Flexible Fitting of Atomic Models into Cryo-EM Density Maps Guided by Helix Correspondences

Hang Dou, Derek W. Burrows, Matthew L. Baker, Tao Ju

Research output: Contribution to journalArticlepeer-review

11 Scopus citations


Although electron cryo-microscopy (cryo-EM) has recently achieved resolutions of better than 3 Å, at which point molecular modeling can be done directly from the density map, analysis and annotation of a cryo-EM density map still primarily rely on fitting atomic or homology models to the density map. In this article, we present, to our knowledge, a new method for flexible fitting of known or modeled protein structures into cryo-EM density maps. Unlike existing methods that are guided by local density gradients, our method is guided by correspondences between the α-helices in the density map and model, and does not require an initial rigid-body fitting step. Compared with current methods on both simulated and experimental density maps, our method not only achieves greater accuracy for proteins with large deformations but also runs as fast or faster than many of the other flexible fitting routines.

Original languageEnglish
Pages (from-to)2479-2493
Number of pages15
JournalBiophysical Journal
Issue number12
StatePublished - Jun 20 2017


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