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

Eur Biophys J. 2023 Jul;52(4-5):225-232. doi: 10.1007/s00249-023-01636-1. Epub 2023 Feb 28.

Abstract

At the 25th International Analytical Ultracentrifugation Workshop and Symposium, we described the recent implementation of the UltraScan SOlution MOdeler AlphaFold (US-SOMO-AF) database, containing hydrodynamic, structural, CD calculations, and other ancillary information, performed on the entire AF v2 database of predicted protein structures, containing more than 1,000,000 entries. The scope of the US-SOMO-AF database was that of providing direct access to pre-calculated physicochemical parameters for rapid assessment against their experimentally determined counterparts to test the compatibility in solution of predicted AlphaFold structures. In the meantime, the AlphaFold consortium has extended its database of predicted structures to an astonishing > 200 million entries, making it quite impractical for their coverage in the US-SOMO-AF database. Therefore, we have created the US-SOMO-Web site, allowing the rapid calculations of all the properties, as present in the US-SOMO-AF database, on user-supplied PDB and mmCIF structures, as well as allowing direct processing of the latest AlphaFold models. Major features on the website are described, along with current limitations and potential future developments.

Keywords: AlphaFold; Circular dichroism; Distance distribution function; Hydrodynamic properties; Science gateway.

MeSH terms

  • Circular Dichroism
  • Databases, Protein
  • Hydrodynamics*
  • Proteins* / chemistry
  • Ultracentrifugation

Substances

  • Proteins