Simple, yet Efficient Conformational Sampling Methods for Reproducing/Predicting Biologically Rare Events of Proteins

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Abstract

<p>The biological functions of proteins are strongly related to their conformational transitions. To elucidate the essential dynamics, molecular dynamics (MD) simulation has become a powerful tool. However, it might still be difficult to address the relevant conformational transitions of proteins with the conventional MD (CMD) because the accessible time scales of CMD are far from those of the biological functions. Furthermore, the essential transitions are induced as stochastic processes in the long time scales, i.e. the conformational transitions are regarded as biologically relevant rare events. To reproduce/predict the rare events, we have proposed several enhanced conformational sampling methods. Our strategy to detect the rare events is based on cycles of the following conformational resampling consisting of two steps. (1) Selections of essential initial structures. (2) Restarting of short-time MD simulations from the initial structures. The cycles of conformational resampling increase the transition probabilities, promoting the rare events. In the present article, we review the enhanced conformational sampling methods developed by us, i.e. parallel cascade selection MD (PaCS-MD), fluctuation flooding method (FFM), taboo search algorithm (TBSA), outlier flooding method (OFLOOD), structural dissimilarity sampling (SDS), and self-avoiding conformational sampling (SACS). Furthermore, we introduce representative applications using our methods for several biological systems.</p>

Journal

  • Bulletin of the Chemical Society of Japan

    Bulletin of the Chemical Society of Japan 91(9), 1436-1450, 2018

    The Chemical Society of Japan

Codes

  • NII Article ID (NAID)
    130007484183
  • NII NACSIS-CAT ID (NCID)
    AA00580132
  • Text Lang
    ENG
  • ISSN
    0009-2673
  • NDL Article ID
    029212431
  • NDL Call No.
    Z53-B35
  • Data Source
    NDL  J-STAGE 
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