Structural Models of the Rhodopseudomonas palustris Proteome

Davidson, Russell B; Coletti, Mark; Gao, Mu; Sedova, Ada

doi:10.13139/ORNLNCCS/1988165

Title: Structural Models of the Rhodopseudomonas palustris Proteome

Dataset
Other Related Research

Abstract

This dataset contains the structural models for the primary transcripts of the Rhodopseudomonas palustris proteome. 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. palustris proteome to those available in the AlphaFold Protein Structure Database.

Authors:

Davidson, Russell B; Coletti, Mark; Gao, Mu; Sedova, Ada

ORNL-OLCF

Publication Date:: Wed Jul 12 00:00:00 EDT 2023

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

OSTI Identifier:: 1988165

DOI:: https://doi.org/10.13139/ORNLNCCS/1988165

Citation Formats


                    Davidson, Russell B, Coletti, Mark, Gao, Mu, and Sedova, Ada. Structural Models of the Rhodopseudomonas palustris Proteome.  United States: N. p., 2023. 
        Web.  doi:10.13139/ORNLNCCS/1988165.

Copy to clipboard


                    Davidson, Russell B, Coletti, Mark, Gao, Mu, & Sedova, Ada. Structural Models of the Rhodopseudomonas palustris Proteome.  United States.  doi:https://doi.org/10.13139/ORNLNCCS/1988165

Copy to clipboard


                    Davidson, Russell B, Coletti, Mark, Gao, Mu, and Sedova, Ada. 2023.  
"Structural Models of the Rhodopseudomonas palustris Proteome".  United States.  doi:https://doi.org/10.13139/ORNLNCCS/1988165.  https://www.osti.gov/servlets/purl/1988165. Pub date:Wed Jul 12 00:00:00 EDT 2023

Copy to clipboard


                    
@article{osti_1988165,

  title        = {Structural Models of the Rhodopseudomonas palustris 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 Rhodopseudomonas palustris proteome. 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. palustris proteome to those available in the AlphaFold Protein Structure Database.},

  doi          = {10.13139/ORNLNCCS/1988165},

  journal      = {},

  number       = ,

  volume       = ,

  place        = {United States},

  year         = {Wed Jul 12 00:00:00 EDT 2023},

  month        = {Wed Jul 12 00:00:00 EDT 2023}

}

Copy to clipboard

Dataset:

View Dataset

DOI: https://doi.org/10.13139/ORNLNCCS/1988165

Save / Share:

Export Metadata

Save to My Library

Similar records in DOE Data Explorer and OSTI.GOV collections:

Rhodopseudomonas palustris evolution for photoheterotrophic metabolism of syringic acid

Dataset Oshlag, Julian
Identifying genomic changes in Rhodopseudomonas palustris strains that confer ability for anaerobic degradation of syringic acid

Dataset Noguera, Daniel
Structural models and functional annotations for the Sphagnum divinum proteome.

Dataset Davidson, Russell B ; Coletti, Mark ; Gao, Mu ; ...

This dataset contains the structural models for the primary transcripts of the Sphagnum divinum proteome. Additionally, for a subset of these proteins, sequence and structural alignment results are provided. This dataset represents the most thorough structural study of a Sphagnum species, also known as peat mosses, by providing three-dimensional atomic resolution structures of the majority of the encoded proteins as well as structural alignment results used in the application of annotating the proteome.
Structural Models and Sequence Alignment Results of the Rhodospirillum rubrum Proteome

Dataset Davidson, Russell B ; Coletti, Mark ; Gao, Mu ; ...

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 frommore »« less
Structural Models and Sequence Alignment Results of the Desulfovibrio vulgaris Proteome

Dataset Davidson, Russell B ; Coletti, Mark ; Gao, Mu ; ...

This dataset contains the structural models for the primary transcripts of the Desulfovibrio vulgaris 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 D. vulgaris proteome to those available in the AlphaFold Protein Structure Database (AFDB). This is a bit more complicated since the proteins reporting inmore »« less

Similar Records