Beyond the US-SOMO-AF database: a new website for hydrodynamic, structural, and circular dichroism calculations on...

Area of Science:

• Biophysics
• Structural Biology
• Computational Biology

Background:

• The AlphaFold v2 database initially contained over 1 million predicted protein structures.
• The UltraScan Solution Modeler AlphaFold (US-SOMO-AF) database was developed to provide physicochemical parameters for these structures.
• The AlphaFold database has since expanded to over 200 million entries, making comprehensive pre-calculation impractical.

Purpose of the Study:

• To introduce the US-SOMO-Web site, a new platform for calculating protein properties.
• To enable rapid assessment of the solution compatibility of predicted protein structures.
• To provide access to physicochemical parameters for user-supplied and the latest AlphaFold models.

Main Methods:

• Implementation of the US-SOMO-AF database with hydrodynamic and structural information.
• Development of the US-SOMO-Web site for on-demand property calculations.
• Processing of user-supplied PDB/mmCIF files and AlphaFold models.

Main Results:

• The US-SOMO-AF database provided pre-calculated parameters for over 1 million AlphaFold v2 structures.
• The US-SOMO-Web site enables rapid calculation of physicochemical properties for new and existing protein structure models.
• The website facilitates direct processing of the latest AlphaFold predictions.

Conclusions:

• The US-SOMO-Web site addresses the challenge of an exponentially growing protein structure database.
• It offers a practical solution for assessing the biophysical properties of predicted protein structures.
• Future developments aim to expand the site's capabilities and address current limitations.