Ancona Nicolas, Bastola Ananta, Alexov Emil
Department of Biological Sciences, College of Science, Clemson University, 105 Sikes Hall, Address, Clemson, SC 29634, United States of America.
School of Computing, College of Engineering, Computing and Applied Sciences, Clemson University, 105 Sikes Hall, SC 29634, United States of America.
J Comput Biophys Chem. 2023 Aug;22(5):515-524. doi: 10.1142/s2737416523500230. Epub 2023 Apr 25.
Almost all biological reactions are pH dependent and understanding the origin of pH dependence requires knowledge of the pKa's of ionizable groups. Here we report a new edition of PKAD, the PKAD-2, which is a database of experimentally measured pKa's of proteins, both wild type and mutant proteins. The new additions include 117 wild type and 54 mutant pKa values, resulting in total 1742 experimentally measured pKa's. The new edition of PKAD-2 includes 8 new wild type and 12 new mutant proteins, resulting in total of 220 proteins. This new edition incorporates a visual 3D image of the highlighted residue of interest within the corresponding protein or protein complex. Hydrogen bonds were identified, counted, and implemented as a search feature. Other new search features include the number of neighboring residues <4A from the heaviest atom of the side chain of a given amino acid. Here, we present PKAD-2 with the intention to continuously incorporate novel features and current data with the goal to be used as benchmark for computational methods.
几乎所有的生物反应都依赖于pH值，而要理解pH值依赖性的起源需要了解可电离基团的pKa值。在此，我们报告了PKAD的新版本PKAD - 2，它是一个关于野生型和突变型蛋白质实验测量pKa值的数据库。新增内容包括117个野生型和54个突变型pKa值，使实验测量的pKa值总数达到1742个。PKAD - 2的新版本包括8种新的野生型和12种新的突变型蛋白质，总数达到220种蛋白质。这个新版本包含了相应蛋白质或蛋白质复合物中感兴趣的突出残基的可视化3D图像。识别、计数氢键并将其作为搜索功能。其他新的搜索功能包括与给定氨基酸侧链重原子距离<4A的相邻残基数量。在此，我们展示PKAD - 2，目的是不断纳入新特性和当前数据，目标是用作计算方法的基准。
