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Comparison of Charge Derivation Methods Applied to Amino Acid Parameterization.

ABSTRACT: When using non-natural amino acids in computational simulations of proteins, it is necessary to ensure appropriate parameterization of the new amino acids toward the creation of appropriate input files. In particular, the charges on the atoms may have to be derived de novo and ad hoc for the new species. As there are many variables in the charge derivation process, an investigation was devised to compare different approaches and determine their effect on simulations. This was done with the purpose to identify the methods which produced results compatible with the existing parameters. It was found in this study that all analyzed charge derivation methods reproduce with sufficient accuracy the literature values and can be used with confidence when parameterizing novel species.

SUBMITTER: Aronica PGA

PROVIDER: S-EPMC6641686 | biostudies-literature | 2018 Apr

REPOSITORIES: biostudies-literature

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Comparison of Charge Derivation Methods Applied to Amino Acid Parameterization.

Aronica Pietro G A PGA Fox Stephen J SJ Verma Chandra S CS

ACS omega 20180427 4

When using non-natural amino acids in computational simulations of proteins, it is necessary to ensure appropriate parameterization of the new amino acids toward the creation of appropriate input files. In particular, the charges on the atoms may have to be derived de novo and ad hoc for the new species. As there are many variables in the charge derivation process, an investigation was devised to compare different approaches and determine their effect on simulations. This was done with the purpo ...[more]

PMID: 31458687

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Dataset Information

Comparison of Charge Derivation Methods Applied to Amino Acid Parameterization.

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Comparison of Charge Derivation Methods Applied to Amino Acid Parameterization.

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