ArticleJournal of computational chemistry2016
Adding energy minimization strategy to peptide-design algorithm enables better search for RNA-binding peptides: Redesigned λ N peptide binds boxB RNA.
Article in Journal of computational chemistry, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed, 19 citations in OpenAlex.
- Integrating biophysical modeling, quantum computing, and AI to discover plastic-binding peptides that combat microplastic pollution.PNAS nexus · 2025Article
- In Silico Design and Analysis of Plastic-Binding Peptides.The journal of physical chemistry. B · 2023Article
- Design of 8-mer peptides that block Clostridioides difficile toxin A in intestinal cells.Communications biology · 2023Article
- Design of 8-mer Peptides that BlockbioRxiv : the preprint server for biology · 2023Article
- Sequence patterns and signatures: Computational and experimental discovery of amyloid-forming peptides.PNAS nexus · 2022Article
- Article
- De novo design of peptides that coassemble into β sheet-based nanofibrils.Science advances · 2021Article
- Extended Concerted Rotation Technique Enhances the Sampling Efficiency of the Computational Peptide-Design Algorithm.Journal of chemical theory and computation · 2017Article
- Simulation study of the ability of a computationally-designed peptide to recognize target tRNAProtein science : a publication of the Protein Society · 2016Article
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4 authors at 2 institutions in 1 country.
Funding
Abstract
Our previously developed peptide-design algorithm was improved by adding an energy minimization strategy which allows the amino acid sidechains to move in a broad configuration space during sequence evolution. In this work, the new algorithm was used to generate a library of 21-mer peptides which could substitute for λ N peptide in binding to boxB RNA. Six potential peptides were obtained from the algorithm, all of which exhibited good binding capability with boxB RNA. Atomistic molecular dynamics simulations were then conducted to examine the ability of the λ N peptide and three best evolved peptides, viz. Pept01, Pept26, and Pept28, to bind to boxB RNA. Simulation results demonstrated that our evolved peptides are better at binding to boxB RNA than the λ N peptide. Sequence searches using the old (without energy minimization strategy) and new (with energy minimization strategy) algorithms confirm that the new algorithm is more effective at finding good RNA-binding peptides than the old algorithm. © 2016 Wiley Periodicals, Inc.
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