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- W2949127989 endingPage "e00161" @default.
- W2949127989 startingPage "e00161" @default.
- W2949127989 abstract "Predicting crystallographic B-factors of a protein from a conventional molecular dynamics simulation is challenging, in part because the B-factors calculated through sampling the atomic positional fluctuations in a picosecond molecular dynamics simulation are unreliable, and the sampling of a longer simulation yields overly large root mean square deviations between calculated and experimental B-factors. This article reports improved B-factor prediction achieved by sampling the atomic positional fluctuations in multiple picosecond molecular dynamics simulations that use uniformly increased atomic masses by 100-fold to increase time resolution. Using the third immunoglobulin-binding domain of protein G, bovine pancreatic trypsin inhibitor, ubiquitin, and lysozyme as model systems, the B-factor root mean square deviations (mean ± standard error) of these proteins were 3.1 ± 0.2–9 ± 1 Å2 for Cα and 7.3 ± 0.9–9.6 ± 0.2 Å2 for Cγ, when the sampling was done for each of these proteins over 20 distinct, independent, and 50-picosecond high-mass molecular dynamics simulations with AMBER forcefield FF12MC or FF14SB. These results suggest that sampling the atomic positional fluctuations in multiple picosecond high-mass molecular dynamics simulations may be conducive to a priori prediction of crystallographic B-factors of a folded globular protein." @default.
- W2949127989 created "2019-06-27" @default.
- W2949127989 creator A5062493231 @default.
- W2949127989 date "2016-09-01" @default.
- W2949127989 modified "2023-10-16" @default.
- W2949127989 title "Use of multiple picosecond high-mass molecular dynamics simulations to predict crystallographic B-factors of folded globular proteins" @default.
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- W2949127989 doi "https://doi.org/10.1016/j.heliyon.2016.e00161" @default.
- W2949127989 hasPubMedCentralId "https://www.ncbi.nlm.nih.gov/pmc/articles/5035356" @default.
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- W2949127989 hasPublicationYear "2016" @default.
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