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Prediction of compound-target interactions of natural products using large-scale drug and protein information

Jongsoo Keum, Sunyong Yoo, Doheon Lee, Hojung Nam
2016 BMC Bioinformatics  
Finally, the interactions of compounds from natural products were predicted using the constructed classification models.  ...  Verifying the proteins that are targeted by compounds of natural herbs will be helpful to select natural herb-based drug candidates.  ...  In more recent years, compounds derived from natural products have shown promising effects in drug discovery and drug development.  ... 
doi:10.1186/s12859-016-1081-y pmid:27490208 pmcid:PMC4965709 fatcat:cbzu2k6muzbtdb52r6qmwajyv4

Prediction of Compound-Target Interactions of Natural Products Using Large-scale Drug and Protein Information

Jongsoo Keum, Sunyong Yoo, Hojung Nam
2015 Proceedings of the ACM Ninth International Workshop on Data and Text Mining in Biomedical Informatics - DTMBIO '15  
Finally, the interactions of compounds from natural products were predicted using the constructed classification models.  ...  Verifying the proteins that are targeted by compounds of natural herbs will be helpful to select natural herb-based drug candidates.  ...  In more recent years, compounds derived from natural products have shown promising effects in drug discovery and drug development.  ... 
doi:10.1145/2811163.2811172 dblp:conf/cikm/KeumYN15 fatcat:6k627v4fnjboli2x7ry3kvf7eq

Use of Natural Products as Chemical Library for Drug Discovery and Network Pharmacology

Jiangyong Gu, Yuanshen Gui, Lirong Chen, Gu Yuan, Hui-Zhe Lu, Xiaojie Xu, Dermot Cox
2013 PLoS ONE  
Natural products have vast chemical diversity, good drug-like properties and can interact with multiple cellular target proteins.  ...  indicated that natural products had large quantity of potential lead compounds.  ...  Typically, natural products, especially high-degree compounds, would interact with several target proteins and target protein would concern a lot of diseases.  ... 
doi:10.1371/journal.pone.0062839 pmid:23638153 pmcid:PMC3636197 fatcat:ssnn5elxonbx3nmt4damwie464

In silico target identification of biologically active compounds using an inverse docking simulation

Youngjin Choi
This methodology can be applied in the field of target fishing and toxicity prediction for herbal compounds as well as known drug molecules.  ...  Identification of target protein is an important procedure in the course of drug discovery.  ...  ACKNOWLEDGEMENTS This work was supported by Basic Science Research Program through the National Research Foundation of Korea (NRF) funded by the Ministry of Education, Science and Technology (2010-0004820  ... 
doi:10.5667/tang.2013.0008 fatcat:obc2k7q4ibg53ji3l76fvfz6ha

Identification of drug candidates and repurposing opportunities through compound–target interaction networks

Anna Cichonska, Juho Rousu, Tero Aittokallio
2015 Expert Opinion on Drug Discovery  
Janica Wakkinen and Dr. Simon Anders for many useful discussions about different types of experimental assays and computational models.  ...  [26] are illustrative examples of large-scale binding and functional assays, respectively, both generating kinome-scale compound--target interaction maps.  ...  New compound--target links can be inferred by Regularized Least Squares model using a Kronecker product of constructed drug and target kernels.  ... 
doi:10.1517/17460441.2015.1096926 pmid:26429153 fatcat:vtz37pji6jcnlmcuw6k3v7t3kq

KampoDB, database of predicted targets and functional annotations of natural medicines

Ryusuke Sawada, Michio Iwata, Masahito Umezaki, Yoshihiko Usui, Toshikazu Kobayashi, Takaki Kubono, Shusaku Hayashi, Makoto Kadowaki, Yoshihiro Yamanishi
2018 Scientific Reports  
Potential target proteins of these constituent compounds were predicted by docking simulations and machine learning methods based on large-scale omics data (e.g., genome, proteome, metabolome, interactome  ...  formulas Kampo medicines, constituent herbal drugs, constituent compounds, and target proteins of these constituent compounds.  ...  structures and large-scale chemical-protein interactome data in the framework of chemogenomics.  ... 
doi:10.1038/s41598-018-29516-1 pmid:30046160 pmcid:PMC6060122 fatcat:5lykrwv2ubgyhbx2gb6jqgmvsu

A hybrid approach for hot spot prediction and deep representation of hematological protein – drug interactions

Bipin Nair B.J, Lijo Joy
2018 International Journal of Engineering & Technology  
finally using machine learning algorithm predicting which drug will interact with the help of a hybrid approach.  ...  In our research work we will collect the data of drugs as well as protein regarding hematic diseases, then applying feature extraction as well as classification, predict hot spot and non-hot spot then  ...  The similarity-based approach used to predict the interaction of their compound and sequence similarity of the protein.  ... 
doi:10.14419/ijet.v7i1.9.9752 fatcat:lh34szujqvecpokepx5kw7b774

Prediction of Medicinal Properties Using Mathematical Models and Computation, and Selection of Plant Materials [chapter]

Sanjoy S. Ningthoujam, Anupam D. Talukdar, Satyajit D. Sarker, Lutfun Nahar, Manabendra D. Choudhury
2018 Computational Phytochemistry  
Importance of database-driven information sharing in drug discovery can be demonstrated by large-scale production of taxol ( Fig. 2.8) .  ...  Application of network mapping to a wide array of drugs to protein targets both before and after modelling with chemical drug-ligand interactions helps in prediction of new targets.  ... 
doi:10.1016/b978-0-12-812364-5.00002-x fatcat:3snqntam4jdrnkb7ahnfhd4vo4

Drug-target interaction prediction from chemical, genomic and pharmacological data in an integrated framework

Y. Yamanishi, M. Kotera, M. Kanehisa, S. Goto
2010 Bioinformatics  
We then develop a new method to predict unknown drug-target interactions from chemical, genomic and pharmacological data on a large scale.  ...  Our comprehensively predicted drug-target interaction networks enable us to suggest many potential drug-target interactions and to increase research productivity toward genomic drug discovery.  ...  ACKNOWLEDGEMENTS Computational resources were provided by the Bioinformatics Center, Institute for Chemical Research and the Super Computer Laboratory, Kyoto University.  ... 
doi:10.1093/bioinformatics/btq176 pmid:20529913 pmcid:PMC2881361 fatcat:2gzxu62n6ram7jkqqjysqooiey

CancerHSP: anticancer herbs database of systems pharmacology

Weiyang Tao, Bohui Li, Shuo Gao, Yaofei Bai, Piar Ali Shar, Wenjuan Zhang, Zihu Guo, Ke Sun, Yingxue Fu, Chao Huang, Chunli Zheng, Jiexin Mu (+4 others)
2015 Scientific Reports  
Further, the protein targets of the compounds are predicted by state-of-art methods or collected from literatures.  ...  As a holistic approach, computer-based systems approach integrates large scale experimental studies and computational analyses to provide a mechanistic understanding of drug action across multiple scales  ...  At molecular level, protein targets of the ingredients are obtained through computational predictions and literatures.  ... 
doi:10.1038/srep11481 pmid:26074488 pmcid:PMC4466901 fatcat:mtnaxkbgsbajbmi3qu2cepy4s4

In silico docking and drug design of herbal ligands for anticancer property

Sandeep Waghulde, MK Kale, VR Patil
2018 Journal of Pharmacognosy and Phytochemistry  
It helps to give the existing information to model disease pathway and identifies precise targets of the selected drugs.  ...  Here, we consider the significance of available databases of medicinal plants and chemo and bioinformatics tools for in silico drug discovery beyond the traditional use of medicines.  ...  Introduction Natural products have been used in folk medicine for thousands of years.  ... 
doi:10.22271/phyto.2018.v7.isp6.1.19 fatcat:t5ftebge4jdmlayqll4bgjvb4a

Chemical ligands, genomics and drug discovery

George R Lenz, Huw M Nash, Satish Jindal
2000 Drug Discovery Today  
This approach enables the use of a wide variety of synthetic reactions, together with multiple-connection chemistries that yield large compound libraries based on a complex natural product scaffold.  ...  leads for most targets of interest (a 'universal' library in the absolute sense) • Prediction of molecular binding to protein surfaces as yet unexplored (e.g. protein-protein interactions and novel genomic  ... 
doi:10.1016/s1359-6446(00)01468-9 pmid:10729820 fatcat:adajciynejctnfd2ko6taeosda

A Brief Review of Machine Learning-Based Bioactive Compound Research

Jihye Park, Bo Ram Beck, Hoo Hyun Kim, Sangbum Lee, Keunsoo Kang
2022 Applied Sciences  
, such as those in natural products (NPs).  ...  This review introduces how machine learning approaches can be used for the identification and evaluation of bioactive compounds.  ...  applications, which predict target proteins of a given compound.  ... 
doi:10.3390/app12062906 fatcat:5ootoacaxzeh7etmwk3gwvokci

Quantitative and systems pharmacology 4. Network-based analysis of drug pleiotropy on coronary artery disease

Jiansong Fang, Chuipu Cai, Yanting Chai, Jingwei Zhou, Yujie Huang, Li Gao, Qi Wang, Feixiong Cheng
2019 European Journal of Medicinal Chemistry  
The use of genomics and systems biology approaches to inform drug discovery and development have offered the possibilities for new target identification and in silico drug repurposing.  ...  Specifically, we build in silico models by integrating known drug-target interactions, CAD genes derived from the genetic and genomic studies, and the human protein-protein interactome.  ...  and Open Tending Project for the Construction of High-Level University (A1-AFD018171Z11027) and the National Heart, Lung, and Blood Institute of the National Institutes of Health under Award Number K99HL138272  ... 
doi:10.1016/j.ejmech.2018.10.020 pmid:30359818 pmcid:PMC6263141 fatcat:77dak7mdm5bkxjv6cfnnjpwvum

In silico approach in reveal traditional medicine plants pharmacological material basis

Fan Yi, Li Li, Li-jia Xu, Hong Meng, Yin-mao Dong, Hai-bo Liu, Pei-gen Xiao
2018 Chinese Medicine  
In the process of new drug discovery, the application of virtual screening and network pharmacology can enrich active compounds among the candidates and adequately indicate the mechanism of action of medicinal  ...  In recent years, studies of traditional medicinal plants have gradually increased worldwide because the natural sources and variety of such plants allow them to complement modern pharmacological approaches  ...  Jun Xu (Research Centerfor Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou) for his valuable suggestions.  ... 
doi:10.1186/s13020-018-0190-0 pmid:29946351 pmcid:PMC6006786 fatcat:btf7nau2wbeyrkrgxvuvvkn26i
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