Huang; Thomas E Ferrin; Patricia C Babbitt
Journal:  Pac Symp Biocomput       Date:  2005

7.  Chemical markup, XML, and the world wide web. 6. CMLReact, an XML vocabulary for chemical reactions.

Authors:  Gemma L Holliday; Peter Murray-Rust; Henry S Rzepa
Journal:  J Chem Inf Model       Date:  2006 Jan-Feb       Impact factor: 4.956

8.  CATH--a hierarchic classification of protein domain structures.

Authors:  C A Orengo; A D Michie; S Jones; D T Jones; M B Swindells; J M Thornton
Journal:  Structure       Date:  1997-08-15       Impact factor: 5.006

9.  EzCatDB: the Enzyme Catalytic-mechanism Database.

Authors:  Nozomi Nagano
Journal:  Nucleic Acids Res       Date:  2005-01-01       Impact factor: 16.971
  9 in total
  18 in total

1.  Structure-based identification of catalytic residues.

Authors:  Ran Yahalom; Dan Reshef; Ayana Wiener; Sagiv Frankel; Nir Kalisman; Boaz Lerner; Chen Keasar
Journal:  Proteins       Date:  2011-04-12

2.  Quantitative comparison of catalytic mechanisms and overall reactions in convergently evolved enzymes: implications for classification of enzyme function.

Authors:  Daniel E Almonacid; Emmanuel R Yera; John B O Mitchell; Patricia C Babbitt
Journal:  PLoS Comput Biol       Date:  2010-03-12       Impact factor: 4.475

3.  Quantitative global studies of reactomes and metabolomes using a vectorial representation of reactions and chemical compounds.

Authors:  Juan C Triviño; Florencio Pazos
Journal:  BMC Syst Biol       Date:  2010-04-20

Review 4.  A global analysis of function and conservation of catalytic residues in enzymes.

Authors:  António J M Ribeiro; Jonathan D Tyzack; Neera Borkakoti; Gemma L Holliday; Janet M Thornton
Journal:  J Biol Chem       Date:  2019-12-03       Impact factor: 5.157

5.  Using reaction mechanism to measure enzyme similarity.

Authors:  Noel M O'Boyle; Gemma L Holliday; Daniel E Almonacid; John B O Mitchell
Journal:  J Mol Biol       Date:  2007-03-02       Impact factor: 5.469

6.  Exploring the evolution of protein function in Archaea.

Authors:  Alexander Goncearenco; Igor N Berezovsky
Journal:  BMC Evol Biol       Date:  2012-05-30       Impact factor: 3.260

7.  Comparing the chemical spaces of metabolites and available chemicals: models of metabolite-likeness.

Authors:  Sunil Gupta; João Aires-de-Sousa
Journal:  Mol Divers       Date:  2007-02-16       Impact factor: 3.364

8.  The semantics of Chemical Markup Language (CML): dictionaries and conventions.

Authors:  Peter Murray-Rust; Joe A Townsend; Sam E Adams; Weerapong Phadungsukanan; Jens Thomas
Journal:  J Cheminform       Date:  2011-10-14       Impact factor: 5.514

Review 9.  Characterizing the complexity of enzymes on the basis of their mechanisms and structures with a bio-computational analysis.

Authors:  Gemma L Holliday; Julia D Fischer; John B O Mitchell; Janet M Thornton
Journal:  FEBS J       Date:  2011-06-13       Impact factor: 5.542

10.  MACiE: exploring the diversity of biochemical reactions.

Authors:  Gemma L Holliday; Claudia Andreini; Julia D Fischer; Syed Asad Rahman; Daniel E Almonacid; Sophie T Williams; William R Pearson
Journal:  Nucleic Acids Res       Date:  2011-11-03       Impact factor: 16.971
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