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Contact-based molecular dynamics of structured and disordered proteins in a coarse-grained model: fixed contacts, switchable contacts and those described by pseudo-improper-dihedral angles
- Source :
- Comput Phys Commun 284:108611 (2023)
- Publication Year :
- 2024
-
Abstract
- We present a coarse-grained C$\alpha$-based protein model that can be used to simulate structured, intrinsically disordered and partially disordered proteins. We use a Go-like potential for the structured parts and two different variants of a transferable potential for the disordered parts. The first variant uses dynamic structure-based (DSB) contacts that form and disappear quasi-adiabatically during the simulation. By using specific structural criteria we distinguish sidechain-sidechain, sidechain-backbone and backbone-backbone contacts. The second variant is a non-radial multi-body pseudo-improper-dihedral (PID) potential that does not include time-dependent terms but requires more computational resources. Our model can simulate in reasonable time thousands of residues on millisecond time scales.
- Subjects :
- Condensed Matter - Soft Condensed Matter
Subjects
Details
- Database :
- arXiv
- Journal :
- Comput Phys Commun 284:108611 (2023)
- Publication Type :
- Report
- Accession number :
- edsarx.2404.04431
- Document Type :
- Working Paper
- Full Text :
- https://doi.org/10.1016/j.cpc.2022.108611