Caron Giulia, Nurisso Alessandra, Ermondi Giuseppe
CASMedChem Laboratory, Dipartimento di Scienza e Tecnologia del Farmaco, Università di Torino, Via P. Giuria 9, I-10125 Torino, Italy.
ChemMedChem. 2009 Jan;4(1):29-36. doi: 10.1002/cmdc.200800259.
Many computational tools routinely used in chemistry could successfully be applied to the biosciences since protein-protein and protein-ligand interactions are governed by the laws of chemistry. This paper shows that it is possible to extend the use of existing computational tools from their traditional application field (e.g. chemistry) to culturally-related research areas by the implementation of simple but well-designed utilities. In particular, a computational strategy obtained by combining GRID (the program originally designed by Peter Goodford, and now distributed by Molecular Discovery Ltd.) and BIOCUBE4mf (an application freely available at www.casmedchem.unito.it) was used to a) characterize the surface properties of the cavity of the Bacillus anthracis protective antigen heptameric prepore; b) suggest how to design mutagenesis experiments; c) quantitatively show the selectivity of the KvAP channel for K(+) over Na(+) ions and d) rationalize the pharmacokinetic behavior of 1,4-DHP third-generation drugs.
由于蛋白质-蛋白质和蛋白质-配体相互作用受化学规律支配，化学领域常用的许多计算工具可成功应用于生物科学。本文表明，通过实施简单但设计良好的实用程序，有可能将现有计算工具的使用从其传统应用领域（如化学）扩展到与文化相关的研究领域。特别是，通过结合GRID（最初由彼得·古德福德设计，现由分子发现有限公司发行的程序）和BIOCUBE4mf（可在www.casmedchem.unito.it免费获取的应用程序）获得的一种计算策略被用于：a）表征炭疽芽孢杆菌保护性抗原七聚体前孔腔的表面性质；b）提出如何设计诱变实验；c）定量显示KvAP通道对K(+) 比对Na(+) 离子的选择性；d）阐明1,4 -二氢吡啶第三代药物的药代动力学行为。
