School of Computational Sciences, Korea Institute for Advanced Study (KIAS), Seoul, Korea.
CPIS, the Graduate University for Advanced Studies (Sokendai), Hayama, Japan.
Sci Rep. 2019 Feb 7;9(1):1588. doi: 10.1038/s41598-018-36992-y.
We constructed a standardized protein folding kinetics database (PFDB) in which the logarithmic rate constants of all listed proteins are calculated at the standard temperature (25 °C). A temperature correction based on the Eyring-Kramers equation was introduced for proteins whose folding kinetics were originally measured at temperatures other than 25 °C. We verified the temperature correction by comparing the logarithmic rate constants predicted and experimentally observed at 25 °C for 14 different proteins, and the results demonstrated improvement of the quality of the database. PFDB consists of 141 (89 two-state and 52 non-two-state) single-domain globular proteins, which has the largest number among the currently available databases of protein folding kinetics. PFDB is thus intended to be used as a standard for developing and testing future predictive and theoretical studies of protein folding. PFDB can be accessed from the following link: http://lee.kias.re.kr/~bala/PFDB .
我们构建了一个标准化的蛋白质折叠动力学数据库（PFDB），其中列出的所有蛋白质的对数速率常数均在标准温度（25°C）下计算。对于折叠动力学最初在 25°C 以外的温度下测量的蛋白质，我们引入了基于 Eyring-Kramers 方程的温度校正。我们通过比较在 25°C 下预测的和实验观察到的 14 种不同蛋白质的对数速率常数来验证温度校正，结果表明数据库的质量得到了提高。PFDB 包含 141 种（89 种二态和 52 种非二态）单域球状蛋白质，是目前可用的蛋白质折叠动力学数据库中数量最多的。因此，PFDB 旨在用作开发和测试未来蛋白质折叠预测和理论研究的标准。PFDB 可以从以下链接访问：http://lee.kias.re.kr/~bala/PFDB。
