ArticleScientific reports2015
Multiple Simulated Annealing-Molecular Dynamics (MSA-MD) for Conformational Space Search of Peptide and Miniprotein.
Article in Scientific reports, 2015. 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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Who cites it
13 citing papers in PubMed.
- A Review of Global Optimization Methods for Molecular Structures: Algorithms, Applications and Perspectives.Journal of computational chemistry · 2025Review
- Molecular dynamics as a tool for unveiling protein-like folding behavior in urethane-based macromolecules: the effect of chain length on the secondary structure of oligourethanes.Polymer chemistry · 2025Article
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- Iterative deep learning design of human enhancers exploits condensed sequence grammar to achieve cell-type specificity.Cell systems · 2025Article
- How does the conformational landscape change on replacement in tetralin? A computational investigation with oxygen, sulfur, and selenium.Journal of molecular modeling · 2025Article
- Molecular Modelling in Bioactive Peptide Discovery and Characterisation.Biomolecules · 2025Review
- Developing novel indoles as antitubercular agents and simulated annealing-based analysis of their binding with MmpL3.Future medicinal chemistry · 2025Article
- The adsorption of drugs on nanoplastics has severe biological impact.Scientific reports · 2024Article
- Surrogate Based Genetic Algorithm Method for Efficient Identification of Low-Energy Peptide Structures.Journal of chemical theory and computation · 2023Article
- Structure and Dynamics of Human Chemokine CCL16-Implications for Biological Activity.Biomolecules · 2022Article
- Insight into the mechanism of molecular recognition between human Integrin-Linked Kinase and Cpd22 and its implication at atomic level.Journal of computer-aided molecular design · 2022Article
- Fast activation maximization for molecular sequence design.BMC bioinformatics · 2021Article
- Article
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4 authors.
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Abstract
Protein and peptide structure predictions are of paramount importance for understanding their functions, as well as the interactions with other molecules. However, the use of molecular simulation techniques to directly predict the peptide structure from the primary amino acid sequence is always hindered by the rough topology of the conformational space and the limited simulation time scale. We developed here a new strategy, named Multiple Simulated Annealing-Molecular Dynamics (MSA-MD) to identify the native states of a peptide and miniprotein. A cluster of near native structures could be obtained by using the MSA-MD method, which turned out to be significantly more efficient in reaching the native structure compared to continuous MD and conventional SA-MD simulation.
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