ArticleRSC advances2019
Using molecular dynamics simulations to evaluate active designs of cephradine hydrolase by molecular mechanics/Poisson-Boltzmann surface area and molecular mechanics/generalized Born surface area methods.
Article in RSC advances, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
10 citing papers in PubMed.
- Solar-hybrid biocatalyst for methane hydroxylation to methanol.Nature communications · 2025Article
- 3D-QSAR, design, molecular docking and dynamics simulation studies of novel 6-hydroxybenzothiazole-2-carboxamides as potentially potent and selective monoamine oxidase B inhibitors.Frontiers in pharmacology · 2025Article
- Rational design of an anti-cancer peptide inhibiting CD147 / Cyp A interaction.Journal of molecular structure · 2023Article
- Identification of 13 Guanidinobenzoyl- or Aminidinobenzoyl-Containing Drugs to Potentially Inhibit TMPRSS2 for COVID-19 Treatment.International journal of molecular sciences · 2021Article
- Computational design of SARS-CoV-2 spike glycoproteins to increase immunogenicity by T cell epitope engineering.Computational and structural biotechnology journal · 2021Article
- Recent Developments in Free Energy Calculations for Drug Discovery.Frontiers in molecular biosciences · 2021Review
- Identification of promising molecules against MurD ligase from Acinetobacter baumannii: insights from comparative protein modelling, virtual screening, molecular dynamics simulations and MM/PBSA analysis.Journal of molecular modeling · 2020Article
- Design of novel ROCK inhibitors using fragment-based de novo drug design approach.Journal of molecular modeling · 2020Article
- Binding modes of cabazitaxel with the different human β-tubulin isotypes: DFT and MD studies.Journal of molecular modeling · 2020Article
- Molecular dynamics and binding energy analysis of Vatairea guianensis lectin: a new tool for cancer studies.Journal of molecular modeling · 2020Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
The poor predictive accuracy of current computational enzyme design methods has led to low success rates of producing highly active variants that target non-natural substrates. In this report, a quantitative assessment approach based on molecular dynamics (MD) simulations was developed to eliminate false-positive enzyme designs at the computational stage. Taking cephradine hydrolase as an example, the apparent Michaelis binding constant (
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What OpenQuestion holds
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.