The capability of current force fields to reproduce RNA structural dynamics is limited. Several methods have been developed to take advantage of experimental data in order to enforce agreement with experiments. Here, we extend an existing framework which allows arbitrarily chosen force-field correction terms to be fitted by quantification of the discrepancy between observables back-calculated from simulation and corresponding experiments. We apply a robust regularization protocol to avoid overfitting and additionally introduce and compare a number of different regularization strategies, namely, L1, L2, Kish size, relative Kish size, and relative entropy penalties. The training set includes a GACC tetramer as well as more challenging systems, namely, gcGAGAgc and gcUUCGgc RNA tetraloops. Specific intramolecular hydrogen bonds in the AMBER RNA force field are corrected with automatically determined parameters that we call gHBfixopt. A validation involving a separate simulation of a system present in the training set (gcUUCGgc) and new systems not seen during training (CAAU and UUUU tetramers) displays improvements regarding the native population of the tetraloop as well as good agreement with NMR experiments for tetramers when using the new parameters. Then, we simulate folded RNAs (a kink-turn and L1 stalk rRNA) including hydrogen bond types not sufficiently present in the training set. This allows a final modification of the parameter set which is named gHBfix21 and is suggested to be applicable to a wider range of RNA systems.

Automatic Learning of Hydrogen-Bond Fixes in the AMBER RNA Force Field / Froehlking, Thorben; Mlýnský, Vojtěch; Janeček, Michal; Kührová, Petra; Krepl, Miroslav; Banáš, Pavel; Šponer, Jiří; Bussi, Giovanni. - In: JOURNAL OF CHEMICAL THEORY AND COMPUTATION. - ISSN 1549-9626. - 18:7(2022), pp. 4490-4502. [10.1021/acs.jctc.2c00200]

Automatic Learning of Hydrogen-Bond Fixes in the AMBER RNA Force Field

Froehlking, Thorben;Bussi, Giovanni
2022

Abstract

The capability of current force fields to reproduce RNA structural dynamics is limited. Several methods have been developed to take advantage of experimental data in order to enforce agreement with experiments. Here, we extend an existing framework which allows arbitrarily chosen force-field correction terms to be fitted by quantification of the discrepancy between observables back-calculated from simulation and corresponding experiments. We apply a robust regularization protocol to avoid overfitting and additionally introduce and compare a number of different regularization strategies, namely, L1, L2, Kish size, relative Kish size, and relative entropy penalties. The training set includes a GACC tetramer as well as more challenging systems, namely, gcGAGAgc and gcUUCGgc RNA tetraloops. Specific intramolecular hydrogen bonds in the AMBER RNA force field are corrected with automatically determined parameters that we call gHBfixopt. A validation involving a separate simulation of a system present in the training set (gcUUCGgc) and new systems not seen during training (CAAU and UUUU tetramers) displays improvements regarding the native population of the tetraloop as well as good agreement with NMR experiments for tetramers when using the new parameters. Then, we simulate folded RNAs (a kink-turn and L1 stalk rRNA) including hydrogen bond types not sufficiently present in the training set. This allows a final modification of the parameter set which is named gHBfix21 and is suggested to be applicable to a wider range of RNA systems.
18
7
4490
4502
10.1021/acs.jctc.2c00200
https://arxiv.org/abs/2201.04078
Froehlking, Thorben; Mlýnský, Vojtěch; Janeček, Michal; Kührová, Petra; Krepl, Miroslav; Banáš, Pavel; Šponer, Jiří; Bussi, Giovanni
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Utilizza questo identificativo per citare o creare un link a questo documento: http://hdl.handle.net/20.500.11767/129230
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