PredictONCO: a web tool supporting decision-making in precision oncology by extending the bioinformatics predictions with advanced computing and machine learning

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Authors

ŠTOURAČ Jan BORKO Simeon KHAN Rayyan Tariq POKORNÁ Petra DOBIÁŠ Adam PLANAS IGLESIAS Joan MAZURENKO Stanislav RANGEL PAMPLONA PIZARRO PINTO José Gaspar SZOTKOWSKÁ Veronika ŠTĚRBA Jaroslav SLABÝ Ondřej DAMBORSKÝ Jiří BEDNÁŘ David

Year of publication 2024
Type Article in Periodical
Magazine / Source Briefings in Bioinformatics
MU Faculty or unit

Faculty of Science

Citation
Web https://academic.oup.com/bib/article/25/1/bbad441/7463300?login=true
Doi http://dx.doi.org/10.1093/bib/bbad441
Keywords cancer; oncology; personalized medicine; single-nucleotide polymorphism; targeted therapy
Attached files
Description PredictONCO 1.0 is a unique web server that analyzes effects of mutations on proteins frequently altered in various cancer types. The server can assess the impact of mutations on the protein sequential and structural properties and apply a virtual screening to identify potential inhibitors that could be used as a highly individualized therapeutic approach, possibly based on the drug repurposing. PredictONCO integrates predictive algorithms and state-of-the-art computational tools combined with information from established databases. The user interface was carefully designed for the target specialists in precision oncology, molecular pathology, clinical genetics and clinical sciences. The tool summarizes the effect of the mutation on protein stability and function and currently covers 44 common oncological targets. The binding affinities of Food and Drug Administration/ European Medicines Agency -approved drugs with the wild-type and mutant proteins are calculated to facilitate treatment decisions. The reliability of predictions was confirmed against 108 clinically validated mutations. The server provides a fast and compact output, ideal for the often time-sensitive decision-making process in oncology. Three use cases of missense mutations, (i) K22A in cyclin-dependent kinase 4 identified in melanoma, (ii) E1197K mutation in anaplastic lymphoma kinase 4 identified in lung carcinoma and (iii) V765A mutation in epidermal growth factor receptor in a patient with congenital mismatch repair deficiency highlight how the tool can increase levels of confidence regarding the pathogenicity of the variants and identify the most effective inhibitors. The server is available at https://loschmidt.chemi.muni.cz/predictonco.
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