U.S. Department of EnergyOffice of Scientific and Technical Information
Deep Green Unannotated Protein Structures
Abstract
The Deep Green list is based on the identification and curation of conserved unannotated proteins in three green lineage (Viridiplantae) model organisms; Arabidopsis thaliana, Chlamydomonas reinhardtii, and Setaria viridis. Preliminary characterization of Deep Green proteins and genes was done using various informatics tools and published data sets and is presented in Knoshaug, Sun, et al., 2023, submitted. The structures of these unannotated proteins were also predicted using AlphaFold (Jumper et al., 2021). The data deposited here are the AlphaFold structural predictions having the highest pLDDT score and thus identified as the best folded structure (ranked_0). These data enable others to do in-depth structural characterizations to aid in functional characterization leading to deeper understanding of plant biology. References: Jumper, J., Evans, R., Pritzel, A., Green, T., Figurnov, M., Ronneberger, O., Tunyasuvunakool, K., Bates, R., Žídek, A., Potapenko, A., Bridgland, A., Meyer, C., Kohl, S. A. A., Ballard, A. J., Cowie, A., Romera-Paredes, B., Nikolov, S., Jain, R., Adler, J., Back, T., Petersen, S., Reiman, D., Clancy, E., Zielinski, M., Steinegger, M., Pacholska, M., Berghammer, T., Bodenstein, S., Silver, D., Vinyals, O., Senior, A. W., Kavukcuoglu, K., Kohli, P. and Hassabis, D. (2021) Highly accurate protein structure prediction with AlphaFold. Nature, 596:583-589.more »
- Authors:
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- Biosciences Center; National Renewable Energy Laboratory
- Donald Danforth Plant Science Center
- Computational Science
- University of Missouri - Columbia
- NREL, now at NVIDIA Corp.
- Donald Danforth Plant Sciences Center
- Publication Date:
- Other Number(s):
- ERW9098
- Research Org.:
- National Renewable Energy Laboratory - Data (NREL-DATA), Golden, CO (United States); National Renewable Energy Laboratory (NREL), Golden, CO (United States)
- Sponsoring Org.:
- National Renewable Energy Laboratory (NREL), Golden, CO (United States)
- Subject:
- 09 BIOMASS FUELS; 59 BASIC BIOLOGICAL SCIENCES; AlphaFold; Arabidopsis thaliana; Chlamydomonas reinhardtii; Donald Danforth Plant Science Center; Setaria viridis; energy crop; green lineage; model species; protein structure; unannotated proteins
- OSTI Identifier:
- 1970473
- DOI:
- https://doi.org/10.7799/1970473
Citation Formats
Knoshaug, Eric, Sun, Peipei, Nag, Ambarish, Nguyen, Huong, Mattoon, Erin, Zhang, Ningning, Liu, Jian, Chen, Chen, Cheng, Jianlin, Zhang, Ru, St. John, Peter, and Umen, James. Deep Green Unannotated Protein Structures. United States: N. p., 2023.
Web. doi:10.7799/1970473.
Knoshaug, Eric, Sun, Peipei, Nag, Ambarish, Nguyen, Huong, Mattoon, Erin, Zhang, Ningning, Liu, Jian, Chen, Chen, Cheng, Jianlin, Zhang, Ru, St. John, Peter, & Umen, James. Deep Green Unannotated Protein Structures. United States. doi:https://doi.org/10.7799/1970473
Knoshaug, Eric, Sun, Peipei, Nag, Ambarish, Nguyen, Huong, Mattoon, Erin, Zhang, Ningning, Liu, Jian, Chen, Chen, Cheng, Jianlin, Zhang, Ru, St. John, Peter, and Umen, James. 2023.
"Deep Green Unannotated Protein Structures". United States. doi:https://doi.org/10.7799/1970473. https://www.osti.gov/servlets/purl/1970473. Pub date:Wed Apr 19 00:00:00 EDT 2023
@article{osti_1970473,
title = {Deep Green Unannotated Protein Structures},
author = {Knoshaug, Eric and Sun, Peipei and Nag, Ambarish and Nguyen, Huong and Mattoon, Erin and Zhang, Ningning and Liu, Jian and Chen, Chen and Cheng, Jianlin and Zhang, Ru and St. John, Peter and Umen, James},
abstractNote = {The Deep Green list is based on the identification and curation of conserved unannotated proteins in three green lineage (Viridiplantae) model organisms; Arabidopsis thaliana, Chlamydomonas reinhardtii, and Setaria viridis. Preliminary characterization of Deep Green proteins and genes was done using various informatics tools and published data sets and is presented in Knoshaug, Sun, et al., 2023, submitted. The structures of these unannotated proteins were also predicted using AlphaFold (Jumper et al., 2021). The data deposited here are the AlphaFold structural predictions having the highest pLDDT score and thus identified as the best folded structure (ranked_0). These data enable others to do in-depth structural characterizations to aid in functional characterization leading to deeper understanding of plant biology. References: Jumper, J., Evans, R., Pritzel, A., Green, T., Figurnov, M., Ronneberger, O., Tunyasuvunakool, K., Bates, R., Žídek, A., Potapenko, A., Bridgland, A., Meyer, C., Kohl, S. A. A., Ballard, A. J., Cowie, A., Romera-Paredes, B., Nikolov, S., Jain, R., Adler, J., Back, T., Petersen, S., Reiman, D., Clancy, E., Zielinski, M., Steinegger, M., Pacholska, M., Berghammer, T., Bodenstein, S., Silver, D., Vinyals, O., Senior, A. W., Kavukcuoglu, K., Kohli, P. and Hassabis, D. (2021) Highly accurate protein structure prediction with AlphaFold. Nature, 596:583-589. Knoshaug, E. P., Sun, P., Nag, A., Nguyen, H., Mattoon, E. M., Zhang, N., Liu, J., Chen, C., Cheng, J., Zhang, R., St. John, P., and Umen, J. (submitted) Identification and preliminary characterization of conserved uncharacterized proteins from Chlamydomonas reinhardtii, Arabidopsis thaliana, and Setaria viridis.},
doi = {10.7799/1970473},
journal = {},
number = ,
volume = ,
place = {United States},
year = {Wed Apr 19 00:00:00 EDT 2023},
month = {Wed Apr 19 00:00:00 EDT 2023}
}