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

Area of Science:

• Structural biology
• Computational biology
• Biophysics

Background:

• Determining complex molecular machine structures requires integrating diverse experimental data.
• Specialized software is crucial for handling data from methods like cryo-electron microscopy (cryo-EM) and mass spectrometry (MS).
• Previous work introduced PowerFit for rigid body fitting and DisVis for analyzing distance restraints.

Purpose of the Study:

• To report recent advancements in the GPGPU-accelerated software packages PowerFit and DisVis.
• To enhance the capabilities for analyzing structural data from molecular machines.
• To improve accessibility through user-friendly web portals.

Main Methods:

• PowerFit: Rigid body fitting of atomic structures into cryo-EM density maps, incorporating Fisher z-transformation for reliability indicators.
• DisVis: Quantifying information content of distance restraints (from chemical cross-linking coupled with MS) and identifying false positives.
• Web portal implementation utilizing local CPU and EGI grid resources for GPGPU acceleration.

Main Results:

• PowerFit now provides reliability indicators for fitting success using confidence intervals.
• DisVis analysis extended to include putative interface residues and average ligand shape prediction.
• Web portals offer user-friendly interfaces, minimizing computational demands and providing interactive results.

Conclusions:

• Advanced PowerFit and DisVis software packages significantly improve structural determination of molecular machines.
• Integrated computational tools and web portals enhance accessibility and data analysis for the scientific community.
• These developments facilitate a more accurate and efficient understanding of complex biological structures.