U.S. Department of EnergyOffice of Scientific and Technical Information
Structural Models and Sequence Alignment Results of the Rhodospirillum rubrum Proteome
Abstract
This dataset contains the structural models for the primary transcripts of the Rhodospirillum rubrum proteome as well as sequence alignment results for a subset of the encoded proteins. For each protein, the five models inferred from AlphaFold 2 are provided. The largest pTM-scoring model for each protein was energy minimized; this minimized structure as well as its AlphaFold pickle output file are also provided. This set of structures represent an alternate source of models for the R. rubrum proteome to those available in the AlphaFold Protein Structure Database. For proteins that have been annotated as "hypothetical", sequence alignment results from the HHblits and SAdLSA alignment methods are provided. These methods are often more capable to resolve sequence homology than other methods. Therefore, the results from both HHblits and SAdLSA are provided to identify possible homologs for these challenging proteins. Numerous sequence databases are utilized for these alignments.
- Authors:
-
- ORNL-OLCF
- Publication Date:
- Research Org.:
- Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States). Oak Ridge Leadership Computing Facility (OLCF); Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)
- Sponsoring Org.:
- Office of Science (SC); Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; 74 ATOMIC AND MOLECULAR PHYSICS; 97 MATHEMATICS AND COMPUTING; Protein Structure Prediction, Protein Sequence Alignment, Functional Annotation
- OSTI Identifier:
- 1987876
- DOI:
- https://doi.org/10.13139/ORNLNCCS/1987876
Citation Formats
Davidson, Russell B, Coletti, Mark, Gao, Mu, and Sedova, Ada. Structural Models and Sequence Alignment Results of the Rhodospirillum rubrum Proteome. United States: N. p., 2023.
Web. doi:10.13139/ORNLNCCS/1987876.
Davidson, Russell B, Coletti, Mark, Gao, Mu, & Sedova, Ada. Structural Models and Sequence Alignment Results of the Rhodospirillum rubrum Proteome. United States. doi:https://doi.org/10.13139/ORNLNCCS/1987876
Davidson, Russell B, Coletti, Mark, Gao, Mu, and Sedova, Ada. 2023.
"Structural Models and Sequence Alignment Results of the Rhodospirillum rubrum Proteome". United States. doi:https://doi.org/10.13139/ORNLNCCS/1987876. https://www.osti.gov/servlets/purl/1987876. Pub date:Fri Jul 07 00:00:00 EDT 2023
@article{osti_1987876,
title = {Structural Models and Sequence Alignment Results of the Rhodospirillum rubrum Proteome},
author = {Davidson, Russell B and Coletti, Mark and Gao, Mu and Sedova, Ada},
abstractNote = {This dataset contains the structural models for the primary transcripts of the Rhodospirillum rubrum proteome as well as sequence alignment results for a subset of the encoded proteins. For each protein, the five models inferred from AlphaFold 2 are provided. The largest pTM-scoring model for each protein was energy minimized; this minimized structure as well as its AlphaFold pickle output file are also provided. This set of structures represent an alternate source of models for the R. rubrum proteome to those available in the AlphaFold Protein Structure Database. For proteins that have been annotated as "hypothetical", sequence alignment results from the HHblits and SAdLSA alignment methods are provided. These methods are often more capable to resolve sequence homology than other methods. Therefore, the results from both HHblits and SAdLSA are provided to identify possible homologs for these challenging proteins. Numerous sequence databases are utilized for these alignments.},
doi = {10.13139/ORNLNCCS/1987876},
journal = {},
number = ,
volume = ,
place = {United States},
year = {Fri Jul 07 00:00:00 EDT 2023},
month = {Fri Jul 07 00:00:00 EDT 2023}
}