ArticleJournal of molecular biology2007
Using reaction mechanism to measure enzyme similarity.
Article in Journal of molecular biology, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- SimCAL: a flexible tool to compute biochemical reaction similarity.BMC bioinformatics · 2018Article
- Simultaneous prediction of enzyme orthologs from chemical transformation patterns for de novo metabolic pathway reconstruction.Bioinformatics (Oxford, England) · 2016Article
- Evolutionary Conserved Positions Define Protein Conformational Diversity.PLoS computational biology · 2016Article
- Metabolic pathway reconstruction strategies for central metabolism and natural product biosynthesis.Biophysics and physicobiology · 2016Review
- Characterising Complex Enzyme Reaction Data.PloS one · 2016Article
- EC-BLAST: a tool to automatically search and compare enzyme reactions.Nature methods · 2014Article
- Is EC class predictable from reaction mechanism?BMC bioinformatics · 2012Article
- Assignment of EC numbers to enzymatic reactions with reaction difference fingerprints.PloS one · 2012Article
- MACiE: exploring the diversity of biochemical reactions.Nucleic acids research · 2012Article
- Toward mechanistic classification of enzyme functions.Current opinion in chemical biology · 2011Review
- Non-homologous isofunctional enzymes: a systematic analysis of alternative solutions in enzyme evolution.Biology direct · 2010Article
- Quantitative global studies of reactomes and metabolomes using a vectorial representation of reactions and chemical compounds.BMC systems biology · 2010Article
- Quantitative comparison of catalytic mechanisms and overall reactions in convergently evolved enzymes: implications for classification of enzyme function.PLoS computational biology · 2010Article
- Evolutionarily conserved substrate substructures for automated annotation of enzyme superfamilies.PLoS computational biology · 2008Article
- Exploring the structure and function paradigm.Current opinion in structural biology · 2008Review
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Authors and funding
4 authors.
Funding
Abstract
The concept of reaction similarity has been well studied in terms of the overall transformation associated with a reaction, but not in terms of mechanism. We present the first method to give a quantitative measure of the similarity of reactions based upon their explicit mechanisms. Two approaches are presented to measure the similarity between individual steps of mechanisms: a fingerprint-based approach that incorporates relevant information on each mechanistic step; and an approach based only on bond formation, cleavage and changes in order. The overall similarity for two reaction mechanisms is then calculated using the Needleman-Wunsch alignment algorithm. An analysis of MACiE, a database of enzyme mechanisms, using our measure of similarity identifies some examples of convergent evolution of chemical mechanisms. In many cases, mechanism similarity is not reflected by similarity according to the EC system of enzyme classification. In particular, little mechanistic information is conveyed by the class level of the EC system.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.