Schmidt, Michael ; Schroeder, Indra ; Bauer, Daniel ; Thiel, Gerhard ; Hamacher, Kay (2024)
Inferring functional units in ion channel pores via relative entropy.
In: European Biophysics Journal, 2021, 50 (1)
doi: 10.26083/tuprints-00023470
Artikel, Zweitveröffentlichung, Verlagsversion
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Kurzbeschreibung (Abstract)
Coarse-grained protein models approximate the first-principle physical potentials. Among those modeling approaches, the relative entropy framework yields promising and physically sound results, in which a mapping from the target protein structure and dynamics to a model is defined and subsequently adjusted by an entropy minimization of the model parameters. Minimization of the relative entropy is equivalent to maximization of the likelihood of reproduction of (configurational ensemble) observations by the model. In this study, we extend the relative entropy minimization procedure beyond parameter fitting by a second optimization level, which identifies the optimal mapping to a (dimension-reduced) topology. We consider anisotropic network models of a diverse set of ion channels and assess our findings by comparison to experimental results.
| Typ des Eintrags: | Artikel |
|---|---|
| Erschienen: | 2024 |
| Autor(en): | Schmidt, Michael ; Schroeder, Indra ; Bauer, Daniel ; Thiel, Gerhard ; Hamacher, Kay |
| Art des Eintrags: | Zweitveröffentlichung |
| Titel: | Inferring functional units in ion channel pores via relative entropy |
| Sprache: | Englisch |
| Publikationsjahr: | 3 September 2024 |
| Ort: | Darmstadt |
| Publikationsdatum der Erstveröffentlichung: | 2021 |
| Ort der Erstveröffentlichung: | Berlin ; Heidelberg ; New York |
| Verlag: | Springer International Publishing |
| Titel der Zeitschrift, Zeitung oder Schriftenreihe: | European Biophysics Journal |
| Jahrgang/Volume einer Zeitschrift: | 50 |
| (Heft-)Nummer: | 1 |
| DOI: | 10.26083/tuprints-00023470 |
| URL / URN: | https://tuprints.ulb.tu-darmstadt.de/23470 |
| Zugehörige Links: | |
| Herkunft: | Zweitveröffentlichung DeepGreen |
| Kurzbeschreibung (Abstract): | Coarse-grained protein models approximate the first-principle physical potentials. Among those modeling approaches, the relative entropy framework yields promising and physically sound results, in which a mapping from the target protein structure and dynamics to a model is defined and subsequently adjusted by an entropy minimization of the model parameters. Minimization of the relative entropy is equivalent to maximization of the likelihood of reproduction of (configurational ensemble) observations by the model. In this study, we extend the relative entropy minimization procedure beyond parameter fitting by a second optimization level, which identifies the optimal mapping to a (dimension-reduced) topology. We consider anisotropic network models of a diverse set of ion channels and assess our findings by comparison to experimental results. |
| Freie Schlagworte: | Potassium channel (pores), Mechanical coupling relative entropy, Anisotropic network model |
| Status: | Verlagsversion |
| URN: | urn:nbn:de:tuda-tuprints-234702 |
| Sachgruppe der Dewey Dezimalklassifikatin (DDC): | 500 Naturwissenschaften und Mathematik > 530 Physik 500 Naturwissenschaften und Mathematik > 570 Biowissenschaften, Biologie |
| Fachbereich(e)/-gebiet(e): | 10 Fachbereich Biologie 10 Fachbereich Biologie > Biologie der Algen und Protozoen 10 Fachbereich Biologie > Computational Biology and Simulation |
| Hinterlegungsdatum: | 03 Sep 2024 13:51 |
| Letzte Änderung: | 04 Sep 2024 05:33 |
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- Inferring functional units in ion channel pores via relative entropy. (deposited 03 Sep 2024 13:51) [Gegenwärtig angezeigt]
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