ChaperISM: improved chaperone binding prediction using position-independent scoring matrices
Open accessAbstract
Motivation: Understanding the mechanisms of client protein interaction with Hsp70 chaperones is essential to analyze the complex dynamics in the context of normal or dysregulated metabolism. Because Hsp70 can bind millions of proteins, including key molecules involved in processes of stemness, tumorigenesis and survival, in silico prediction of Hsp70 interactions has great value in validating possible new clients. Currently, two algorithms are available to predict binding to DnaK—the bacterial Hsp70—but both are based on amino acid sequence and energy calculations of qualitative information—binders and non-binders. Results: We introduce a new algorithm to identify Hsp70 binding sequences in proteins—ChaperISM—a position-independent scoring matrix trained on either qualitative or quantitative chemiluminescence data previously published, which were obtained from the interaction between DnaK and different ligands. Both versions of ChaperISM, qualitative or quantitative, resulted in an improved performance in comparison to other state-of-the-art chaperone binding predictors. Availability and implementation: ChaperISM is implemented in Python version 3. The source code of ChaperISM is freely available for download at https://github.com/BioinfLab/ChaperISM. Supplementary information: Supplementary data are available at Bioinformatics online.
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Two 7-residue GR segments, SIVPATL and IVPATLP, in the GRpre-Helix 1 strand are predicted by two algorithms to be Hsp70-binding sites.
“Two 7-residue GR segments (SIVPATL and IVPATLP) of a continuous sequence (residues 519–526; note that residue 519 in the native GR sequence is T, not S) in the GRpre-Helix 1 strand are predicted to be Hsp70-binding sites by two state-of-the-art algorithms (BiPPred58 and ChaperISM59) (Extended Data Fig. 9a).”
From Structure of Hsp90–Hsp70–Hop–GR reveals the Hsp90 client-loading mechanism (2022) · cites this paper as [59]
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Structure of Hsp90–Hsp70–Hop–GR reveals the Hsp90 client-loading mechanism
Wang, R. Y.-R., Noddings, C. M., Kirschke, E., Myasnikov, A. G., Johnson, J. L., & Agard, D. A. (2022) · Nature · doi:10.1038/s41586-021-04252-1 · Cited by 213 · see citing works
- Authors
- Gutierres, M. B. B., Bonorino, C. B. C., & Rigo, M. M.
- Affiliations
- Universidade Federal de Ciências da Saúde de Porto Alegre (BR)
- Pontifícia Universidade Católica do Rio Grande do Sul (BR)
- Corresponding author
- Rigo, M M
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2019-08-28
- Volume
- 36
- Issue
- 3
- Pages
- 735-741
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- OpenAlex
- W2971253990
- Cited by
- 29
- References
- 26
- Citations by year
- 2026: 4 · 2025: 7 · 2024: 1 · 2023: 4 · 2022: 7 · 2021: 4 · 2020: 1 · 2012: 1
- FWCI
- 0.99
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model (vor)
- Locations
- Bioinformatics (publishedVersion)
- PubMed (publishedVersion)
- Funders
- Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) and Financiadora de Inovação e Pesquisa
- Coordenação de Aperfeiçoamento de Pessoal de Nível Superior
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Heat shock proteins research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Machine Learning in Bioinformatics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Keywords
- Hsp70 chaperones, DnaK, protein-protein interaction, chemiluminescence, binding affinity
- MeSH terms
- Algorithms, Amino Acid Sequence, Protein Binding, Software, HSP70 Heat-Shock Proteins
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