title: The DisVis and PowerFit Web Servers: Explorative and Integrative Modeling of Biomolecular Complexes.
abstract: 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.
authors.affiliation: Bijvoet Center for Biomolecular Research, Faculty of Science - Chemistry, Utrecht University, Padualaan 8, 3584CH Utrecht, The Netherlands.
authors.forename: G C P
authors.initials: GC
authors.lastname: van Zundert
authors.affiliation: Bijvoet Center for Biomolecular Research, Faculty of Science - Chemistry, Utrecht University, Padualaan 8, 3584CH Utrecht, The Netherlands.
authors.forename: M
authors.initials: M
authors.lastname: Trellet
authors.affiliation: Bijvoet Center for Biomolecular Research, Faculty of Science - Chemistry, Utrecht University, Padualaan 8, 3584CH Utrecht, The Netherlands.
authors.forename: J
authors.initials: J
authors.lastname: Schaarschmidt
authors.affiliation: Bijvoet Center for Biomolecular Research, Faculty of Science - Chemistry, Utrecht University, Padualaan 8, 3584CH Utrecht, The Netherlands.
authors.forename: Z
authors.initials: Z
authors.lastname: Kurkcuoglu
authors.affiliation: LIP - Laboratório de Instrumentação e Física Experimental de Particulãs, Avenida Elias Garcia 14, 1000 Lisbon, Portugal.
authors.forename: M
authors.initials: M
authors.lastname: David
authors.affiliation: Istituto Nazionale di Fisica Nucleare - Sezione di Padova, Via Marzolo 8, 35131 Padova, Italy.
authors.forename: M
authors.initials: M
authors.lastname: Verlato
authors.affiliation: Magnetic Resonance Center and Department of Chemistry "Ugo Schiff", University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy.
authors.forename: A
authors.initials: A
authors.lastname: Rosato
authors.affiliation: Bijvoet Center for Biomolecular Research, Faculty of Science - Chemistry, Utrecht University, Padualaan 8, 3584CH Utrecht, The Netherlands. Electronic address: a.m.j.j.bonvin@uu.nl.
authors.forename: A M J J
authors.initials: AM
authors.lastname: Bonvin
mesh_terms: D019295:Computational Biology; D020285:Cryoelectron Microscopy; D030562:Databases, Protein; D020407:Internet; D046911:Macromolecular Substances / Q000737:chemistry*; D013058:Mass Spectrometry; D008958:Models, Molecular; D011487:Protein Conformation; D015203:Reproducibility of Results; D012984:Software
chemical_list: D046911:Macromolecular Substances
keywords: GPGPU acceleration; chemical cross-links coupled with mass spectrometry; cryo-electron microscopy; fast Fourier transform