ArticleProtein science : a publication of the Protein Society2011
A matching algorithm for catalytic residue site selection in computational enzyme design.
Article in Protein science : a publication of the Protein Society, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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13 citing papers in PubMed.
- Computational loop reconstruction based design of efficient PET hydrolases.Communications biology · 2025Article
- Computational design of highly efficient thermostable MHET hydrolases and dual enzyme system for PET recycling.Communications biology · 2023Article
- A computational method for design of connected catalytic networks in proteins.Protein science : a publication of the Protein Society · 2019Article
- Computational design of enhanced detoxification activity of a zearalenone lactonase fromRSC advances · 2019Article
- Article
- 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
- Computational study of a model system of enzyme-mediated [4+2] cycloaddition reaction.PloS one · 2015Article
- Evaluation of active designs of cephalosporin C acylase by molecular dynamics simulation and molecular docking.Journal of molecular modeling · 2014Article
- Systematic optimization model and algorithm for binding sequence selection in computational enzyme design.Protein science : a publication of the Protein Society · 2013Article
- A solvated ligand rotamer approach and its application in computational protein design.Journal of molecular modeling · 2013Article
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3 authors.
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Abstract
A loop closure-based sequential algorithm, PRODA_MATCH, was developed to match catalytic residues onto a scaffold for enzyme design in silico. The computational complexity of this algorithm is polynomial with respect to the number of active sites, the number of catalytic residues, and the maximal iteration number of cyclic coordinate descent steps. This matching algorithm is independent of a rotamer library that enables the catalytic residue to take any required conformation during the reaction coordinate. The catalytic geometric parameters defined between functional groups of transition state (TS) and the catalytic residues are continuously optimized to identify the accurate position of the TS. Pseudo-spheres are introduced for surrounding residues, which make the algorithm take binding into account as early as during the matching process. Recapitulation of native catalytic residue sites was used as a benchmark to evaluate the novel algorithm. The calculation results for the test set show that the native catalytic residue sites were successfully identified and ranked within the top 10 designs for 7 of the 10 chemical reactions. This indicates that the matching algorithm has the potential to be used for designing industrial enzymes for desired reactions.
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