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Mechanism Modeling and Investigation

Computer-aided mechanism modeling uses molecular simulation to study the specific catalytic mechanism of an enzyme by defining the catalytic-binding pockets for cofactors and substrates. Starting from modeling and deriving specific proteins structural features, molecular mechanisms and the functional conservation of proteins, especially from the same family, can be analyzed thoroughly. The merit of this study allows targeting and engineering specific biocatalysts with novel activities and unique specificity for valuable manufacturing processes.

Various algorithms, softwares, and databases have been developed for molecular modeling of different aspects, examples including domain architecture analyses, secondary structure prediction, homology modeling, protein docking process, clustering analysis, and many others. In general, mechanism modeling provides a comprehensive understanding of (i) the structure and characterization of target biocatalyst; (ii) the structure similarities and differences of target biocatalyst to its family members; (iii) the implications of the polymorphism; (iv) the molecular environment of the substrate-binding pocket of target protein for cofactor and substrate recognition and interaction; (v) catalytic mechanism modeling; (vi) the structural and molecular basis for engineering biosynthetic tailoring enzyme reactions for generating new active compounds; (vii) the implications of the molecular variability of epitopes.

Creative Enzymes offers computer-aided molecular design for the study of catalytic mechanism, as well as other characterization of target biocatalysts. Enabled by our advanced algorithm and databases, we offer professional one-stop services:


  1. Jimenez-Lopez, J.C., Kotchoni, S.O., Hernandez-Soriano, M.C., Gachomo, E.W., Alché, J.D. (2013) Structural functionality, catalytic mechanism modeling and molecular allergenicity of phenylcoumaran benzylic ether reductase, an olive pollen (Ole e 12) allergen. Journal of Computer-Aided Molecular Design. 27: 873-895.

Computational modeling is widely used to mimic and investigate details of biocatalytic reactions

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