About
HermiteFit is a new docking algorithm for rapid fitting atomic structures into cryo-EM density maps using 3D orthogonal Hermite functions. HermiteFit uses the cross-correlation or the Laplacian-filtered cross-correlation as the fitting criterion. HermiteFit exhaustively rotates the protein density in the Hermite space and then converts the expansion coefficients into the Fourier space for the subsequent fast FFT-based correlation computations.
Authors
Georgy Derevyanko and Sergei Grudinin,
Institute of Complex Systems (ICS-6), Forschungszentrum Jülich, Jülich, Germany.CEA, Institut de Biologie Structurale (IBS), F-38027 Grenoble, France.
CNRS, UMR 5075, IBS, Grenoble, France.
Université Joseph Fourier – Grenoble 1, IBS, Grenoble, France.
NANO-D, INRIA Grenoble — Rhone-Alpes, 38334 Saint Ismier Cedex, Montbonnot, France.
Laboratoire Jean Kuntzmann, B.P. 53, 38041 Grenoble Cedex 9, France.
E-mail: Sergei.Grudinin @ inria.fr
Download
Linux executables verified on Fedora, x86-64 architecture, multi-threaded and single-threaded versions. An updated version under BSD-compatible license without dependences and a GUI SAMSON module are in preparation.
Examples
GroEL example (input PDB files + cryo-EM map) GroEL data
A standard fitting example with automatically chosen parameters:
Another fitting example with automatically chosen parameters, the protein is rotated and translated to exclude the rotational bias:
A rapid coarse fitting:
Results can be visualised using PyMol:
To see all models in PyMol do:
To split the first 14 models in PyMol type (in the command prompt):
License
Currently the license is being changed to a BSD-compatible one.
Reference
G. Derevyanko, and S. Grudinin. “HermiteFit: Fast fitting atomic structures into cryo-EM density maps using 3D orthogonal Hermite functions“. Acta Crystallographica Section D70: 2069-84, 2014. DOI :10.1107/S1399004714011493.Download PDF.
