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Nucleic Acids Res. 2018 Jul 2;46(W1):W310-W314. doi: 10.1093/nar/gky424.

FragFit: a web-application for interactive modeling of protein segments into cryo-EM density maps.

Author information

1
Institute of Medical Physics and Biophysics, Charité University Medicine Berlin, Berlin 10117, Germany.
2
Institute of Medical Physics and Biophysics, Medical University Leipzig, Leipzig, Sachsen 04107, Germany.

Abstract

Cryo-electron microscopy (cryo-EM) is a standard method to determine the three-dimensional structures of molecular complexes. However, easy to use tools for modeling of protein segments into cryo-EM maps are sparse. Here, we present the FragFit web-application, a web server for interactive modeling of segments of up to 35 amino acids length into cryo-EM density maps. The fragments are provided by a regularly updated database containing at the moment about 1 billion entries extracted from PDB structures and can be readily integrated into a protein structure. Fragments are selected based on geometric criteria, sequence similarity and fit into a given cryo-EM density map. Web-based molecular visualization with the NGL Viewer allows interactive selection of fragments. The FragFit web-application, accessible at http://proteinformatics.de/FragFit, is free and open to all users, without any login requirements.

PMID:
29788317
PMCID:
PMC6030921
DOI:
10.1093/nar/gky424
[Indexed for MEDLINE]
Free PMC Article

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