Efficient multi-task chemogenomics for drug specificity prediction.
PLoS One
; 13(10): e0204999, 2018.
Article
em En
| MEDLINE
| ID: mdl-30286165
ABSTRACT
Adverse drug reactions, also called side effects, range from mild to fatal clinical events and significantly affect the quality of care. Among other causes, side effects occur when drugs bind to proteins other than their intended target. As experimentally testing drug specificity against the entire proteome is out of reach, we investigate the application of chemogenomics approaches. We formulate the study of drug specificity as a problem of predicting interactions between drugs and proteins at the proteome scale. We build several benchmark datasets, and propose NN-MT, a multi-task Support Vector Machine (SVM) algorithm that is trained on a limited number of data points, in order to solve the computational issues or proteome-wide SVM for chemogenomics. We compare NN-MT to different state-of-the-art methods, and show that its prediction performances are similar or better, at an efficient calculation cost. Compared to its competitors, the proposed method is particularly efficient to predict (protein, ligand) interactions in the difficult double-orphan case, i.e. when no interactions are previously known for the protein nor for the ligand. The NN-MT algorithm appears to be a good default method providing state-of-the-art or better performances, in a wide range of prediction scenario that are considered in the present study proteome-wide prediction, protein family prediction, test (protein, ligand) pairs dissimilar to pairs in the train set, and orphan cases.
Texto completo:
1
Coleções:
01-internacional
Base de dados:
MEDLINE
Assunto principal:
Preparações Farmacêuticas
/
Genômica
Tipo de estudo:
Diagnostic_studies
/
Prognostic_studies
/
Risk_factors_studies
Idioma:
En
Revista:
PLoS One
Assunto da revista:
CIENCIA
/
MEDICINA
Ano de publicação:
2018
Tipo de documento:
Article
País de afiliação:
França
País de publicação:
EEUU
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ESTADOS UNIDOS
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ESTADOS UNIDOS DA AMERICA
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EUA
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UNITED STATES
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UNITED STATES OF AMERICA
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US
/
USA