{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,27]],"date-time":"2025-10-27T15:50:47Z","timestamp":1761580247704},"reference-count":21,"publisher":"Oxford University Press (OUP)","issue":"6","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2005,3,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: As a first step toward the elucidation of the systems biology of complex biological systems, it was our goal to mathematically model common enzyme catalytic and regulatory mechanisms that repeatedly appear in biological processes such as signal transduction and metabolic pathways.<\/jats:p>\n               <jats:p>Results: We describe kMech, a Cellerator language extension that describes a suite of enzyme mechanisms. Each enzyme mechanism is parsed by kMech into a set of fundamental association\u2013dissociation reactions that are translated by Cellerator into ordinary differential equations that are numerically solved by Mathematica\u2122. In addition, we present methods that use commonly available kinetic measurements to estimate rate constants required to solve these differential equations.<\/jats:p>\n               <jats:p>Availability: A Mathematica\u2122 executable kMech.m file is available at the University of California, Irvine, Institute for Genomics and Bioinformatics website, http:\/\/www.igb.uci.edu\/servers\/sb.html. Cellerator, free of charge to academic, US government, and other non-profit organizations, can be obtained at the Cellerator website, (http:\/\/www-aig.jpl.nasa.gov\/public\/mls\/cellerator\/feedback.html).<\/jats:p>\n               <jats:p>Contact: Biology correspondence should be addressed to gwhatfie@uci.edu. Computation correspondence should be addressed to emj@uci.edu.<\/jats:p>\n               <jats:p>Supplementary information: \u00a0http:\/\/www.igb.uci.edu\/servers\/sb.html.<\/jats:p>","DOI":"10.1093\/bioinformatics\/bti068","type":"journal-article","created":{"date-parts":[[2004,10,28]],"date-time":"2004-10-28T00:23:01Z","timestamp":1098922981000},"page":"774-780","source":"Crossref","is-referenced-by-count":36,"title":["An enzyme mechanism language for the mathematical modeling of metabolic pathways"],"prefix":"10.1093","volume":"21","author":[{"given":"Chin-Rang","family":"Yang","sequence":"first","affiliation":[]},{"given":"Bruce E.","family":"Shapiro","sequence":"additional","affiliation":[]},{"given":"Eric D.","family":"Mjolsness","sequence":"additional","affiliation":[]},{"given":"G. 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