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• W2017562024 abstract "The multibody terms pertaining to the correlation between backbone−local and backbone−electrostatic interactions in the UNRES force field for energy-based protein-structure prediction, developed in our laboratory, were reparametrized on the basis of the results of high-level ab initio calculations on relevant model systems. MP2/6-31G(d,p) ab initio calculations were carried out to evaluate the energy surfaces of pairs consisting of N-acetyl-N‘-methylacetamide molecules (AcNHMe, which model a regular peptide group) and N-acetyl-N‘,N‘-dimethylacetamide molecules (AcNMe2, which model a peptide group preceding proline) at various intermolecular distances and orientations. For each pair, the calculated ab initio energy surface was subsequently fitted by a sum of Coulombic and Lennard-Jones components. Then, the restricted free-energy (RFE) surfaces of pairs of free peptide groups as well as the RFE factors corresponding to the coupling of backbone−local and backbone−electrostatic interactions in model tetrapeptides were calculated by numerical integration, with the use of the ab initio-fitted simplified energy functions and the ab initio energy maps of model terminally blocked amino acid residues calculated recently (Ołdziej, S.; Kozłowska, U.; Liwo, A.; Scheraga, H. A. J. Phys. Chem. B, in press, 2003). Next, analytical expressions based on Kubo's generalized cumulant theory from our previous work were fitted to the resulting RFE surfaces to parametrize the backbone−electrostatic and multibody terms in the UNRES force field. The computed coefficients of the cumulant-based expressions are different from those derived earlier, which had been based on the ECEPP/3 force field. To complete the force-field parametrization, the weights of the energy terms were determined, and the coefficients of the cumulant-based expressions were refined simultaneously by using our recently developed method of hierarchical optimization of a protein energy landscape using the protein 1IGD. The resulting force field was able to predict significant portions of the structures of proteins with α, β as well as both α and β structure correctly." @default.
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• W2017562024 date "2004-03-26" @default.
• W2017562024 modified "2023-10-18" @default.
• W2017562024 title "Parametrization of Backbone−Electrostatic and Multibody Contributions to the UNRES Force Field for Protein-Structure Prediction from Ab Initio Energy Surfaces of Model Systems" @default.
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• W2017562024 doi "https://doi.org/10.1021/jp030844f" @default.
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