3MTK — Moscow Molecular Modeling Toolkit

Moscow Molecular Modeling Toolkit (3MTK) is a software for computer-aided reconstruction of the atomistic models of bio-macromolecules and their complexes on the base of low-resolution electron density maps.

The main features of 3MTK are:

  • Segmentation of electron density maps to distinguish large molecular structures (domains)
  • Database of the protein domains extracted from Protein Data Bank
  • Calculation of form characteristics of the domains based on the moments
  • Fitting known domains into the electron density map
  • Homology search using BLAST
  • Molecular docking using HEX
  • Calculation of the scoring function to determine quality of the reconstruction
  • Volume rendering of electron density maps based on the Voreen framework
  • Stereoscopic 3D-rendering based on NVIDIA Quadro and NVIDIA 3D Vision
  • 6-coordinate spacial manipulation of electron density maps and atomistic structures using 3DConnexion SpaceNavigator
  • Distribution under the GPL license
  • Cross-platform compilation

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