Schlick Tamar
Department of Chemistry and Courant Institute of Mathematical Sciences, New York University 251 Mercer Street, New York, NY 10012 USA.
F1000 Biol Rep. 2009 Jun 29;1:48. doi: 10.3410/B1-48.
The rugged energy landscape of biomolecules and associated large-scale conformational changes have triggered the development of many innovative enhanced sampling methods, either based or not based on molecular dynamics (MD) simulations. Surveyed here are methods in the latter class - including Monte Carlo methods, harmonic approximations, and coarse graining - many of which yield valuable conformational insights into biomolecular structure and flexibility, despite altered kinetics. MD-based methods are surveyed in an upcoming issue of F1000 Biology Reports.
生物分子崎岖的能量图景以及相关的大规模构象变化引发了许多创新的增强采样方法的发展，这些方法有的基于分子动力学（MD）模拟，有的则不基于此。本文考察的是后一类方法——包括蒙特卡罗方法、谐波近似法和粗粒化方法——尽管动力学有所改变，但其中许多方法都能为生物分子结构和灵活性提供有价值的构象见解。基于MD的方法将在即将出版的《F1000生物学报告》中进行考察。
