Empirical force fields for biomolecular systems are usually derived from quantum chemistry calculations and validated against experimental data. We here show how it is possible to refine the full dihedral-angle potential of the Amber RNA force field by using solution NMR data as well as stability of known structural motifs. The procedure can be used to mix multiple systems and heterogeneous experimental information and crucially depends on a regularization term chosen with a cross-validation procedure. By fitting corrections to the dihedral angles on the order of less than 1 kJ/mol per angle, it is possible to increase the stability of difficult-to-fold RNA tetraloops by more than 1 order of magnitude.

Fitting Corrections to an RNA Force Field Using Experimental Data / Cesari, A.; Bottaro, S.; Lindorff-Larsen, K.; Banas, P.; Sponer, J.; Bussi, G.. - In: JOURNAL OF CHEMICAL THEORY AND COMPUTATION. - ISSN 1549-9618. - 15:6(2019), pp. 3425-3431. [10.1021/acs.jctc.9b00206]

Fitting Corrections to an RNA Force Field Using Experimental Data

Cesari A.;Bussi G.
2019

Abstract

Empirical force fields for biomolecular systems are usually derived from quantum chemistry calculations and validated against experimental data. We here show how it is possible to refine the full dihedral-angle potential of the Amber RNA force field by using solution NMR data as well as stability of known structural motifs. The procedure can be used to mix multiple systems and heterogeneous experimental information and crucially depends on a regularization term chosen with a cross-validation procedure. By fitting corrections to the dihedral angles on the order of less than 1 kJ/mol per angle, it is possible to increase the stability of difficult-to-fold RNA tetraloops by more than 1 order of magnitude.
15
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3425
3431
Cesari, A.; Bottaro, S.; Lindorff-Larsen, K.; Banas, P.; Sponer, J.; Bussi, G.
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Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/20.500.11767/95974
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