Speaker
Prof.
Alexandre Bonvin
(Utrecht University)
Description
Structure determination of complex molecular machines requires combination of an increasing number of experimental methods with highly specialized software geared towards each data source to properly handle the gathered data. Recently we introduced the two software packages PowerFit [1,2] and DisVis [3]. These combine high-resolution structures of atomic subunits with density maps from cryo-electron microscopy or distance restraints, typically acquired by chemical cross-linking coupled with mass spectrometry, respectively. To facilitate their use by a broad community, they have been implemented as web portals harvesting both local CPU resources and GPGPU-accelerated EGI HTC resources [4], making use of GPGPU-enabled Docker containers developed under the MoBrain competence center of EGI-Engage[5] and the INDIGO-Datacloud EU project [6]. The web portals offer user-friendly interfaces, while minimizing computational requirements, and provide a first interactive view of the results. The portals can be accessed freely after registration via http://milou.science.uu.nl/services/DISVIS and http://milou.science.uu.nl/services/POWERFIT.
1. 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).
2. 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).
3. G.C.P. van Zundert and A.M.J.J. Bonvin. DisVis: Quantifying and
visualizing accessible interaction space of distance-restrained
biomolecular complexes.
*Bioinformatics*. **31**, 3222-3224 (2015).
4. http://www.egi.eu
5. https://mobrain.egi.eu
6. http://www.indigo-datacloud.eu
Primary author
Prof.
Alexandre Bonvin
(Utrecht University)
Co-authors
Prof.
Antonio Rosato
(University of Florence, Italy)
Dr
Gydo van Zundert
(Utrecht University, the Netherlands)
Dr
Joerg Schaarschmidt
(Utrecht University, the Netherlands)
Dr
Marco Verlato
(INFN, Padova, Italy)
Dr
Mario David
(LIP, Lisbon, Portugal)
Dr
Mikael Trellet
(Utrecht University, the Netherlands)
Dr
Seynep Kurkcuoglu
(Utrecht University, the Netherlands)
