De Novo Atomic-Detail Structure Prediction for Proteins Guided by Medium Resolution Density Maps
Year: 2011
Type: article
Abstract: EM-Fold is a software algorithm that folds proteins into medium resolution density maps obtained by cryo-electron microscopy (cryo-EM) or X-ray crystallography [1].Models built by EM-Fold and refined by Rosetta generally have root mean square distance deviations (RMSDs) between 4 Å and 7 Å over the full length of the protein.These results demonstrate that it is possible to use computational methods to generate models for proteins that have the correct topology from a medium resolution density map and the primary sequence alone.In short, EM-Fold is capable to use the experimental data to deduct the topology of the protein by adding helix directionality and connectivity not visibly in the density map.While, side chain conformations in selected helix-helix interfaces were predicted correctly, the models were accurate at atomic detail only in limited regions.Often predicted helices lacked bends or differed in length from helices in the experimental structure.Furthermore, even though the true topology could be enriched by selection of low energy models, it could not be identified by virtue of score alone.On the other hand, the high-resolution experimental structures had considerably better scores than any of the models built using the EM-Fold protocol.
Source: Microscopy and Microanalysis
Authors: J Meiler, S Lindert, P Stewart
Institution: Vanderbilt University
Language: English
Subfield: Structural Biology
Domain: Life Sciences
Open Access status: bronze
OpenAlex ID: W2168928264