Quantification of protein surfaces, volumes and atom-atom contacts using a constrained Voronoi procedure
Quantification of protein surfaces, volumes and atom-atom contacts using a constrained Voronoi procedure
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DOI：
10.1093/bioinformatics/18.10.1365
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发表时间：
2002-10-01
期刊：
影响因子：
5.8
通讯作者：
Edelman, M
中科院分区：
文献类型：
--
作者：
McConkey, BJ;Sobolev, V;Edelman, M
动机：蛋白质和配体的几何表示，包括原子体积、原子-原子接触和溶剂可及表面，可用于表征蛋白质、配体和溶剂之间及其内部的相互作用。Voronoi算法允许通过将结构划分为与组成原子一一对应的单元来量化这些性质。由于没有普遍接受的原子-原子接触的度量，原子间接触的连续分析表示将是有用的。改进的几何算法也将有助于提高迭代建模算法的速度和精度。结果：我们提出了基于Voronoi过程的计算方法，为大分子中溶剂可及表面、体积和原子接触提供了快速和准确的解。此外，我们定义了一种与溶剂可及表面的计算一致的原子-原子接触的度量，允许将溶剂可及性和原子间接触集成到一个连续的度量中。该算法的速度和精度与现有的计算溶剂可及表面和体积的方法进行了比较。与数值和近似解析表面计算算法相比，该算法具有更少的执行时间和更高的精度，而与现有的计算原子表面和体积的Voronoi方法相比，执行时间更短，精度更接近。
Motivation: Geometric representations of proteins and ligands, including atom volumes, atom-atom contacts and solvent accessible surfaces, can be used to characterize interactions between and within proteins, ligands and solvent. Voronoi algorithms permit quantification of these properties by dividing structures into cells with a one-to-one correspondence with constituent atoms. As there is no generally accepted measure of atom-atom contacts, a continuous analytical representation of inter-atomic contacts will be useful. Improved geometric algorithms will also be helpful in increasing the speed and accuracy of iterative modeling algorithms.Results: We present computational methods based on the Voronoi procedure that provide rapid and exact solutions to solvent accessible surfaces, volumes, and atom contacts within macromolecules. Furthermore, we define a measure of atom-atom contact that is consistent with the calculation of solvent accessible surfaces, allowing the integration of solvent accessibility and inter-atomic contacts into a continuous measure. The speed and accuracy of the algorithm is compared to existing methods for calculating solvent accessible surfaces and volumes. The presented algorithm has a reduced execution time and greater accuracy compared to numerical and approximate analytical surface calculation algorithms, and a reduced execution time and similar accuracy to existing Voronoi procedures for calculating atomic surfaces and volumes.