Reciprocal Best Structure Hits (RBSH)

Repository URI
https://www.repository.cam.ac.uk/handle/1810/341254
Repository DOI
https://doi.org/10.17863/CAM.87873
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Files
AlphaFold RBSH predictions added to PomBase curated orthologs.xlsx (38.19 KB)
H_sapiens_C_elegans_results.xlsx (151.79 KB)
H_sapiens_D_melanogaster_results.xlsx (167.51 KB)
H_sapiens_S_cerevisiae_results.xlsx (77.63 KB)
H_sapiens_S_pombe_results.xlsx (82.57 KB)
Type
Dataset
Change log
Authors
Monzon, Vivian 
Paysan-Lafosse, Typhaine 
Wood, Valerie 
Bateman, Alex 
Description

In this work, we are using AlphaFold structure models to find the closest homologues proteins between Homo sapiens and D. melanogaster, C. elegans, S. cerevisiae and S. pombe as well as between S. cerevisiae and S. pombe. We are using the structure aligner Foldseek to run all against all and search for the best scoring hit in both directions to detect the Reciprocal Best Structure Hits (RBSH). We compare the results to protein pairs detected by their sequence similarity as Reciprocal Best Hits (RBH) and verify the results using the PANTHER family classification files.

 

Note: This dataset is an updated version of the dataset at https://doi.org/10.17863/CAM.85487.

Version
Software / Usage instructions
We used the structure aligner Foldseek to find the RBSH as well as the sequence aligner BLASTP to find the RBH.
Keywords
AlphaFold database, Protein homology, Schizosaccharomyces pombe, Structure comparison
Publisher
Rights
Attribution 4.0 International (CC BY 4.0) Repository logo
Relationships
https://doi.org/10.1101/2022.07.04.498216
Supplements:
https://www.repository.cam.ac.uk/handle/1810/341511
https://doi.org/10.1093/bioadv/vbac072
Is new version of:
https://doi.org/10.17863/CAM.85487
Collections
Data - European Bioinformatics Institute (EMBL-EBI)