Literature DB >> 10812475

History of the enzyme nomenclature system.

K Tipton1, S Boyce.   

Abstract

Naming things is essential for people to understand one another, no matter what language or field of interest is involved. This is as true for enzymes, genes and chemicals as it is for birds, food, flowers, etc. Effective communication requires a lack of ambiguity, but, in practice, ambiguities abound even between people who use the same language in different parts of the world, or even within the same country. Whereas ambiguities in the words used for common objects or actions have been the basis for many, more-or-less memorable jokes, they can also cause a great deal of confusion. Such linguistic chaos is welcomed by many as being a part of a diverse heritage that should be preserved at all costs to prevent us from descending into Orwellian 'newspeak'. However, in the sciences, there are distinct advantages in others being able to understand what one is doing. Many groups have stressed the need for standardized, universally accepted systems of nomenclature in chemistry, genetics, enzymology, etc. However, it is the universal acceptance that usually causes the problem. It is rare to find people who will admit that they find nomenclature to be an interesting subject, but many who profess contempt for it will get very excited if it is suggested that their pet nomenclature should be changed in the interest of clarity or uniformity. This account will consider the development of the enzyme nomenclature system, its benefits, shortcomings and future prospects.

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Year:  2000        PMID: 10812475     DOI: 10.1093/bioinformatics/16.1.34

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


  28 in total

1.  IntEnz, the integrated relational enzyme database.

Authors:  Astrid Fleischmann; Michael Darsow; Kirill Degtyarenko; Wolfgang Fleischmann; Sinéad Boyce; Kristian B Axelsen; Amos Bairoch; Dietmar Schomburg; Keith F Tipton; Rolf Apweiler
Journal:  Nucleic Acids Res       Date:  2004-01-01       Impact factor: 16.971

2.  Evolutionary constraints on structural similarity in orthologs and paralogs.

Authors:  Mark E Peterson; Feng Chen; Jeffery G Saven; David S Roos; Patricia C Babbitt; Andrej Sali
Journal:  Protein Sci       Date:  2009-06       Impact factor: 6.725

3.  Remodeling adipose tissue through in silico modulation of fat storage for the prevention of type 2 diabetes.

Authors:  Thierry Chénard; Frédéric Guénard; Marie-Claude Vohl; André Carpentier; André Tchernof; Rafael J Najmanovich
Journal:  BMC Syst Biol       Date:  2017-06-12

4.  Reconstruction of metabolic network in the bovine mammary gland tissue.

Authors:  Changfa Wang; Ji Wang; Zhihua Ju; Ruiyan Zhai; Lei Zhou; Qiuling Li; Jianbin Li; Rongling Li; Jinming Huang; Jifeng Zhong
Journal:  Mol Biol Rep       Date:  2012-02-12       Impact factor: 2.316

5.  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

6.  Computational evaluation of factors governing catalytic 2-keto acid decarboxylation.

Authors:  Di Wu; Dajun Yue; Fengqi You; Linda J Broadbelt
Journal:  J Mol Model       Date:  2014-06-10       Impact factor: 1.810

Review 7.  The Classification and Evolution of Enzyme Function.

Authors:  Sergio Martínez Cuesta; Syed Asad Rahman; Nicholas Furnham; Janet M Thornton
Journal:  Biophys J       Date:  2015-05-15       Impact factor: 4.033

8.  Sequence-based feature prediction and annotation of proteins.

Authors:  Agnieszka S Juncker; Lars J Jensen; Andrea Pierleoni; Andreas Bernsel; Michael L Tress; Peer Bork; Gunnar von Heijne; Alfonso Valencia; Christos A Ouzounis; Rita Casadio; Søren Brunak
Journal:  Genome Biol       Date:  2009-02-02       Impact factor: 13.583

9.  E-zyme: predicting potential EC numbers from the chemical transformation pattern of substrate-product pairs.

Authors:  Yoshihiro Yamanishi; Masahiro Hattori; Masaaki Kotera; Susumu Goto; Minoru Kanehisa
Journal:  Bioinformatics       Date:  2009-06-15       Impact factor: 6.937

10.  ExplorEnz: the primary source of the IUBMB enzyme list.

Authors:  Andrew G McDonald; Sinéad Boyce; Keith F Tipton
Journal:  Nucleic Acids Res       Date:  2008-09-06       Impact factor: 16.971

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