Combining Network-based and Matrix Factorization to Predict Novel Drug-target Interactions: A Case Study Using the Brazilian Natural Chemical Database

矩阵分解 计算机科学 化学信息学 水准点(测量) 药物发现 因式分解 数据挖掘 机器学习 人工智能 生物信息学 算法 生物 特征向量 物理 大地测量学 量子力学 地理
作者
Ronald Sodré Martins,Marcelo Ferreira da Costa Gomes,Ernesto R. Caffarena
出处
期刊:Current Bioinformatics [Bentham Science Publishers]
卷期号:17 (9): 793-803 被引量:3
标识
DOI:10.2174/1574893617666220820105258
摘要

Background: Chemogenomic techniques use mathematical calculations to predict new DrugTarget Interactions (DTIs) based on drugs' chemical and biological information and pharmacological targets. Compared to other structure-based computational methods, they are faster and less expensive. Network analysis and matrix factorization are two practical chemogenomic approaches for predicting DTIs from many drugs and targets. However, despite the extensive literature introducing various chemogenomic techniques and methodologies, there is no consensus for predicting interactions using a drug or a target, a set of drugs, and a dataset of known interactions Methods: This study predicted novel DTIs from a limited collection of drugs using a heterogeneous ensemble based on network and matrix factorization techniques. We examined three network-based approaches and two matrix factorization-based methods on benchmark datasets. Then, we used one network approach and one matrix factorization technique on a small collection of Brazilian plant-derived pharmaceuticals. Results: We have discovered two novel DTIs and compared them to the Therapeutic Target Database to detect linked disorders, such as breast cancer, prostate cancer, and Cushing syndrome, with two drugs (Quercetin and Luteolin) originating from Brazilian plants. Conclusion: The suggested approach allows assessing the performance of approaches only based on their sensitivity, independent of their unfavorable interactions. Findings imply that integrating network and matrix factorization results might be a helpful technique in bioinformatics investigations involving the development of novel medicines from a limited range of drugs.
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