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PROCEDIA
2010
140views more  PROCEDIA 2010»
13 years 1 months ago
Theoretical enzyme design using the Kepler scientific workflows on the Grid
One of the greatest challenges in computational chemistry is the design of enzymes to catalyze non-natural chemical reactions. We focus on harnessing the distributed parallel comp...
Jianwu Wang, Prakashan Korambath, Seonah Kim, Scot...
BMCBI
2004
89views more  BMCBI 2004»
13 years 6 months ago
Network analysis of metabolic enzyme evolution in Escherichia coli
Background: The two most common models for the evolution of metabolism are the patchwork evolution model, where enzymes are thought to diverge from broad to narrow substrate speci...
Sara Light, Per Kraulis
BMCBI
2005
90views more  BMCBI 2005»
13 years 6 months ago
DSD - An integrated, web-accessible database of Dehydrogenase Enzyme Stereospecificities
Background: Dehydrogenase enzymes belong to the oxidoreductase class and utilise the coenzymes NAD and NADP. Stereo-selectivity is focused on the C4 hydrogen atoms of the nicotina...
Christopher P. Toseland, Helen M. McSparron, Darre...
BMCBI
2007
102views more  BMCBI 2007»
13 years 6 months ago
qPIPSA: Relating enzymatic kinetic parameters and interaction fields
Background: The simulation of metabolic networks in quantitative systems biology requires the assignment of enzymatic kinetic parameters. Experimentally determined values are ofte...
Razif R. Gabdoulline, Matthias Stein, Rebecca C. W...
BMCBI
2006
144views more  BMCBI 2006»
13 years 6 months ago
Association algorithm to mine the rules that govern enzyme definition and to classify protein sequences
Background: The number of sequences compiled in many genome projects is growing exponentially, but most of them have not been characterized experimentally. An automatic annotation...
Shih-Hau Chiu, Chien-Chi Chen, Gwo-Fang Yuan, Thy-...
BMCBI
2006
89views more  BMCBI 2006»
13 years 6 months ago
ORENZA: a web resource for studying ORphan ENZyme activities
Background: Despite the current availability of several hundreds of thousands of amino acid sequences, more than 36% of the enzyme activities (EC numbers) defined by the Nomenclat...
Olivier Lespinet, Bernard Labedan
BMCBI
2010
82views more  BMCBI 2010»
13 years 6 months ago
Predicting the network of substrate-enzyme-product triads by combining compound similarity and functional domain composition
Background: Metabolic pathway is a highly regulated network consisting of many metabolic reactions involving substrates, enzymes, and products, where substrates can be transformed...
Lei Chen, Kai-Yan Feng, Yu-Dong Cai, Kuo-Chen Chou...
BMCBI
2010
162views more  BMCBI 2010»
13 years 6 months ago
SNP-RFLPing 2: an updated and integrated PCR-RFLP tool for SNP genotyping
Background: PCR-restriction fragment length polymorphism (RFLP) assay is a cost-effective method for SNP genotyping and mutation detection, but the manual mining for restriction e...
Hsueh-Wei Chang, Yu-Huei Cheng, Li-Yeh Chuang, Che...
CSB
2005
IEEE
128views Bioinformatics» more  CSB 2005»
13 years 8 months ago
Application of a Generalized MWC Model for the Mathematical Simulation of Metabolic Pathways Regulated by Allosteric Enzymes
In our effort to elucidate the systems biology of the model organism, Escherichia coli, we have developed a mathematical model that simulates the allosteric regulation for threoni...
Tarek S. Najdi, Chin-Rang Yang, Bruce E. Shapiro, ...