Department of Computer Science, University of Texas at Austin, Austin, TX, USA.
Bioinformatics. 2011 Jan 1;27(1):55-62. doi: 10.1093/bioinformatics/btq627. Epub 2010 Nov 25.
We present the 'Dynamic Packing Grid' (DPG), a neighborhood data structure for maintaining and manipulating flexible molecules and assemblies, for efficient computation of binding affinities in drug design or in molecular dynamics calculations.
DPG can efficiently maintain the molecular surface using only linear space and supports quasi-constant time insertion, deletion and movement (i.e. updates) of atoms or groups of atoms. DPG also supports constant time neighborhood queries from arbitrary points. Our results for maintenance of molecular surface and polarization energy computations using DPG exhibit marked improvement in time and space requirements.
我们提出了“动态填充网格”（DPG），这是一种用于维护和操作柔性分子和组装体的邻域数据结构，可用于有效地计算药物设计或分子动力学计算中的结合亲和力。
DPG 仅使用线性空间即可有效地维护分子表面，并支持原子或原子组的准恒定时间插入、删除和移动（即更新）。DPG 还支持从任意点进行恒定时间邻域查询。我们使用 DPG 进行分子表面维护和极化能计算的结果在时间和空间需求方面都有显著的改进。
