Artikel ; Online: Performance efficient macromolecular mechanics via sub-nanometer shape based coarse graining.
2023 Band 14, Heft 1, Seite(n) 2014
Abstract: Dimensionality reduction via coarse grain modeling is a valuable tool in biomolecular research. For large assemblies, ultra coarse models are often knowledge-based, relying on a priori information to parameterize models thus hindering general predictive ... ...
| Abstract | Dimensionality reduction via coarse grain modeling is a valuable tool in biomolecular research. For large assemblies, ultra coarse models are often knowledge-based, relying on a priori information to parameterize models thus hindering general predictive capability. Here, we present substantial advances to the shape based coarse graining (SBCG) method, which we refer to as SBCG2. SBCG2 utilizes a revitalized formulation of the topology representing network which makes high-granularity modeling possible, preserving atomistic details that maintain assembly characteristics. Further, we present a method of granularity selection based on charge density Fourier Shell Correlation and have additionally developed a refinement method to optimize, adjust and validate high-granularity models. We demonstrate our approach with the conical HIV-1 capsid and heteromultimeric cofilin-2 bound actin filaments. Our approach is available in the Visual Molecular Dynamics (VMD) software suite, and employs a CHARMM-compatible Hamiltonian that enables high-performance simulation in the GPU-resident NAMD3 molecular dynamics engine. |
|---|---|
| Sprache | Englisch |
| Erscheinungsdatum | 2023-04-10 |
| Erscheinungsland | England |
| Dokumenttyp | Journal Article |
| ZDB-ID | 2553671-0 |
| ISSN | 2041-1723 ; 2041-1723 |
| ISSN (online) | 2041-1723 |
| ISSN | 2041-1723 |
| DOI | 10.1038/s41467-023-37801-5 |
| Datenquelle | MEDical Literature Analysis and Retrieval System OnLINE |
Zusatzmaterialien
Kategorien
Über subito bestellen
Dieser Service ist kostenpflichtig (siehe Lieferbedingungen von subito). Bestellungen, die einen Artikel nebst Supplementary Material umfassen, werden grundsätzlich wie mehrfache Bestellungen bearbeitet. Gebühren fallen in diesen Fällen für jede einzelne Bestellung an.