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

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...

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Bibliographic Details
Published in:European biophysics journal 2023-07, Vol.52 (4-5), p.225-232
Main Authors: Brookes, Emre H., Rocco, Mattia
Format: Article
Language:English
Subjects:
Assessments
Biochemistry
Biological and Medical Physics
Biomedical and Life Sciences
Biophysics
Cell Biology
Circular Dichroism
Databases, Protein
Dichroism
Hydrodynamics
Life Sciences
Membrane Biology
Methods Paper
Nanotechnology
Neurobiology
Physicochemical properties
Proteins - chemistry
Ultracentrifugation
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Summary: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.
ISSN:0175-7571
1432-1017
1432-1017
DOI:10.1007/s00249-023-01636-1