Comparison of charge derivation methods applied to amino acid parameterization
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 spe...
| Main Authors: | , , |
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| Other Authors: | |
| Format: | Journal Article |
| Language: | English |
| Published: |
2019
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| Online Access: | https://hdl.handle.net/10356/106848 http://hdl.handle.net/10220/49658 |
| _version_ | 1811688206418051072 |
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| author | Aronica, Pietro G. A. Fox, Stephen J. Verma, Chandra Shekhar |
| author2 | School of Biological Sciences |
| author_facet | School of Biological Sciences Aronica, Pietro G. A. Fox, Stephen J. Verma, Chandra Shekhar |
| author_sort | Aronica, Pietro G. A. |
| collection | NTU |
| description | 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. |
| first_indexed | 2024-10-01T05:28:31Z |
| format | Journal Article |
| id | ntu-10356/106848 |
| institution | Nanyang Technological University |
| language | English |
| last_indexed | 2024-10-01T05:28:31Z |
| publishDate | 2019 |
| record_format | dspace |
| spelling | ntu-10356/1068482023-02-28T17:06:43Z Comparison of charge derivation methods applied to amino acid parameterization Aronica, Pietro G. A. Fox, Stephen J. Verma, Chandra Shekhar School of Biological Sciences Parameterization Charge Derivation Science::Biological sciences 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. ASTAR (Agency for Sci., Tech. and Research, S’pore) Published version 2019-08-15T07:01:05Z 2019-12-06T22:19:39Z 2019-08-15T07:01:05Z 2019-12-06T22:19:39Z 2018 Journal Article Aronica, P. G. A., Fox, S. J., & Verma, C. S. (2018). Comparison of charge derivation methods applied to amino acid parameterization. ACS Omega, 3(4), 4664-4673. doi:10.1021/acsomega.8b00438 https://hdl.handle.net/10356/106848 http://hdl.handle.net/10220/49658 10.1021/acsomega.8b00438 en ACS Omega © 2018 American Chemical Society. This is an open access article published under an ACS AuthorChoice License, which permits copying and redistribution of the article or any adaptations for non-commercial purposes. 10 p. application/pdf |
| spellingShingle | Parameterization Charge Derivation Science::Biological sciences Aronica, Pietro G. A. Fox, Stephen J. Verma, Chandra Shekhar Comparison of charge derivation methods applied to amino acid parameterization |
| title | Comparison of charge derivation methods applied to amino acid parameterization |
| title_full | Comparison of charge derivation methods applied to amino acid parameterization |
| title_fullStr | Comparison of charge derivation methods applied to amino acid parameterization |
| title_full_unstemmed | Comparison of charge derivation methods applied to amino acid parameterization |
| title_short | Comparison of charge derivation methods applied to amino acid parameterization |
| title_sort | comparison of charge derivation methods applied to amino acid parameterization |
| topic | Parameterization Charge Derivation Science::Biological sciences |
| url | https://hdl.handle.net/10356/106848 http://hdl.handle.net/10220/49658 |
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