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

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


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, is free and open to all users, without any login requirements.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acids / chemistry
  • Amino Acids / genetics
  • Cryoelectron Microscopy
  • Internet*
  • Models, Molecular
  • Protein Conformation
  • Proteins / chemistry*
  • Proteins / genetics
  • Software*


  • Amino Acids
  • Proteins