IVS2vec: A tool of Inverse Virtual Screening based on word2vec and deep learning techniques

Zhang, Haiping2; Liao, Linbu2,3; Cai, Yunting1; Hu, Yuhui1; Wang, Hao1

2019-08-15

10.1016/j.ymeth.2019.03.012

METHODS   影响因子和分区

1046-2023

1095-9130

Inverse Virtual Screening is a powerful technique in the early stage of drug discovery process. This technique can provide important clues for biologically active molecules, which is useful in the following researches of durg discovery. In this work, combining with Word2vec, a natural language processing technique, dense fully connected neural network (DFCNN) algorithm is utilized to build up a prediction model. This model is able to perform a binary classification. Based on the query molecule, the input protein candidates can be classified into two subsets. One set is that potential targets with high possibilities to bind with the query molecule and the other one is that the proteins with low possibilities to bind with the query molecule. This model is named as IVS2vec. IVS2vec also can output a score reflecting binding possibility of the association between a protein and a molecule, which is useful to improve efficiency of research. We applied IVS2vec on several databases related to drug development and shown that our model can detect possible therapeutic targets. In addition, our model can identify targets related to adverse drug reactions which is useful to improve medication safety and repurpose drugs. Moreover, IVS2vec can give a very fast speed to perform prediction jobs. It is suitable for processing a large number of compounds in the chemical databases. We also find that IVS2vec has potential capabilities and outperform other state-of-the-art docking tools such as Autodock vina. In this study, IVS2vec brings many convincing results than Autodock vina in the reverse target searching case of Quercetin.

SCI

英语

通讯

Shenzhen Science and Technology Innovation Commission Project[JCYJ20180302174235893]

Biochemistry & Molecular Biology

Biochemical Research Methods ; Biochemistry & Molecular Biology

WOS:000483008800007

ACADEMIC PRESS INC ELSEVIER SCIENCE

BIOLOGY & BIOCHEMISTRY

Web of Science

1.Southern Univ Sci & Technol, Dept Biol, 1088 Xueyuan Rd, Shenzhen 518055, Guangdong, Peoples R China
2.Chinese Acad Sci, Shenzhen Inst Adv Technol, Joint Engn Res Ctr Hlth Big Data Intelligent Anal, Shenzhen 518055, Guangdong, Peoples R China
3.Zhejiang Univ, Coll Software Technol, Hangzhou 315048, Zhejiang, Peoples R China

Zhang, Haiping,Liao, Linbu,Cai, Yunting,et al. IVS2vec: A tool of Inverse Virtual Screening based on word2vec and deep learning techniques[J]. METHODS,2019,166:57-65.

Zhang, Haiping,Liao, Linbu,Cai, Yunting,Hu, Yuhui,&Wang, Hao.(2019).IVS2vec: A tool of Inverse Virtual Screening based on word2vec and deep learning techniques.METHODS,166,57-65.

Zhang, Haiping,et al."IVS2vec: A tool of Inverse Virtual Screening based on word2vec and deep learning techniques".METHODS 166(2019):57-65.