Computational Enzymology

Computational enzymology is a rapidly developing area, and is testing theories of catalysis, and identifying novel catalytic mechanisms. Increasingly, modelling is contributing directly to experimental studies of enzyme-catalysed reactions. Potential practical applications include interpretation of experimental data, catalyst design and drug development.

Computational Enzymology

Recent advances in computational methods and the availability of fast, affordable computers have made the modelling of enzymatic reactions practical. Molecular modelling and simulation can give atomic-level understanding of the fundamental mechanisms of enzyme catalysis, which are changing the science of enzymology. For example, modelling can identify likely enzyme reaction mechanisms, analyse catalytic interactions, and identify determinants of reactivity and specificity. Combined quantum mechanics/molecular mechanics (QM/MM) methods are an important technique in this maturing field of computational enzymology. By coupling quantum chemical (electronic structure) calculations on the active site with a simpler, empirical 'molecular mechanics' treatment of the rest of the protein, including the enzyme environment, QM/MM methods allow the modelling of enzyme reactions. A range of QM/MM methods can be used for molecular dynamics simulations to investigate fundamental problems in enzymology. QM/MM methods can also contribute to the practical development and application of enzymology in the interpretation and prediction of the effects of mutagenesis.

Learn more about our QM/MM Simulation Service

Computational enzymology can now reliably and accurately model and predict properties and reactions at or beyond the limits of the experiment, answering important biochemical questions and challenges. Our experts have the expertise, educational backgrounds, and solid experience especially in the field of computational biology, bioinformatics, or a combination of computational biology and quantitative genetics.

What do we focus on?

  • Enzymatic Mechanisms and Inhibition
  • Thermochemistry
  • QM/MM Simulation
  • Molecular Dynamics
  • QM-Cluster

Computational Strategies in Drug Design

Some fundamental stages of rational drug design can be addressed by our experts' team, namely the atomic level understanding on disease-related enzymatic mechanisms and inhibition. Computational alanine-scanning mutagenesis of protein-protein interfacial residues can be a very powerful method for drug design, since protein-protein interactions form the basis for most biological processes and molecular docking using total flexibility of ligand and receptor, which can all be regarded as a pre-requisite to any attempt to rationally design new, better enzyme inhibitors.

Computational Alanine Scanning of Protein-Protein Interfaces. Figure 1 Computational Alanine Scanning of Protein-Protein Interfaces. (TANJA KORTEMME, et al. 2004.)

CD ComputaBio offers comprehensive computational enzymology services. We also have multiple resources including academic research and preclinical works in the identification of a suitable disease target and its corresponding hit.

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Reference

  1. TANJA KORTEMME, DAVID E. KIM, DAVID BAKER. Computational Alanine Scanning of Protein-Protein Interfaces. Science Signaling. 2004.
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