TY - JOUR
T1 - Beyond the US-SOMO-AF database
T2 - a new website for hydrodynamic, structural, and circular dichroism calculations on user-supplied structures
AU - Brookes, Emre H.
AU - Rocco, Mattia
N1 - Funding Information:
Funding was provided by National Institutes of Health (US) (Grant No. GM120600) and Directorate for Computer and Information Science and Engineering (Grant No. 1912444).
Funding Information:
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.
Publisher Copyright:
© 2023, European Biophysical Societies' Association.
PY - 2023
Y1 - 2023
N2 - 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.
AB - 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.
KW - AlphaFold
KW - Circular dichroism
KW - Distance distribution function
KW - Hydrodynamic properties
KW - Science gateway
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U2 - 10.1007/s00249-023-01636-1
DO - 10.1007/s00249-023-01636-1
M3 - Article
C2 - 36853343
AN - SCOPUS:85148999664
SN - 0175-7571
JO - European Biophysics Journal
JF - European Biophysics Journal
ER -