ArticleInternational journal of molecular sciences2013
Combining coarse-grained protein models with replica-exchange all-atom molecular dynamics.
Article in International journal of molecular sciences, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 citing papers in PubMed.
- Challenges of conventional iterative all-atom and coarse-grained multiscale molecular dynamics.Scientific reports · 2026Article
- Automated Protein Secondary Structure Assignment from CBiomolecules · 2022Article
- Modeling of Disordered Protein Structures Using Monte Carlo Simulations and Knowledge-Based Statistical Force Fields.International journal of molecular sciences · 2019Review
- Role of Resultant Dipole Moment in Mechanical Dissociation of Biological Complexes.Molecules (Basel, Switzerland) · 2018Article
- Coarse-Grained Modeling of Peptide Docking Associated with Large Conformation Transitions of the Binding Protein: Troponin I Fragment-Troponin C System.Molecules (Basel, Switzerland) · 2015Article
- CABS-flex predictions of protein flexibility compared with NMR ensembles.Bioinformatics (Oxford, England) · 2014Article
- Structure prediction of the second extracellular loop in G-protein-coupled receptors.Biophysical journal · 2014Article
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Authors and funding
5 authors.
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Abstract
We describe a combination of all-atom simulations with CABS, a well-established coarse-grained protein modeling tool, into a single multiscale protocol. The simulation method has been tested on the C-terminal beta hairpin of protein G, a model system of protein folding. After reconstructing atomistic details, conformations derived from the CABS simulation were subjected to replica-exchange molecular dynamics simulations with OPLS-AA and AMBER99sb force fields in explicit solvent. Such a combination accelerates system convergence several times in comparison with all-atom simulations starting from the extended chain conformation, demonstrated by the analysis of melting curves, the number of native-like conformations as a function of time and secondary structure propagation. The results strongly suggest that the proposed multiscale method could be an efficient and accurate tool for high-resolution studies of protein folding dynamics in larger systems.
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