Table 1.
Comparisons of current natural product databases
| Database | Data source | Advantage | Disadvantage | Web service | Web link |
|---|---|---|---|---|---|
| NPACT | Chinese herb | Experimentally determined in vitro and in vivo biological activity | Only 1574 entries |
Similarity search Java‐based Molecular Editor tool draw structure to be searched in the database |
http://crdd.osdd.net/raghava/npact/ |
| Database specified for cancer therapy | Online submission | ||||
| HIT | Chinese herbs | Protein targets related to herbs are included | All information is covered by other DB except the key feature | Text mining and curation(scan abstracts) | http://lifecenter.sgst.cn/hit/ |
| Compound similarity search (Tanimoto coefficient) | |||||
| AfroDb | African medicinal plants | Covers the entire continent of Africa | Data from traditional healers have no words based on | MOE software generated 3D structure | N/A |
| Classified with ‘Drug‐like’, ‘lead‐like’ and ‘fragment‐like’ subsets | |||||
| CVDHD | Herbs(FDA approved drugs derived from natural products) | Contains integrated medicinal herbs, natural products, CVD‐related target proteins, docking results, diseases and clinical biomarkers | \ | Available for downloading docking scores of all molecules and single target proteins | http://pkuxxj.pku.edu.cn/ |
| API for Cytoscape is integrated | |||||
| CamMedNP | Plants | Plant sources ware collected from geographical collection sites | \ | Generate 3D structures using MOE and energyz MMFF94 | N/A |
| NuBBE | Brazilian plants | ‘Rule of five’ drug‐likeness evaluate compounds were grouped by acquisition source | No functions or diseases related to these compounds | Molecular drawing interface WebME | http://nubbe.iq.unesp.br/nubbeDB.html |
| Substructure search engine:CDK | |||||
| 3DMET | Natural product | 3D structure display | Short for drug features of compounds | JME molecular editor applet for a graphical input | http://www.3dmet.dna.affrc.go.jp/ |
| TTD | drug data | data sources of interaction with targets comparison with succeed drugs | Absence of interactions of targets | N/A | http://bidd.nus.edu.sg/group/ttd/ttd.asp |
| SuperToxic | Toxic compounds | Be used to evaluate the risk of use for compounds | Mechanisms of toxin is absent | MyChem/OpenBabel chemical function | http://bioinformatics.charite.de/supertoxic |
| MarvinSketch drawing and uploading function | |||||
| JMol inspection compound | |||||
| SuperNatural | Various sources | Large and comprehensive | \ | ChemDoodle integrated for structure drawing | http://bioinformatics.charite.de/supernatural |
| Chemistry development kit calculate fingerprint | |||||
| Tanimoto coefficient similarity measure | |||||
| TCMID | Chinese herb | Having the largest data set for related field | Unable to display network on the web page | Self‐developed network‐display tools which can show Herb–disease network, Herbal ingredients—targets interaction network, Herbal ingredient–target–disease–drug network | http://www.megabionet.org/tcmid/ |
| Compounds and disease‐specific functions interaction networks bridge the gap between TCM and modern western medicine | |||||
| Chem‐TCM | Chinese herb | \ | \ | http://www.chemtcm.com/ | |
| CEMTDD | Chinese ethnic minorities’ herb | The most complete database structure among database above include herb‐compound, compound‐target, herb‐disease | Disease cannot be used as the keyword for query | Cytoscape Web integrated for network displaying | http://www.cemtdd.com/ |
| TCMDB@Taiwan | Chinese herbs | Possess the largest traditional Chinese medicine data source | Only shows the relation between herb, ingredients and compound | ChemAxon: user can draw compound structure and query | http://tcm.cmu.edu.tw/ |
| Users can download the structure of the molecule in cdx (2D) or mol2 (3D) |