Kunzmann, Patrick ; Anter, Jacob Marcel ; Hamacher, Kay (2022)
Adding hydrogen atoms to molecular models via fragment superimposition.
In: Algorithms for molecular biology : AMB, 17 (1)
doi: 10.1186/s13015-022-00215-x
Artikel, Bibliographie
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Kurzbeschreibung (Abstract)
BACKGROUND
Most experimentally determined structures of biomolecules lack annotated hydrogen positions due to their low electron density. However, thorough structure analysis and simulations require knowledge about the positions of hydrogen atoms. Existing methods for their prediction are either limited to a certain range of molecules or only work effectively on small compounds.
RESULTS
We present a novel algorithm that compiles fragments of molecules with known hydrogen atom positions into a library. Using this library the method is able to predict hydrogen positions for molecules with similar moieties. We show that the method is able to accurately assign hydrogen atoms to most organic compounds including biomacromolecules, if a sufficiently large library is used.
CONCLUSIONS
We bundled the algorithm into the open-source Python package and command line program Hydride. Since usually no additional parametrization is necessary for the problem at hand, the software works out-of-box for a wide range of molecular systems usually within a few seconds of computation time. Hence, we believe that Hydride could be a valuable tool for structural biologists and biophysicists alike.
| Typ des Eintrags: | Artikel |
|---|---|
| Erschienen: | 2022 |
| Autor(en): | Kunzmann, Patrick ; Anter, Jacob Marcel ; Hamacher, Kay |
| Art des Eintrags: | Bibliographie |
| Titel: | Adding hydrogen atoms to molecular models via fragment superimposition |
| Sprache: | Englisch |
| Publikationsjahr: | 29 März 2022 |
| Titel der Zeitschrift, Zeitung oder Schriftenreihe: | Algorithms for molecular biology : AMB |
| Jahrgang/Volume einer Zeitschrift: | 17 |
| (Heft-)Nummer: | 1 |
| DOI: | 10.1186/s13015-022-00215-x |
| Zugehörige Links: | |
| Kurzbeschreibung (Abstract): | BACKGROUND Most experimentally determined structures of biomolecules lack annotated hydrogen positions due to their low electron density. However, thorough structure analysis and simulations require knowledge about the positions of hydrogen atoms. Existing methods for their prediction are either limited to a certain range of molecules or only work effectively on small compounds. RESULTS We present a novel algorithm that compiles fragments of molecules with known hydrogen atom positions into a library. Using this library the method is able to predict hydrogen positions for molecules with similar moieties. We show that the method is able to accurately assign hydrogen atoms to most organic compounds including biomacromolecules, if a sufficiently large library is used. CONCLUSIONS We bundled the algorithm into the open-source Python package and command line program Hydride. Since usually no additional parametrization is necessary for the problem at hand, the software works out-of-box for a wide range of molecular systems usually within a few seconds of computation time. Hence, we believe that Hydride could be a valuable tool for structural biologists and biophysicists alike. |
| ID-Nummer: | pmid:35351165 |
| Fachbereich(e)/-gebiet(e): | 10 Fachbereich Biologie 10 Fachbereich Biologie > Computational Biology and Simulation |
| Hinterlegungsdatum: | 05 Apr 2022 06:56 |
| Letzte Änderung: | 03 Jul 2024 02:57 |
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| Suche nach Titel in: | TUfind oder in Google |
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Adding hydrogen atoms to molecular models via fragment superimposition. (deposited 25 Mai 2022 12:27)
- Adding hydrogen atoms to molecular models via fragment superimposition. (deposited 05 Apr 2022 06:56) [Gegenwärtig angezeigt]
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