| Autor: |
Sakuraba, Shun, Iwakiri, Junichi, Hamada, Michiaki, Kameda, Tomoshi, Tsuji, Genichiro, Kimura, Yasuaki, Abe, Hiroshi, Asai, Kiyoshi |
| Jazyk: |
angličtina |
| Rok vydání: |
2020 |
| Předmět: |
|
| Zdroj: |
Journal of the Computational and Theoretical Chemistry. 16(9):5925-5935 |
| ISSN: |
1549-9618 |
| Popis: |
Can current simulations quantitatively predict the stability of ribonucleic acids (RNAs)? In this research, we apply a free-energy perturbation simulation of RNAs containing inosine, a modified ribonucleic base, to the derivation of RNA nearest-neighbor parameters. A parameter set derived solely from 30 simulations was used to predict the free-energy difference of the RNA duplex with a mean unbiased error of 0.70 kcal/mol, which is a level of accuracy comparable to that obtained with parameters derived from 25 experiments. We further show that the error can be lowered to 0.60 kcal/mol by combining the simulation-derived free-energy differences with experimentally measured differences. This protocol can be used as a versatile method for deriving nearest-neighbor parameters of RNAs with various modified bases. |
| Databáze: |
OpenAIRE |
| Externí odkaz: |
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