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

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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.

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Data availability

There is no stored “data”. The data are produced dynamically on the website by calculating properties from user supplied structures or from structures obtained from other sources (e.g. AlphaFold database).

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Acknowledgements

EB was funded by the National Institutes of Health, National Institute of General Medical Sciences grant GM120600 and the National Science Foundation Grant 1912444. This work used the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by National Science Foundation Grant Number ACI-1548562 and utilized Jetstream2 at Indiana University through allocation TG-MCB17057 to EB. This work benefited from CCP-SAS (software developed through a joint EPSRC (EP/K039121/1) and NSF (CHE-1265821) Grant.

Funding

Funding was provided by National Institutes of Health (US) (Grant No. GM120600) and Directorate for Computer and Information Science and Engineering (Grant No. 1912444).

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  1. Department of Chemistry and Biochemistry, University of Montana, Missoula, MT, 59812, USA

    Emre H. Brookes

  2. Retired, Proteomica e Spettrometria di Massa, IRCCS Ospedale Policlinico San Martino, Largo R. Benzi 10, 16132, Genova, Italy

    Mattia Rocco

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Brookes, E.H., Rocco, M. Beyond the US-SOMO-AF database: a new website for hydrodynamic, structural, and circular dichroism calculations on user-supplied structures. Eur Biophys J 52, 225–232 (2023). https://doi.org/10.1007/s00249-023-01636-1

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