Department of Chemistry, Federal University of Paraíba, João Pessoa - PB 58051-900, Brazil.
Department of Chemistry, Federal University of Pernambuco, Recife - PE 50670-901, Brazil.
J Chem Inf Model. 2020 Dec 28;60(12):5885-5890. doi: 10.1021/acs.jcim.0c00655. Epub 2020 Nov 13.
Plenty of enzymes with structural data do not have their mechanism of catalysis elucidated. Reactivity descriptors, theoretical quantities generated from resolved electronic structure, provide a way to predict and rationalize chemical processes of such systems. In this Application Note, we present PRIMoRDiA (MoRDiA acromolecular eactivity escriptors ccess), a software built to calculate the reactivity descriptors of large biosystems by employing an efficient and accurate treatment of the large output files produced by quantum chemistry packages. Here, we show the general implementation details and the software main features. Calculated descriptors were applied for a set of enzymatic systems in order to show their relevance for biological studies and the software potential for use in large scale. Also, we test PRIMoRDiA to aid in the interaction depiction between the SARS-CoV-2 main protease and a potential inhibitor.
许多具有结构数据的酶的催化机制尚未阐明。反应性描述符是从解析的电子结构中产生的理论量，为预测和合理化此类系统的化学过程提供了一种方法。在本应用说明中，我们介绍了 PRIMoRDiA（MoRDiA acromolecular eactivity escriptors ccess），这是一款软件，通过采用量子化学软件包生成的大型输出文件的高效准确处理，用于计算大型生物系统的反应性描述符。在这里，我们展示了一般的实现细节和软件的主要功能。计算得到的描述符应用于一组酶系统，以展示它们在生物学研究中的相关性以及该软件在大规模应用中的潜力。此外，我们还测试了 PRIMoRDiA 以帮助描绘 SARS-CoV-2 主要蛋白酶和潜在抑制剂之间的相互作用。
