IDPpi: Protein-Protein Interaction Analyses of Human Intrinsically Disordered Proteins
2018
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Authors
Perović, VladimirSumonja, Neven
Marsh, Lindsey A.
Radovanović, Sandro
Vukićević, Milan
Roberts, Stefan G. E.
Veljković, Nevena
Article (Published version)
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Intrinsically disordered proteins (IDPs) are characterized by the lack of a fixed tertiary structure and are involved in the regulation of key biological processes via binding to multiple protein partners. IDPs are malleable, adapting to structurally different partners, and this flexibility stems from features encoded in the primary structure. The assumption that universal sequence information will facilitate coverage of the sparse zones of the human interactome motivated us to explore the possibility of predicting protein-protein interactions (PPIs) that involve IDPs based on sequence characteristics. We developed a method that relies on features of the interacting and non-interacting protein pairs and utilizes machine learning to classify and predict IDP PPIs. Consideration of both sequence determinants specific for conformational organizations and the multiplicity of IDP interactions in the training phase ensured a reliable approach that is superior to current state-of-the-art metho...ds. By applying a strict evaluation procedure, we confirm that our method predicts interactions of the IDP of interest even on the proteome-scale. This service is provided as a web tool to expedite the discovery of new interactions and IDP functions with enhanced efficiency.
Source:
Scientific Reports, 2018, 8Publisher:
- Nature Portfolio, Berlin
Funding / projects:
- BBSRC [BB/K000446/1]
- COST Action [BM1405]
- BBSRC [BB/K000446/1] Funding Source: UKRI
- Application of the EIIP/ISM bioinformatics platform in discovery of novel therapeutic targets and potential therapeutic molecules (RS-MESTD-Basic Research (BR or ON)-173001)
- Interraction of etiopathogenetic mechanisms of periodontal disease and periimplantitis with the systemic disorders of the present day (RS-MESTD-Integrated and Interdisciplinary Research (IIR or III)-41008)
- Multimodal Biometry in Identity Management (RS-MESTD-Technological Development (TD or TR)-32013)
DOI: 10.1038/s41598-018-28815-x
ISSN: 2045-2322
PubMed: 30002402
WoS: 000438343600073
Scopus: 2-s2.0-85049874911
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Fakultet organizacionih naukaTY - JOUR AU - Perović, Vladimir AU - Sumonja, Neven AU - Marsh, Lindsey A. AU - Radovanović, Sandro AU - Vukićević, Milan AU - Roberts, Stefan G. E. AU - Veljković, Nevena PY - 2018 UR - https://rfos.fon.bg.ac.rs/handle/123456789/1804 AB - Intrinsically disordered proteins (IDPs) are characterized by the lack of a fixed tertiary structure and are involved in the regulation of key biological processes via binding to multiple protein partners. IDPs are malleable, adapting to structurally different partners, and this flexibility stems from features encoded in the primary structure. The assumption that universal sequence information will facilitate coverage of the sparse zones of the human interactome motivated us to explore the possibility of predicting protein-protein interactions (PPIs) that involve IDPs based on sequence characteristics. We developed a method that relies on features of the interacting and non-interacting protein pairs and utilizes machine learning to classify and predict IDP PPIs. Consideration of both sequence determinants specific for conformational organizations and the multiplicity of IDP interactions in the training phase ensured a reliable approach that is superior to current state-of-the-art methods. By applying a strict evaluation procedure, we confirm that our method predicts interactions of the IDP of interest even on the proteome-scale. This service is provided as a web tool to expedite the discovery of new interactions and IDP functions with enhanced efficiency. PB - Nature Portfolio, Berlin T2 - Scientific Reports T1 - IDPpi: Protein-Protein Interaction Analyses of Human Intrinsically Disordered Proteins VL - 8 DO - 10.1038/s41598-018-28815-x UR - conv_2065 ER -
@article{ author = "Perović, Vladimir and Sumonja, Neven and Marsh, Lindsey A. and Radovanović, Sandro and Vukićević, Milan and Roberts, Stefan G. E. and Veljković, Nevena", year = "2018", abstract = "Intrinsically disordered proteins (IDPs) are characterized by the lack of a fixed tertiary structure and are involved in the regulation of key biological processes via binding to multiple protein partners. IDPs are malleable, adapting to structurally different partners, and this flexibility stems from features encoded in the primary structure. The assumption that universal sequence information will facilitate coverage of the sparse zones of the human interactome motivated us to explore the possibility of predicting protein-protein interactions (PPIs) that involve IDPs based on sequence characteristics. We developed a method that relies on features of the interacting and non-interacting protein pairs and utilizes machine learning to classify and predict IDP PPIs. Consideration of both sequence determinants specific for conformational organizations and the multiplicity of IDP interactions in the training phase ensured a reliable approach that is superior to current state-of-the-art methods. By applying a strict evaluation procedure, we confirm that our method predicts interactions of the IDP of interest even on the proteome-scale. This service is provided as a web tool to expedite the discovery of new interactions and IDP functions with enhanced efficiency.", publisher = "Nature Portfolio, Berlin", journal = "Scientific Reports", title = "IDPpi: Protein-Protein Interaction Analyses of Human Intrinsically Disordered Proteins", volume = "8", doi = "10.1038/s41598-018-28815-x", url = "conv_2065" }
Perović, V., Sumonja, N., Marsh, L. A., Radovanović, S., Vukićević, M., Roberts, S. G. E.,& Veljković, N.. (2018). IDPpi: Protein-Protein Interaction Analyses of Human Intrinsically Disordered Proteins. in Scientific Reports Nature Portfolio, Berlin., 8. https://doi.org/10.1038/s41598-018-28815-x conv_2065
Perović V, Sumonja N, Marsh LA, Radovanović S, Vukićević M, Roberts SGE, Veljković N. IDPpi: Protein-Protein Interaction Analyses of Human Intrinsically Disordered Proteins. in Scientific Reports. 2018;8. doi:10.1038/s41598-018-28815-x conv_2065 .
Perović, Vladimir, Sumonja, Neven, Marsh, Lindsey A., Radovanović, Sandro, Vukićević, Milan, Roberts, Stefan G. E., Veljković, Nevena, "IDPpi: Protein-Protein Interaction Analyses of Human Intrinsically Disordered Proteins" in Scientific Reports, 8 (2018), https://doi.org/10.1038/s41598-018-28815-x ., conv_2065 .