J Chem Inf Model - Stereochemically consistent reaction mapping and identification of multiple reaction mechanisms through integer linear optimization.

Tópicos

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{ age(1611) year(1155) adult(843) }
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{ group(2977) signific(1463) compar(1072) }
{ data(3008) multipl(1320) sourc(1022) }
{ first(2504) two(1366) second(1323) }
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{ process(1125) use(805) approach(778) }
{ activ(1452) weight(1219) physic(1104) }

Resumo

Reaction mappings are of fundamental importance to researchers studying the mechanisms of chemical reactions and analyzing biochemical pathways. We have developed an automated method based on integer linear optimization, ILP, to identify optimal reaction mappings that minimize the number of bond changes. An alternate objective function is also proposed that minimizes the number of bond order changes. In contrast to previous approaches, our method produces mappings that respect stereochemistry. We also show how to locate multiple reaction mappings efficiently and determine which of those mappings correspond to distinct reaction mechanisms by automatically detecting molecular symmetries. We demonstrate our techniques through a number of computational studies on the GRI-Mech, KEGG LIGAND, and BioPath databases. The computational studies indicate that 99% of the 8078 reactions tested can be addressed within 1 CPU hour. The proposed framework has been incorporated into the Web tool DREAM ( http://selene.princeton.edu/dream/ ), which is freely available to the scientific community.

Resumo Limpo

reaction map fundament import research studi mechan chemic reaction analyz biochem pathway develop autom method base integ linear optim ilp identifi optim reaction map minim number bond chang altern object function also propos minim number bond order chang contrast previous approach method produc map respect stereochemistri also show locat multipl reaction map effici determin map correspond distinct reaction mechan automat detect molecular symmetri demonstr techniqu number comput studi grimech kegg ligand biopath databas comput studi indic reaction test can address within cpu hour propos framework incorpor web tool dream httpseleneprincetonedudream freeli avail scientif communiti

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