Kunzmann, Patrick ; Anter, Jacob Marcel ; Hamacher, Kay (2022)
Adding hydrogen atoms to molecular models via fragment superimposition.
In: Algorithms for Molecular Biology, 2022, 17
doi: 10.26083/tuprints-00021427
Artikel, Zweitveröffentlichung, Verlagsversion
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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: | Zweitveröffentlichung |
| Titel: | Adding hydrogen atoms to molecular models via fragment superimposition |
| Sprache: | Englisch |
| Publikationsjahr: | 2022 |
| Publikationsdatum der Erstveröffentlichung: | 2022 |
| Verlag: | BioMed Central |
| Titel der Zeitschrift, Zeitung oder Schriftenreihe: | Algorithms for Molecular Biology |
| Jahrgang/Volume einer Zeitschrift: | 17 |
| Kollation: | 8 Seiten |
| DOI: | 10.26083/tuprints-00021427 |
| URL / URN: | https://tuprints.ulb.tu-darmstadt.de/21427 |
| Zugehörige Links: | |
| Herkunft: | Zweitveröffentlichung aus gefördertem Golden Open Access |
| 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. |
| Status: | Verlagsversion |
| URN: | urn:nbn:de:tuda-tuprints-214279 |
| Sachgruppe der Dewey Dezimalklassifikatin (DDC): | 500 Naturwissenschaften und Mathematik > 570 Biowissenschaften, Biologie |
| Fachbereich(e)/-gebiet(e): | 10 Fachbereich Biologie 10 Fachbereich Biologie > Computational Biology and Simulation |
| Hinterlegungsdatum: | 25 Mai 2022 12:27 |
| Letzte Änderung: | 27 Mai 2022 06:34 |
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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) [Gegenwärtig angezeigt]
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