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Pipeline for transferring annotations between proteins beyond globular domains
Open accessPreprint — published as 10.1002/pro.4655 · Paper page
Abstract
Background: DisProt is the primary repository of Intrinsically Disordered Proteins. This database is manually curated and the annotations there have strong experimental support. Currently DisProt contains a relatively small number of proteins highlighting the importance of transferring verified disorder and other annotations, in such a way as to increase the number of proteins that could benefit from this valuable information. While the principles and practicalities of homology transfer are well-established for globular proteins, these are largely lacking for disordered proteins. Methods: We used DisProt to evaluate the transferability of the annotation terms to orthologous proteins. For each protein, we looked for their orthologs, with the assumption that they will have a similar function. Then, for each protein and their orthologs we made multiple sequence alignments (MSAs). Global and regional quality of the MSAs was evaluated with the NorMD score. Results: We have designed a pipeline to obtain good quality MSAs and to transfer annotations from any protein to their orthologs. Applying the pipeline to DisProt proteins, from the 1931 entries with 5,623 annotations we can reach 97,555 orthologs and transfer a total of 301,190 terms by homology. We also provide a web server for consulting the results of DisProt proteins and execute the pipeline for any other protein. The server Homology Transfer IDP (HoTIDP) is accessible at http://hotidp.leloir.org.ar .
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Highly accurate protein structure prediction with AlphaFold
Jumper, J., Evans, R., Pritzel, A., Green, T., Figurnov, M., Ronneberger, O., Tunyasuvunakool, K., Bates, R., Žídek, A., Potapenko, A., et al. (2021) · Nature · doi:10.1038/s41586-021-03819-2 · Cited by 43,764
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- 10.1073/pnas.1508380112 · DOI
- 10.1093/NAR/GKAA913 · DOI · Paper page
- 10.1093/nar/gkab408 · DOI
- MobiDB: intrinsically disordered proteins in 2021 | Nucleic Acids Research | Oxford Academic. https://academic.oup.com/nar/article/49/D1/D361/6006190?login=false. · DOI
- 2022, DisProt in 2022: improved quality and accessibility of protein intrinsic disorder annotation, Nucleic Acids Res, 50, D480, 10.1093/nar/gkab1082 · DOI
- 10.1093/nar/gkaa1113 · DOI · Paper page
- 2020, Understanding the causes of errors in eukaryotic protein-coding gene prediction: a case study of primate proteomes, BMC Bioinformatics, 21, 513, 10.1186/s12859-020-03855-1 · DOI
- 2020, A benchmark study of ab initio gene prediction methods in diverse eukaryotic organisms, BMC Genomics, 21, 293, 10.1186/s12864-020-6707-9 · DOI · Paper page
- 10.1371/journal.pone.0018093 · DOI · Paper page
- 10.1093/bioinformatics/bts565 · DOI · Paper page
- 10.1093/bioinformatics/btl158 · DOI
- 10.1093/nar/gkaa1007 · DOI · Paper page
- 10.1093/nar/gky1068 · DOI
- 10.1002/PRO.3290 · DOI · Paper page
- 10.1093/bioinformatics/bty121 · DOI
- 10.1006/jmbi.2001.5187 · DOI
- 2010, AQUA: automated quality improvement for multiple sequence alignments, Bioinforma. Oxf. Engl, 26, 263, 10.1093/bioinformatics/btp651 · DOI
- 10.1093/bioinformatics/btp033 · DOI
Metadata
- Authors
- Martínez-Pérez, E., Pajkos, M., Tosatto, S. C. E., Gibson, T. J., Dosztanyi, Z., & Marino-Buslje, C.
- Affiliations
- Eötvös Loránd University (HU)
- University of Padua (IT)
- European Molecular Biology Laboratory (DE)
- ORCID
- Venue
- Protein Science
- Publisher
- openRxiv
- Published
- 2022-11-09
- Volume
- 32
- Issue
- 7
- Pages
- e4655-e4655
- ISSN
- 0961-8368 (ISSN-L)
- PMC
- PMC10278204
- OpenAlex
- W4376129164
- Cited by
- 4
- References
- 1
- Citations by year
- 2026: 1 · 2024: 1 · 2023: 2
- FWCI
- 0.36
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- cc-by
- Locations
- Protein Science (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Padua Research Archive (University of Padova) (submittedVersion, cc-by)
- Funders
- European Commission (HORIZON2020, H2020, 778247, H2020-MSCA, H2020 MSCA Rise)
- Consejo Nacional de Investigaciones Científicas y Técnicas (H2020-MSCA-RISE)
- Horizon 2020 Framework Programme (H2020-MSCA, H2020-MSCA-RISE, 778247)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
- Keywords
- intrinsically disordered proteins, annotation transfer, orthologs, DisProt, multiple sequence alignment, protein annotation
- MeSH terms
- Databases, Factual, Sequence Alignment, Intrinsically Disordered Proteins
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