Schmidt, Michael ; Schroeder, Indra ; Bauer, Daniel ; Thiel, Gerhard ; Hamacher, Kay (2021)
Inferring functional units in ion channel pores via relative entropy.
In: European biophysics journal : EBJ
doi: 10.1007/s00249-020-01480-7
Artikel, Bibliographie
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: | 2021 |
| Autor(en): | Schmidt, Michael ; Schroeder, Indra ; Bauer, Daniel ; Thiel, Gerhard ; Hamacher, Kay |
| Art des Eintrags: | Bibliographie |
| Titel: | Inferring functional units in ion channel pores via relative entropy |
| Sprache: | Englisch |
| Publikationsjahr: | 1 Februar 2021 |
| Titel der Zeitschrift, Zeitung oder Schriftenreihe: | European biophysics journal : EBJ |
| DOI: | 10.1007/s00249-020-01480-7 |
| 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. |
| ID-Nummer: | pmid:33523249 |
| Fachbereich(e)/-gebiet(e): | 10 Fachbereich Biologie 10 Fachbereich Biologie > Plant Membrane Biophyscis (am 20.12.23 umbenannt in Biologie der Algen und Protozoen) 10 Fachbereich Biologie > Computational Biology and Simulation |
| Hinterlegungsdatum: | 09 Feb 2021 06:33 |
| Letzte Änderung: | 09 Feb 2021 06:33 |
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