TY - JOUR
T1 - The DisVis and PowerFit Web Servers
T2 - Explorative and Integrative Modeling of Biomolecular Complexes
AU - van Zundert, G. C P
AU - Trellet, M.
AU - Schaarschmidt, J.
AU - Kurkcuoglu Soner, Zeynep
AU - David, M.
AU - Verlato, M.
AU - Rosato, A.
AU - Bonvin, A. M J J
PY - 2017/2/3
Y1 - 2017/2/3
N2 - Structure determination of complex molecular machines requires a combination of an increasing number of experimental methods with highly specialized software geared toward each data source to properly handle the gathered data. Recently, we introduced the two software packages PowerFit and DisVis. 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. Here, we report on recent advances in both GPGPU-accelerated software packages: PowerFit is a tool for rigid body fitting of atomic structures in cryo-electron density maps and has been updated to also output reliability indicators for the success of fitting, through the use of the Fisher z-transformation and associated confidence intervals; DisVis aims at quantifying the information content of distance restraints and identifying false-positive restraints. We extended its analysis capabilities to include an analysis of putative interface residues and to output an average shape representing the putative location of the ligand. To facilitate their use by a broad community, they have been implemented as web portals harvesting both local CPU resources and GPGPU-accelerated EGI grid resources. They 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.
AB - Structure determination of complex molecular machines requires a combination of an increasing number of experimental methods with highly specialized software geared toward each data source to properly handle the gathered data. Recently, we introduced the two software packages PowerFit and DisVis. 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. Here, we report on recent advances in both GPGPU-accelerated software packages: PowerFit is a tool for rigid body fitting of atomic structures in cryo-electron density maps and has been updated to also output reliability indicators for the success of fitting, through the use of the Fisher z-transformation and associated confidence intervals; DisVis aims at quantifying the information content of distance restraints and identifying false-positive restraints. We extended its analysis capabilities to include an analysis of putative interface residues and to output an average shape representing the putative location of the ligand. To facilitate their use by a broad community, they have been implemented as web portals harvesting both local CPU resources and GPGPU-accelerated EGI grid resources. They 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.
KW - Chemical cross-links coupled with mass spectrometry
KW - Cryo-electron microscopy
KW - Fast Fourier transform
KW - GPGPU acceleration
UR - https://www.scopus.com/pages/publications/85009349446
U2 - 10.1016/j.jmb.2016.11.032
DO - 10.1016/j.jmb.2016.11.032
M3 - Article
AN - SCOPUS:85009349446
SN - 0022-2836
VL - 429
SP - 399
EP - 407
JO - Journal of Molecular Biology
JF - Journal of Molecular Biology
IS - 3
ER -