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Prediction of compound-target interactions of natural products using large-scale drug and protein information
2016
BMC Bioinformatics
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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
2015
Proceedings of the ACM Ninth International Workshop on Data and Text Mining in Biomedical Informatics - DTMBIO '15
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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
2013
PLoS ONE
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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
2013
TANG [HUMANITAS MEDICINE]
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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
2015
Expert Opinion on Drug Discovery
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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
2018
Scientific Reports
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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
2018
International Journal of Engineering & Technology
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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]
2018
Computational Phytochemistry
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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
2010
Bioinformatics
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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
2015
Scientific Reports
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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
2018
Journal of Pharmacognosy and Phytochemistry
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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
2000
Drug Discovery Today
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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
2022
Applied Sciences
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, 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
2019
European Journal of Medicinal Chemistry
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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
2018
Chinese Medicine
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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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