ArticleProtein science : a publication of the Protein Society2013
Systematic optimization model and algorithm for binding sequence selection in computational enzyme design.
Article in Protein science : a publication of the Protein Society, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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16 citing papers in PubMed.
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- Rational Design of Daunorubicin C-14 Hydroxylase Based on the Understanding of Its Substrate-Binding Mechanism.International journal of molecular sciences · 2023Article
- Co-evolution of β-glucosidase activity and product tolerance for increasing cellulosic ethanol yield.Biotechnology letters · 2020Article
- Enhancing cellulosic ethanol production through coevolution of multiple enzymatic characteristics of β-glucosidase from Penicillium oxalicum 16.Applied microbiology and biotechnology · 2020Article
- FASPR: an open-source tool for fast and accurate protein side-chain packing.Bioinformatics (Oxford, England) · 2020Article
- EvoEF2: accurate and fast energy function for computational protein design.Bioinformatics (Oxford, England) · 2020Article
- Toward the Accuracy and Speed of Protein Side-Chain Packing: A Systematic Study on Rotamer Libraries.Journal of chemical information and modeling · 2020Article
- Computational design of enhanced detoxification activity of a zearalenone lactonase fromRSC advances · 2019Article
- Article
- Computational tools for the evaluation of laboratory-engineered biocatalysts.Chemical communications (Cambridge, England) · 2016Review
- A fast loop-closure algorithm to accelerate residue matching in computational enzyme design.Journal of molecular modeling · 2016Article
- Use of an Improved Matching Algorithm to Select Scaffolds for Enzyme Design Based on a Complex Active Site Model.PloS one · 2016Article
- Computational strategies for the design of new enzymatic functions.Archives of biochemistry and biophysics · 2015Review
- Computational design of enzyme-ligand binding using a combined energy function and deterministic sequence optimization algorithm.Journal of molecular modeling · 2015Article
- Evaluation of active designs of cephalosporin C acylase by molecular dynamics simulation and molecular docking.Journal of molecular modeling · 2014Article
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3 authors.
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Abstract
A systematic optimization model for binding sequence selection in computational enzyme design was developed based on the transition state theory of enzyme catalysis and graph-theoretical modeling. The saddle point on the free energy surface of the reaction system was represented by catalytic geometrical constraints, and the binding energy between the active site and transition state was minimized to reduce the activation energy barrier. The resulting hyperscale combinatorial optimization problem was tackled using a novel heuristic global optimization algorithm, which was inspired and tested by the protein core sequence selection problem. The sequence recapitulation tests on native active sites for two enzyme catalyzed hydrolytic reactions were applied to evaluate the predictive power of the design methodology. The results of the calculation show that most of the native binding sites can be successfully identified if the catalytic geometrical constraints and the structural motifs of the substrate are taken into account. Reliably predicting active site sequences may have significant implications for the creation of novel enzymes that are capable of catalyzing targeted chemical reactions.
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