{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"submitter":["Davidson RB"],"funding":["Oak Ridge National Laboratory, under the Laboratory Directed Research and Development Program","DOE Office of Science User Facility","Oak Ridge Leadership Computing Facility","US DOE Joint Genome Institute","Office of Biological and Environmental Research (BER) Genomic Science program within the US Department of Energy (DOE) Office of Science"],"pagination":["btad511"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC10463551"],"repository":["biostudies-literature"],"omics_type":["Unknown"],"volume":["39(8)"],"pubmed_abstract":["Motivation
Sphagnum-dominated peatlands store a substantial amount of terrestrial carbon. The genus is undersampled and under-studied. No experimental crystal structure from any Sphagnum species exists in the Protein Data Bank and fewer than 200 Sphagnum-related genes have structural models available in the AlphaFold Protein Structure Database. Tools and resources are needed to help bridge these gaps, and to enable the analysis of other structural proteomes now made possible by accurate structure prediction.Results
We present the predicted structural proteome (25 134 primary transcripts) of Sphagnum divinum computed using AlphaFold, structural alignment results of all high-confidence models against an annotated nonredundant crystallographic database of over 90,000 structures, a structure-based classification of putative Enzyme Commission (EC) numbers across this proteome, and the computational method to perform this proteome-scale structure-based annotation.Availability and implementation
All data and code are available in public repositories, detailed at https://github.com/BSDExabio/SAFA. The structural models of the S. divinum proteome have been deposited in the ModelArchive repository at https://modelarchive.org/doi/10.5452/ma-ornl-sphdiv."],"journal":["Bioinformatics (Oxford, England)"],"pubmed_title":["Predicted structural proteome of Sphagnum divinum and proteome-scale annotation."],"pmcid":["PMC10463551"],"funding_grant_id":["DE-AC05-00OR22725","09832","DE-AC02-05CH11231","10.46936/10.25585/60001030","ERKP917","DE-SC0021303"],"pubmed_authors":["Sreedasyam A","Parks JM","Schmutz J","Gao M","Quadir F","Davidson RB","Sedova A","Skolnick J","Piatkowski B","Weston DJ","Coletti M","Cheng J"],"additional_accession":[]},"is_claimable":false,"name":"Predicted structural proteome of Sphagnum divinum and proteome-scale annotation.","description":"Motivation
Sphagnum-dominated peatlands store a substantial amount of terrestrial carbon. The genus is undersampled and under-studied. No experimental crystal structure from any Sphagnum species exists in the Protein Data Bank and fewer than 200 Sphagnum-related genes have structural models available in the AlphaFold Protein Structure Database. Tools and resources are needed to help bridge these gaps, and to enable the analysis of other structural proteomes now made possible by accurate structure prediction.Results
We present the predicted structural proteome (25 134 primary transcripts) of Sphagnum divinum computed using AlphaFold, structural alignment results of all high-confidence models against an annotated nonredundant crystallographic database of over 90,000 structures, a structure-based classification of putative Enzyme Commission (EC) numbers across this proteome, and the computational method to perform this proteome-scale structure-based annotation.Availability and implementation
All data and code are available in public repositories, detailed at https://github.com/BSDExabio/SAFA. The structural models of the S. divinum proteome have been deposited in the ModelArchive repository at https://modelarchive.org/doi/10.5452/ma-ornl-sphdiv.","dates":{"release":"2023-01-01T00:00:00Z","publication":"2023 Aug","modification":"2025-04-04T19:24:04.249Z","creation":"2025-04-04T19:24:04.249Z"},"accession":"S-EPMC10463551","cross_references":{"pubmed":["37589594"],"doi":["10.1093/bioinformatics/btad511"]}}