These tools will no longer be maintained as of December 31, 2024. Archived website can be found here. PubMed4Hh GitHub repository can be found here. Contact NLM Customer Service if you have questions.


Pubmed for Handhelds

PUBMED FOR HANDHELDS

Search MEDLINE/PubMed

  • Title: Ligand docking simulations by generalized-ensemble algorithms.
    Author: Okamoto Y, Kokubo H, Tanaka T.
    Journal: Adv Protein Chem Struct Biol; 2013; 92():63-91. PubMed ID: 23954099.
    Abstract:
    In protein chemistry and structural biology, conventional simulations in physical statistical mechanical ensembles, such as the canonical ensemble with fixed temperature and isobaric-isothermal ensemble with fixed temperature and pressure, face a great difficulty. This is because there exist a huge number of local-minimum-energy states in the system and the conventional simulations tend to get trapped in these states, giving wrong results. Generalized-ensemble algorithms are based on artificial unphysical ensembles and overcome the above difficulty by performing random walks in potential energy, volume, and other physical quantities or their corresponding conjugate parameters such as temperature and pressure. The advantage of generalized-ensemble simulations lies in the fact that they not only avoid getting trapped in states of energy local minima but also allow the calculations of physical quantities as functions of temperature or other parameters from a single simulation run. In this chapter, we review the generalized-ensemble algorithms. Some of their specific examples such as replica-exchange molecular dynamics and replica-exchange umbrella sampling are described in detail. Examples of their applications to drug design are presented.
    [Abstract] [Full Text] [Related] [New Search]