https://3demmethods.i2pc.es/index.php?action=history&feed=atom&title=2024Dahmani_MDFF 2026-05-24T21:14:21Z Revision history for this page on the wiki MediaWiki 1.44.2 https://3demmethods.i2pc.es/index.php?title=2024Dahmani_MDFF&diff=4668&oldid=prev 2024-08-12T06:24:45Z

<p>Created page with &quot;== Citation == Dahmani, Zakaria L. / Scott, Ana Ligia / Vénien-Bryan, Catherine / Perahia, David / Costa, Mauricio G. S. MDFF_NM: Improved Molecular Dynamics Flexible Fitting into Cryo-EM Density Maps with a Multireplica Normal Mode-Based Search. 2024. J. Chemical Information and Modeling, Vol. 64, No. 13, p. 5151-5160 == Abstract == Molecular Dynamics Flexible Fitting (MDFF) is a widely used tool to refine high-resolution structures into cryo-EM density maps. Despit...&quot;</p> <p><b>New page</b></p><div>== Citation ==<br /> <br /> Dahmani, Zakaria L. / Scott, Ana Ligia / Vénien-Bryan, Catherine / Perahia, David / Costa, Mauricio G. S. MDFF_NM: Improved Molecular Dynamics Flexible Fitting into Cryo-EM Density Maps with a Multireplica Normal Mode-Based Search. 2024. J. Chemical Information and Modeling, Vol. 64, No. 13, p. 5151-5160<br /> <br /> == Abstract ==<br /> <br /> Molecular Dynamics Flexible Fitting (MDFF) is a<br /> widely used tool to refine high-resolution structures into cryo-EM<br /> density maps. Despite many successful applications, MDFF is still<br /> limited by its high computational cost, overfitting, accuracy, and<br /> performance issues due to entrapment within wrong local minima.<br /> Modern ensemble-based MDFF tools have generated promising<br /> results in the past decade. In line with these studies, we present<br /> MDFF_NM, a stochastic hybrid flexible fitting algorithm<br /> combining Normal Mode Analysis (NMA) and simulation-based<br /> flexible fitting. Initial tests reveal that, besides accelerating the<br /> fitting process, MDFF_NM increases the diversity of fitting routes<br /> leading to the target, uncovering ensembles of conformations in<br /> closer agreement with experimental data. The potential integration<br /> of MDFF_NM with other existing methods and integrative modeling pipelines is also discussed.<br /> <br /> == Keywords ==<br /> <br /> == Links ==<br /> <br /> https://pubs.acs.org/doi/full/10.1021/acs.jcim.3c02007<br /> <br /> == Related software ==<br /> <br /> == Related methods ==<br /> <br /> == Comments ==</div>

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