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

2018; Oxford University Press; Volume: 46; Issue: W1 Linguagem: Inglês

10.1093/nar/gky424

1362-4962

Johanna K. S. Tiemann, Alexander Rose, Jochen Ismer, Mitra D Darvish, Tarek Hilal, C.M.T. Spahn, Peter W. Hildebrand,

Genomics and Phylogenetic Studies

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.