ArticlePloS one2012
A computational methodology to screen activities of enzyme variants.
Article in PloS one, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed, 24 citations in OpenAlex.
- Evaluating Mechanical-Embedding ML/MM for Predicting Mutation Effects in Chorismate Mutase Catalysis.Journal of chemical theory and computation · 2026Article
- Simulating enzyme catalysis with electrostatically embedded machine learning potentials.Chemical science · 2026Article
- Crius: A novel fragment-based algorithm of de novo substrate prediction for enzymes.Protein science : a publication of the Protein Society · 2018Article
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- BioGPS descriptors for rational engineering of enzyme promiscuity and structure based bioinformatic analysis.PloS one · 2014Article
- Article
- In silico screening of 393 mutants facilitates enzyme engineering of amidase activity in CalB.PeerJ · 2013Article
Corrections and comments
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Authors and funding
5 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We present a fast computational method to efficiently screen enzyme activity. In the presented method, the effect of mutations on the barrier height of an enzyme-catalysed reaction can be computed within 24 hours on roughly 10 processors. The methodology is based on the PM6 and MOZYME methods as implemented in MOPAC2009, and is tested on the first step of the amide hydrolysis reaction catalyzed by the Candida Antarctica lipase B (CalB) enzyme. The barrier heights are estimated using adiabatic mapping and shown to give barrier heights to within 3 kcal/mol of B3LYP/6-31G(d)//RHF/3-21G results for a small model system. Relatively strict convergence criteria (0.5 kcal/(molÅ)), long NDDO cutoff distances within the MOZYME method (15 Å) and single point evaluations using conventional PM6 are needed for reliable results. The generation of mutant structures and subsequent setup of the semiempirical calculations are automated so that the effect on barrier heights can be estimated for hundreds of mutants in a matter of weeks using high performance computing.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.