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PFDB: A standardized protein folding database with temperature correction.

ABSTRACT: 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 .

SUBMITTER: Manavalan B

PROVIDER: S-EPMC6367381 | biostudies-literature | 2019 Feb

REPOSITORIES: biostudies-literature

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PFDB: A standardized protein folding database with temperature correction.

Manavalan Balachandran B Kuwajima Kunihiro K Lee Jooyoung J

Scientific reports 20190207 1

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 diffe ...[more]

PMID: 30733462

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