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University of Illinois at Urbana-Champaign, NIH Resource for Macromolecular Modeling and Bioinformatics Bechman Institute, NAMD Tutorial Windows Version.
http://www.ks.uiuc.edu/Training/Tutorials/

has been cited by the following article:

  • TITLE: Spontaneous Unfolding and Refolding of Plantaricin α-Helix in Molecular Dynamics Simulation

    AUTHORS: Shaomin Yan, Guang Wu

    KEYWORDS: Alpha-Helix, Antimicrobial Peptides, Protein Folding, Plantaricin A

    JOURNAL NAME: Computational Molecular Bioscience, Vol.9 No.1, March 28, 2019

    ABSTRACT: Antimicrobial peptides are promising therapeutic agents in view of increasing resistance to conventional antibiotics. Antimicrobial peptides usually fold in α-helical, β-sheet, and extended/random-coil structures. The α-helical antimicrobial peptides are often unstructured in aqueous solution but become structured on bacterial membrane. The α-helical structure allows the partitioning into bacterial membrane. Therefore it is important to understand the mechanism of unfolding and refolding of α-helical structure in antimicrobial peptides. It is not very easy to obverse and study the process of unfolding and refolding of α-helical antimicrobial peptides because of their rapidity. Therefore, molecular simulation provides a way to observe and explain this phenomenon. Plantaricin A is a 26 amino-acid antimicrobial pheromone peptide and can spontaneously unfold and refold under physiological condition. This study demonstrated the unfolding and refolding of plantaricin A by means of molecular simulation, and its mechanism was discussed with its implication to the Levinthal paradox.