AI Article Synopsis
- A new protocol using molecular dynamics (MD) simulations is introduced for refining structures predicted from templates.
- The method includes applying restraints, averaging results from selected models, and comparing initial and refined structures to gauge success.
- The findings indicate that short MD sampling, coupled with ensemble averaging, leads to reliable but moderate improvements in structure refinement for many CASP targets studied.
Article Abstract
A molecular dynamics (MD) simulation based protocol for structure refinement of template-based model predictions is described. The protocol involves the application of restraints, ensemble averaging of selected subsets, interpolation between initial and refined structures, and assessment of refinement success. It is found that sub-microsecond MD-based sampling when combined with ensemble averaging can produce moderate but consistent refinement for most systems in the CASP targets considered here.
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Source |
|---|---|
| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3603382 | PMC |
| http://dx.doi.org/10.1021/ct300962x | DOI Listing |
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