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

Emre H. Brookes; Mattia Rocco

doi:10.1007/s00249-023-01636-1

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

Emre H. Brookes
, Mattia Rocco

Chemistry and Biochemistry

IRCCS Ospedale Policlinico San Martino

Research output: Contribution to journal › Article › peer-review

3 Scopus citations

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.

Original language	English
Pages (from-to)	225-232
Number of pages	8
Journal	European Biophysics Journal
Volume	52
Issue number	4-5
Early online date	Feb 28 2023
DOIs	https://doi.org/10.1007/s00249-023-01636-1
State	Published - Jul 2023

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). 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.

Funders	Funder number
CHE-1265821, ACI-1548562
GM120600
1912444
TG-MCB17057
Engineering and Physical Sciences Research Council	EP/K039121/1

Keywords

AlphaFold
Circular dichroism
Distance distribution function
Hydrodynamic properties
Science gateway
Proteins/chemistry
Databases, Protein
Hydrodynamics
Ultracentrifugation
Circular Dichroism

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10.1007/s00249-023-01636-1

Cite this

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

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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author = "Brookes, \{Emre H.\} and Mattia Rocco",

note = "Publisher Copyright: {\textcopyright} 2023, European Biophysical Societies' Association.",

year = "2023",

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doi = "10.1007/s00249-023-01636-1",

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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.

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KW - Distance distribution function

KW - Hydrodynamic properties

KW - Science gateway

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KW - Hydrodynamics

KW - Ultracentrifugation

KW - Circular Dichroism

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ER -

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

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