The Methodological Trends of Traditional Herbal Medicine Employing Network Pharmacology
Abstract
:1. Introduction
2. Materials and Methods
2.1. Search Strategy
2.2. Inclusion Criteria
2.3. Study Selection and Data Extraction
2.4. Categorizing Drug-Target Interaction Methods
2.5. Construction of the Co-Author Network and Affiliation Network
3. Results
3.1. Description of the Search
3.2. Methodological Trends in Constructing the Herb-Compound Network
3.3. Methodological Trends for Constructing Compound-Target Networks
3.4. Methodological Trends for Target Interpretation
3.5. Combinatorial Patterns in Methodologies of THM-NP Studies
3.6. Co-Author Network and Affiliation Network
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Conflicts of Interest
References
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---|---|---|---|---|---|---|
H-C | C-T | TI | ||||
TCMSP | ○ | ○ | ○ | A system of pharmacology platforms that provide information about ingredients, ADME-related properties, targets, and diseases of herbal medicines. | http://lsp.nwu.edu.cn/tcmsp.php | 24735618 [26] |
TCMID | ○ | ○ | ○ | An integrative database which stores the information of herbs, herbal compounds, targets, and their related information from different resources and through text-mining method | http://www.megabionet.org/tcmid/ | 23203875 [17] |
TCM Databasetaiwan | ○ | A database that includes the information of molecular properties and substructures, TCM ingredients with their 2D and 3D structures. | http://tcm.cmu.edu.tw/ | 21253603 [27] | ||
PharmMapper | ○ | A web server for potential drug target identification by reversed pharmacophore matching the query compound against an in-house pharmacophore model database | http://lilab.ecust.edu.cn/pharmmapper/ | 20430828 [28] | ||
STITCH | ○ | A database that integrates disparate data sources of interactions between proteins and small molecules | http://stitch.embl.de/ | 18084021 [29] | ||
TTD | ○ | ○ | A database that provides information about the therapeutic targets in the literature, targeted disease condition, and the corresponding drugs/ligands directed at each of these targets. | http://xin.cz3.nus.edu.sg/group/ttd/ttd.asp | 11752352 [30] | |
SEA | ○ | A computational tool that relates proteins and chemicals based on the set-wise chemical similarity among their ligands. | http://sea.bkslab.org/ | 17287757 [31] | ||
HIT | ○ | ○ | A comprehensive and fully curated database for herbal ingredients with protein target information | http://lifecenter.sgst.cn/hit/ | 21097881 [32] | |
Drugbank | ○ | ○ | A unique bioinformatics and cheminformatics resource that combines detailed drug data with comprehensive drug target information | https://www.drugbank.ca/ | 16381955 [33] | |
KEGG | ○ | A database resource for understanding high-level functions and utilities of the biological system from molecular-level information | https://www.genome.jp/kegg/ | 9847135 [34] | ||
Gene ontology | ○ | The world’s largest source of information on the functions of genes | http://geneontology.org/ | 18792943 [35] | ||
OMIM | ○ | A comprehensive and authoritative compendium of human genes and genetic phenotypes | https://www.omim.org/ | 11752252 [36] | ||
PharmGkb | ○ | A database for the aggregation, curation, integration, and dissemination of knowledge regarding the impact of human genetic variation on drug response | https://www.pharmgkb.org/ | 11752281 [37] | ||
Genecards | ○ | A searchable and integrated database of human genes that provides concise genomic related information, on all known and predicted human genes. | https://www.genecards.org/ | 12424129 [38] |
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Lee, W.-Y.; Lee, C.-Y.; Kim, Y.-S.; Kim, C.-E. The Methodological Trends of Traditional Herbal Medicine Employing Network Pharmacology. Biomolecules 2019, 9, 362. https://doi.org/10.3390/biom9080362
Lee W-Y, Lee C-Y, Kim Y-S, Kim C-E. The Methodological Trends of Traditional Herbal Medicine Employing Network Pharmacology. Biomolecules. 2019; 9(8):362. https://doi.org/10.3390/biom9080362
Chicago/Turabian StyleLee, Won-Yung, Choong-Yeol Lee, Youn-Sub Kim, and Chang-Eop Kim. 2019. "The Methodological Trends of Traditional Herbal Medicine Employing Network Pharmacology" Biomolecules 9, no. 8: 362. https://doi.org/10.3390/biom9080362
APA StyleLee, W. -Y., Lee, C. -Y., Kim, Y. -S., & Kim, C. -E. (2019). The Methodological Trends of Traditional Herbal Medicine Employing Network Pharmacology. Biomolecules, 9(8), 362. https://doi.org/10.3390/biom9080362