https://3demmethods.i2pc.es/index.php?action=history&feed=atom&title=2023Park_CSA 2026-05-24T21:07:01Z Revision history for this page on the wiki MediaWiki 1.44.2 https://3demmethods.i2pc.es/index.php?title=2023Park_CSA&diff=4493&oldid=prev 2024-01-03T07:54:15Z

<p>Created page with &quot;== Citation == Park, Jimin / Joung, InSuk / Joo, Keehyoung / Lee, Jooyoung Application of conformational space annealing to the protein structure modeling using cryo-EM maps...&quot;</p> <p><b>New page</b></p><div>== Citation ==<br /> <br /> Park, Jimin / Joung, InSuk / Joo, Keehyoung / Lee, Jooyoung <br /> Application of conformational space annealing to the protein structure modeling using cryo-EM maps <br /> 2023. J. Computational Chemistry, Vol. 44, No. 30, p. 2332-2346 <br /> <br /> == Abstract ==<br /> <br /> Conformational space annealing (CSA), a global optimization method, has been <br /> applied to various protein structure modeling tasks. In this paper, we applied CSA <br /> to the cryo-EM structure modeling task by combining the python subroutine of <br /> CSA (PyCSA) and the fast relax (FastRelax) protocol of PyRosetta. Refinement of <br /> initial structures generated from two methods, rigid fitting of predicted structures <br /> to the Cryo-EM map and de novo protein modeling by tracing the Cryo-EM map, <br /> was performed by CSA. In the refinement of the rigid-fitted structures, the final <br /> models showed that CSA can generate reliable atomic structures of proteins, even <br /> when large movements of protein domains were required. In the de novo modeling <br /> case, although the overall structural qualities of the final models were rather <br /> dependent on the initial models, the final models generated by CSA showed <br /> improved MolProbity scores and cross-correlation coefficients to the maps. These <br /> results suggest that CSA can accomplish flexible fitting and refinement together <br /> by sampling diverse conformations effectively and thus can be utilized for cryo- <br /> EM structure modeling.<br /> <br /> == Keywords ==<br /> <br /> == Links ==<br /> <br /> https://onlinelibrary.wiley.com/doi/full/10.1002/jcc.27200<br /> <br /> == Related software ==<br /> <br /> == Related methods ==<br /> <br /> == Comments ==</div>

WikiSysop