The DisVis and PowerFit Web Servers: Explorative and Integrative Modeling of Biomolecular Complexes

JOURNAL OF MOLECULAR BIOLOGY

卷:429

Article

van Zundert, G. C. P.¹  Trellet, M.¹  Schaarschmidt, J.¹  Kurkcuoglu, Z.¹  David, M.²  Verlato, M.³  Rosato, A.^4,5  Bonvin, A. M. J. J.¹ 

[1] Univ Utrecht, Fac Sci Chem, Bijvoet Ctr Biomol Res, Padualaan 8, NL-3584 CH Utrecht, Netherlands

[2] LIP Lab Instrumentacao & Fis Expt Particulas, Ave Elias Garcia 14, P-1000 Lisbon, Portugal

[3] Ist Nazl Fis Nucl, Sez Padova, Via Marzolo 8, I-35131 Padua, Italy

[4] Univ Florence, Magnet Resonance Ctr, Via L Sacconi 6, I-50019 Sesto Fiorentino, Italy

[5] Univ Florence, Dept Chem Ugo Schiff, Via L Sacconi 6, I-50019 Sesto Fiorentino, Italy

关键词: cryo-electron microscopy;    chemical cross-links coupled with mass spectrometry;    fast Fourier transform;    GPGPU acceleration;   

DOI  :  10.1016/j.jmb.2016.11.032

来源: Elsevier

【 摘 要 】

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. (C) 2016 The Authors. Published by Elsevier Ltd. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).

【 授权许可】

Free