PowerFit web portal 2.0


#1

In connection with the publication of the PowerFit and DisVis webserver in the Journal of Molecular Biology (“The DisVis and PowerFit web servers: Explorative and Integrative Modeling of Biomolecular Complexes” in press) we have all updated the PowerFit web server. The update includes:

  • Improved post-processing and result presentation (colour highlighting, case-dependant messages, etc.)
  • Sigma difference to the best fit on the result page as measure of the quality of the fir
  • tag feature to easily identify your run
  • provision of a json file for each run capturing the key parameters
  • Extended information on the help/manual page
  • More detailed examples
  • mmCIF support

See for yourself at http://milou.science.uu.nl/services/PowerFit/

The PowerFit support team


#2

We are glad to announce the release of our POWERFIT web server.

PowerFit automatically fits high-resolution atomic structures in cryo-EM densities. To this end it performs a full-exhaustive 6-dimensional cross-correlation search between the atomic structure and the density. It takes as input an atomic structure in PDB-format and a cryo-EM density with its resolution; and outputs positions and rotations of the atomic structure corresponding to high correlation values. PowerFit uses the local cross-correlation function as its base score, enhanced by a Laplace pre-filter and/or core-weighting to minimize overlapping densities from neighboring subunits.

Read more about PowerFit in the following publications:

  • G.C.P. van Zundert and A.M.J.J. Bonvin. Fast and sensitive rigid-body fitting into cryo-EM density maps with PowerFit. AIMS Biophysics. 2, 73-87 (2015).

  • G.C.P van Zundert and A.M.J.J. Bonvin. Defining the limits and reliability of rigid-body fitting in cryo-EM maps using multi-scale image pyramids. J. Struct. Biol., 195, 252-258 (2016).

POWERFIT is also freely available for local installation through our GitHub repository: https://github.com/haddocking/powerfit. A Docker container is available from the INDIGO-Datacloud repository: https://github.com/indigo-dc/docker-powerfit.

The POWERFIT web server is powered by EGI (www.egi.eu) GPGPU HTC resources.

Its development was made possible with support from various grants:

Netherlands Organization for Scientific Research (NWO), ECHO grant no.711.011.009
European H2020 e-Infrastructure grant, EGI-Engage, grant no. 654142
European H2020 e-Infrastructure grant, INDIGO-DataCloud, grant no. 653549
European H2020 e-Infrastructure grant, West-Life VRE, grant no. 675858
European H2020 e-Infrastructure grant, BioExcel, grant no. 675728