Review on natural products databases: where to find data in 2020

Sorokina, Maria; Steinbeck, Christoph

doi:10.1186/s13321-020-00424-9

Journal of Cheminformatics

Table 1 List of Natural Products databases cited in scientific literature since 2000. The list is ordered by alphabetical order of the database names, and contains, when available, extended metadata

From: Review on natural products databases: where to find data in 2020

Database name	NP type	Estimated size (number of NP molecules with correct structures)	Number of unique molecules in COCONUT	Percentage of molecules with stereochemistry	Is open (data can be freely browsed)	Recquires a registration	Is maintained (2019)	Is updated
3DMET	Generalistic	18248	x	x	Yes	No	Yes	Yes
AfroCancer	tm, plants, africa	390	365	69.76%	Yes	NA	NA	No
AfroDB	tm, plants, africa	954	874	70.73%	Yes	No	No	No
AfroMalariaDB	tm, plants, africa	265	252	70.93%	yes	NA	NA	no
Afrotryp	tm, plants, drug-like, africa	321	x	x	Unknown	NA	NA	No
Alkamid database	plants, structure	300	x	x	yes	no	yes	no
Ambinter-Greenpharma natural compound library (GPNCL)	Generalistic, industrial	> 150,000	x	x	No	Yes	Yes	Yes
AnalytiCon Discovery MEGx	bacteria, plants, industrial	5147	4908	44.15%	Yes	Yes	Yes	Yes
AntiBase	drug-like	> 40,000	x	x	No	No	Yes	No
AntiMarin	Marine, drug-like	> 60,000	x	x	No	Unknown	No	No
ATBD (Animal Toxin Database)	toxins	1000	x	x	Unknown	Unknown	No	Unknown
Ayurveda	tm, asia	950	x	x	No	Yes	Yes	Unknown
Berdy’s Bioactive Natural Products Database	Generalistic	x	x	x	No	Unknown	No	No
BiGG	Metabolites	7339	x	x	Yes	No	Yes	Yes
Binding DB	Drug-like	x	x	x	Yes	No	Yes	No
BIOFAQUIM	Plant, fungi, america	420	400	59.05%	Yes	No	Yes	Yes
BioPhytMol	Drug-like, plants, asia	633	x	x	Yes	No	Yes	Yes
BitterDB	Food	654	631	14.17%	Yes	No	Yes	Yes
BRENDA	Metabolites	x	x	x	Yes	No	Yes	Yes
CamMedNP	tm, plants, africa	> 2500	x	x	Yes, but proprietary format	No	NA	No
Carotenoids Database	Structure	1174	991	57.63%	Yes	No	Yes	Yes
CAS registry/SciFinder	Chemicals	> 300,000	x	x	No	Yes	Yes	Yes
CEMTDD - Chinese Ethnic Minority Traditional Drug Database	tm, plants, asia	4060	x	x	Yes	No	Yes	No
CHDD (Chinese Traditional Medicinal Herbs database)	tm, plants, asia	> 30,000	x	x	Unknown	Unknown	No	No
ChEBI	Chemicals	15,736	14,621	71.33%	Yes	No	Yes	Yes
Chem-TCM	Plants, tm, asia	> 12,000	x	x	No	Yes	Yes	No
ChemBank	Chemicals	x	x	x	Yes	No	No	No
ChEMBL	Chemicals	1899	1581	91.59%	Yes	No	Yes	Yes
ChemBridge diversity datasets	Generalistic, industrial	x	x	x	No	Yes	No	No
ChemDB	Plants, asia	> 1000	x	x	Unknown	Unknown	No	No
ChemIDplus	Drug-like, toxins	9042	x	x	Yes	No	Yes	Yes
ChemSpider	Chemicals	9732	9029	29.50%	Yes	No	Yes	Yes
CHMIS-C	Plants, tm, asia	> 8000	x	x	Yes	No	No	No
CMAUP	Plants	47,645	20,873	72.37%	Yes	No	Yes	No
CNPD (Chinese Natural Products Database)	Generalistic	> 57,000	x	x	Unknown	Unknown	No	No
ConMedNP	Plants, tm, africa	3118	2504	69.59%	Yes	NA	NA	NA
CSLS/NCI (Chemical Structure Lookup Service)	Metabolites	x	x	x	Yes	No	Yes	No
Database of Indonesian Medicinal Plants	Plants, tm, asia	6776	x	x	Yes	No	Yes	No
DESMSCI (Dragon Exploration System on Marin Sponge Compounds Interactions)	Marine	x	x	x	Yes	No	No	No
DFC (Dictionary of Food COmpounds)	Food	> 41,000	x	x	No	Yes	Yes	Yes
DMNP (Dictionary of Marine Natural Products)	Marine	> 30,000	x	x	No	Yes	Yes	Yes
DNP (Dictionary of Natural Products) by Chapman and Hall (also known as CHEMnetBase)	Generalistic	> 230,000	x	x	No	Yes	Yes	Yes
Drugbank NPs	Drug-like	2617	2617	51.32%	Yes	No	Yes	Yes
eBasis	Food		x	x	No	Yes	Yes	Yes
ETCM (Encyclopedia of Traditional Chinese Medicine)	tm, asia	7274	x	x	Yes	No	Yes	Yes
ETM-DB	tm, plants, africa	1795	1653	40.46%	Yes	No	Yes	Yes
FooDB	Food	24,215	22,223	36.01%	Yes	No	Yes	Yes
GNPS	Dereplication	7619	6708	31.08%	Yes	No	Yes	Yes
HIM (Herbal Ingridients in-vivo Metabolism database)	Drug-like, tm, plants	1261	962	41.62%	Yes	No	No	No
HIT (Herbal Ingridients Targets)	Drug-like, tm, plants	524	472	44.03%	Yes	No	No	No
HMDB	Dereplication	x	x	x	Yes	No	Yes	Yes
IMPPAT	tm, plants, asia	9596	x	x	Yes	No	Yes	Yes
InflamNat	Drug-like	552	536	63.75%	Yes	NA	NA	NA
Indofine Chemical Company Inc. natural products	Generalistic, industrial	56	46	51.06%	Yes	No	Yes
InPACdb	Drug-like, plants, asia	124	121	62.10%	Yes	No	No	No
InterBioScreen Ltd (IBS)	Generalistic, industrial	68,350	67,292	42.17%	Yes	Yes	Yes	Yes
iSMART	tm, plants, asia	x	x	x	Yes	No	Yes	Yes
KEGG	Metabolites	x	x	x	Yes	No	Yes	Yes
KNApSaCK	Plants	10,265	8887	74.76%	Yes	No	Yes	Yes
Lichen Database	Fungi	249	156	26.67%	Yes	No	Yes	No
LOPAC1280 by Merck	Drug-like	1280	x	x	No	Yes	Yes	Yes
MAPS database	Plants, asia	x	x	x	Unknown	Unknown	No	No
Marine Compound Database (MCDB)	Marine	182	x	x	Yes	No	No	No
Marine Natural Product Database (MNPD)	Marine	6000	x	x	Yes	No	No	No
MarineLit	Marine	> 29,000	x	x	No	Yes	Yes	Yes
Massbank	Dereplication	x	x	x	Yes	No	Yes	Yes
MedPServer	Plants, tm, asia, drug-like	1124	x	x	Yes	No	Yes	Yes
MetaCyc	Metabolites	x	x	x	Yes	No	Yes	Yes
METLIN	Dereplication	x	x	x	Yes	Yes	Yes	Yes
Mitishamba database	Plants, africa	1102	1010	23.84%	Yes	No	Yes	No
NADI	tm, plants	3000	x	x	No	Yes	Yes	Unknown
NANPDB	Plants, africa	6832	3913	75.02%	Yes	No	Yes	Yes
NaprAlert	Generalistic	> 15,5000	x	x	No	Yes	Yes	Yes
NAPROC-13	Dereplication	> 18,000	x	x	Yes	No	Yes	Yes
NCI DTP data	Drug-like	418	404	36.76%	Yes	No	Yes	No
NeMedPlant	tm, plants, asia	100	x	x	Yes	No	Yes	No
NIST	Chemicals	x	x	x	No	No	Yes	Yes
NMRDATA	Dereplication	x	x	x	Unknown	Yes	Yes	Yes
NMRShiftDB	Dereplication	1875	x	x	Yes	No	Yes	Yes
Novel Antibiotics database	Drug-like	5430	x	x	Yes	No	Yes	No
NPACT	Plants, drug-like	1573	1453	77.53%	Yes	No	Yes	Yes
NPASS	Plants, bacteria, metazoa, fungi	30,858	27,479	71.58%	Yes	No	Yes	Yes
NPAtlas	Bacteria, fungi	20,035	18,959	67.03%	Yes	No	Yes	Yes
NPCARE	Plants, marine, bacteria, drug-like	1370	1364	0%	Yes	No	Yes (server fails sometimes)	Yes
NPEdia	Generalistic	18,016	16,190	51.83%	Yes	No	Yes	No
NPL (library)	Plants, drug-like	814	x	x	No	NA	NA	NA
NuBBEDB	Plants, insects, america	2215	2022	58.34%	Yes	No	Yes
Open Source Malaria	Drug-like	842	x	x	Yes	No	Yes	Yes
p-ANAPL (Pan-African Natural Product Library )	Plants, africa	538	467	0.86%	Yes	No	NA
PAMDB	Metabolites, bacteria	x	x	x	Yes	No	Yes	Yes
Phenol-explorer	Food	862	681	51.79%	Yes	No	Yes	NA
Phytochemica	Plants, tm, asia	571	x	x	Yes	No	No	No
PhytoHub	Food, plants	1200	x	x	Yes	No	Yes	Yes
Pi Chemicals System Natural Products	Generalistic, industrial	405	x	x	Yes	No	Yes	Yes
Prestwick	Plants, industrial	320	x	x	No	Yes	Yes	Yes
ProCarDB	Structure, bacteria	304	x	x	Yes	No	Yes	No
PubChem	Chemicals	3529	2835	2.33%	Yes	No	Yes	Yes
REAXYS	Chemicals	> 220,000	x	x	No	Yes	Yes
ReSpect	Dereplication	4767	711	0%	Yes	No	Yes	No
SANCDB	Plants, africa	623	592	82.28%	Yes	No	Yes	Yes
Seaweed Metabolite Database (SWMD)	Marine	1110	423	78.53%	Yes	No	Yes	No
Specs Natural Products	Generalistic, industrial	745	745	53.02%	Yes	Yes	Yes	No
Spektraris NMR	Dereplication	248	242	91.53%	Yes	No	Yes	No
StreptomeDB	Bacteria	6415	3610	56.41%	Yes	No	Yes	No
Super Natural II	Generalistic	320,670	235,436	83.55%	Yes	No	Yes	No
Super Scent	Other	2100	x	x	Yes	No	Yes	No
Super Sweet	Food, metabolites	15,000	x	x	Yes	No	Yes	No
TargetMol Natural Compound Library	Generalistic, industrial	1680	x	x	No	Yes	Yes	Yes
TC-MC	tm, asia, plants	> 20,000	x	x	Yes	No	Yes	Yes
TCMDB@Taiwan	tm, asia, plants	58,351	50,891	90.38%	Yes	No	Yes (server fails sometimes)	Yes
TCMID	tm, asia, plants	12,549	10,572	0%	Yes	No	Yes	No
TCMSP	tm, asia, plants	29,384	x	x	Yes	No	No	No
TIM	tm, asia, plants	1829	x	x	No	Unknown	No	No
TIPdb	Asia, plants, drug-like	8656	7752	77.10%	Yes	No	Yes	No
TMDB	Plants, metabolites	1393	x	x	Yes	No	No	No
TPPT	Plants, toxins, europe	1583	1486	76.84%	Yes	No	Yes	No
TriForC	Plants	266	x	x	Yes	No	Yes	No
UEFS	Plants, america	503	481	68.93%	Yes	No	No	No
UNPD (Universal Natural Products Database)	Generalistic	213,100	156,984	12.62%	Yes	No	No	No
VIETHERB	Plants, asia	10,887	x	x	Yes	Unknown	No	No
Yeast Metabolome Database	Metabolites, dereplication	16,042	x	x	Yes	No	Yes	Yes
YaTCM	tm, asia, plants	47,696	x	x	Yes	No	Yes	Yes
ZINC natural products catalogue	Generalistic	85,198	673,36	90.49%	Yes	No	Yes	Yes

Database name	NP type	Estimated size (number of NP molecules with correct structures)	Is commercial	Molecule structures easily retrievable (download link, data packed in one file, bulk download option)	Has extensive metadata (organism, tissue, geo info, …)	Has cross-refs	Most recent publication (citation)	Most recent publication (DOI)
3DMET	Generalistic	18248	No	No	No	Yes	Maeda MH, Kondo K. Three-dimensional structure database of natural metabolites (3DMET): a novel database of curated 3D structures. J Chem Inf Model. 2013 Mar 25;53(3):527–33. https://doi.org/10.1021/ci300309k. Epub 2013 Mar 7. PubMed PMID: 23293959.	https://doi.org/10.1021/ci300309k
AfroCancer	tm, plants, africa	390	No	NA	No	No	Fidele Ntie-Kang, Justina Ngozi Nwodo, Akachukwu Ibezim, Conrad Veranso Simoben, Berin Karaman, Valery Fuh Ngwa, Wolfgang Sippl, Michael Umale Adikwu, Luc Meva’a Mbaze, “Molecular Modeling of Potential Anticancer Agents from African Medicinal Plants”, J. Chem. Inf. Model.20145492433-2450	https://doi.org/10.1021/ci5003697
AfroDB	tm, plants, africa	954	No	Yes	No	No	Ntie-Kang F, Zofou D, Babiaka SB, Meudom R, Scharfe M, Lifongo LL, et al. (2013) AfroDb: A Select Highly Potent and Diverse Natural Product Library from African Medicinal Plants. PLoS ONE 8(10): e78085.	https://doi.org/10.1371/journal.pone.0078085
AfroMalariaDB	tm, plants, africa	265	no	NA	no	no	Onguéné, P.A., Ntie-Kang, F., Mbah, J.A. et al. “The potential of anti-malarial compounds derived from African medicinal plants, part III: an in silico evaluation of drug metabolism and pharmacokinetics profiling”, Org Med Chem Lett (2014) 4: 6.	https://doi.org/10.1186/s13588-014-0006-x
Afrotryp	tm, plants, drug-like, africa	321	No	NA	Unknown	Unknown	Ibezim, A., Debnath, B., Ntie-Kang, F. et al. “Binding of anti-Trypanosoma natural products from African flora against selected drug targets: a docking study” Med Chem Res (2017) 26: 562. https://doi.org/10.1007/s00044-016-1764-y	https://doi.org/10.1007/s00044-016-1764-y
Alkamid database	plants, structure	300	no	no	yes	no	Boonen, J., Bronselaer, A., Nielandt, J., Veryser, L. De Tré, G., De Spiegeleer, B., 2012. Alkamid database: Chemistry, occurrence and functionality of plant N-alkylamides. Journal of Ethnopharmacology 2012; 142(3): 563–590	https://doi.org/10.1016/j.jep.2012.05.038
Ambinter-Greenpharma natural compound library (GPNCL)	Generalistic, industrial	> 150,000	Yes	No	Unknown	Unknown	x	x
AnalytiCon Discovery MEGx	bacteria, plants, industrial	5147	No	Yes	No	No	x	x
AntiBase	drug-like	> 40,000	Yes	Yes	Unknown	Unknown	Laatsch H (2012) Antibase Version 4.0—The natural compound identifier. Wiley-VCH Verlag GmbH & Co. KGaA	x
AntiMarin	Marine, drug-like	> 60,000	Yes	Unknown	Unknown	Unknown	Blunt, J., Munro, M. & Laatsch, H. Antimarin database. University of Canterbury; Christchurch, New Zealand: University of Gottingen; Gottingen, Germany, (2007).	x
ATBD (Animal Toxin Database)	toxins	1000	No	Unknown	Unknown	Unknown	He QY, He QZ, Deng XC, et al. ATDB: a uni-database platform for animal toxins. Nucleic Acids Res. 2008;36(Database issue):D293–D297. https://doi.org/10.1093/nar/gkm832	https://doi.org/10.1093/nar/gkm832
Ayurveda	tm, asia	950	Unknown	Unknown	Unknown	Unknown	Lagunin AA, Druzhilovsky DS, Rudik AV, Filimonov DA, Gawande D, Suresh K, Goel R, Poroikov VV. [Computer evaluation of hidden potential of phytochemicals of medicinal plants of the traditional Indian ayurvedic medicine]. Biomed Khim. 2015 Mar-Apr;61(2):286–97. https://doi.org/10.18097/pbmc20156102286. Russian. PubMed PMID:25978395.	https://doi.org/10.18097/PBMC20156102286
Berdy’s Bioactive Natural Products Database	Generalistic	x	Yes	Unknown	Unknown	Unknown	Berdy J., Kertesz M. (1989) Bioactive natural products database: an aid for natural products identification. In: Collier H.R. (eds) Chemical Information. Springer, Berlin, Heidelberg	https://doi.org/10.1007/978-3-642-75165-3_23
BiGG	Metabolites	7339	No	NA	Yes	Yes	King ZA, Lu JS, Dräger A, Miller PC, Federowicz S, Lerman JA, Ebrahim A, Palsson BO, and Lewis NE. BiGG Models: A platform for integrating, standardizing, and sharing genome-scale models (2016) Nucleic Acids Research 44(D1):D515-D522.	https://doi.org/10.1093/nar/gkv1049
Binding DB	Drug-like	x	No	Yes	Yes	Yes	Gilson MK, Liu T, Baitaluk M, Nicola G, Hwang L, Chong J. BindingDB in 2015: A public database for medicinal chemistry, computational chemistry and systems pharmacology. Nucleic Acids Res. 2016;44(D1):D1045–D1053.	https://doi.org/10.1093/nar/gkv1072
BIOFAQUIM	Plant, fungi, america	420	No	Yes	Yes	No	Pilón-Jiménez, B.A.; Saldívar-González, F.I.; Díaz-Eufracio, B.I.; Medina-Franco, J.L. BIOFACQUIM: A Mexican Compound Database of Natural Products. Biomolecules 2019, 9, 31	https://doi.org/10.3390/biom9010031
BioPhytMol	Drug-like, plants, asia	633	No	No	Yes	No	Sharma A, Dutta P, Sharma M, Rajput NK, Dodiya B, Georrge JJ, Kholia T; OSDD Consortium, Bhardwaj A. BioPhytMol: a drug discovery community resource on anti-mycobacterial phytomolecules and plant extracts. J Cheminform. 2014 Oct 11;6(1):46. eCollection 2014 Dec. PubMed PMID: 25360160; PubMed Central PMCID: PMC4206768.	https://doi.org/10.1186/s13321-014-0046-2
BitterDB	Food	654	No	No	Yes	Yes	Ayana Dagan Wiener, Antonella Di Pizio, Ido Nissim, Malkeet Singh Bahia; Nitzan Dubovski, Eitan Margulis, Masha Y. Niv. BitterDB: Taste ligands and receptors database in 2019. Nucleic Acids Res 2019: gky974.	https://doi.org/10.1093/nar/gky974
BRENDA	Metabolites	x	No	Yes	Yes	Yes	Jeske L, Placzek S, Schomburg I, Chang A, Schomburg D. BRENDA in 2019: a European ELIXIR core data resource. Nucleic Acids Res. 2019;47(D1):D542–D549. doi:10.1093/nar/gky1048	https://doi.org/10.1093/nar/gky1048
CamMedNP	tm, plants, africa	> 2500	No	Yes, but proprietary format (MDB readable by MOE)	Unknown	Unknown	Ntie-Kang F, Mbah JA, Mbaze LM, et al. CamMedNP: building the Cameroonian 3D structural natural products database for virtual screening. BMC Complement Altern Med. 2013;13:88. Published 2013 Apr 16. doi:10.1186/1472-6882-13-88	https://doi.org/10.1186/1472-6882-13-88
Carotenoids Database	Structure	1174	No	Yes	Yes	Yes	Junko Yabuzaki, Carotenoids Database: structures, chemical fingerprints and distribution among organisms, Database, Volume 2017, 2017, bax004	https://doi.org/10.1093/database/bax004
CAS registry/SciFinder	Chemicals	> 300,000	Yes	Unknown	Unknown	Unknown	Gabrielson SW. SciFinder. J Med Libr Assoc. 2018;106(4):588–590. doi:10.5195/jmla.2018.515	https://doi.org/10.5195/jmla.2018.515
CEMTDD - Chinese Ethnic Minority Traditional Drug Database	tm, plants, asia	4060	No	No	Yes	No	Huang J, Zheng Y, Wu W, et al. CEMTDD: The database for elucidating the relationships among herbs, compounds, targets and related diseases for Chinese ethnic minority traditional drugs. Oncotarget. 2015;6(19):17675–17684	https://doi.org/10.18632/oncotarget.3789
CHDD (Chinese Traditional Medicinal Herbs database)	tm, plants, asia	> 30,000	Unknown	Unknown	Unknown	Unknown	Xuebin Qiao, Tingjun Hou, Wei Zhang, SenLi Guo, Xiaojie Xu, “A 3D Structure Database of Components from Chinese Traditional Medicinal Herbs”, J. Chem. Inf. Comput. Sci.2002423481-489	https://doi.org/10.1021/ci010113h
ChEBI	Chemicals	15,736	No	Yes	Yes	Yes	Janna Hastings, Gareth Owen, Adriano Dekker, Marcus Ennis, Namrata Kale, Venkatesh Muthukrishnan, Steve Turner, Neil Swainston, Pedro Mendes, Christoph Steinbeck, ChEBI in 2016: Improved services and an expanding collection of metabolites, Nucleic Acids Research, Volume 44, Issue D1, 4 January 2016, Pages D1214–D1219	https://doi.org/10.1093/nar/gkv1031
Chem-TCM	Plants, tm, asia	> 12,000	Yes	Unknown	Unknown	Unknown	Ehrman, T.; Barlow D.; Hylands, P. In silico search for multi-target anti-inflammatories in Chinese herbs and formulas. J Bioorganic & Med Chem. 2010, 18, Pages 2204–2218. doi:10.1016/j.bmc.2010.01.070	https://doi.org/10.1016/j.bmc.2010.01.070
ChemBank	Chemicals	x	No	Unknown	Unknown	Unknown	Petri Seiler K, Kuehn H, Pat Happ M, Decaprio D, Clemons PA. Using ChemBank to probe chemical biology. Curr Protoc Bioinformatics. 2008 Jun;Chapter 14:Unit 14.5. https://doi.org/10.1002/0471250953.bi1405s22. Review. PubMed PMID: 18551413.	https://doi.org/10.1002/0471250953.bi1405s22
ChEMBL	Chemicals	1899	No	Yes	No	Yes	Anna Gaulton, Anne Hersey, Michał Nowotka, A. Patrícia Bento, Jon Chambers, David Mendez, Prudence Mutowo, Francis Atkinson, Louisa J. Bellis, Elena Cibrián-Uhalte, Mark Davies, Nathan Dedman, Anneli Karlsson, María Paula Magariños, John P. Overington, George Papadatos, Ines Smit, Andrew R. Leach, The ChEMBL database in 2017, Nucleic Acids Research, Volume 45, Issue D1, January 2017, Pages D945–D954	https://doi.org/10.1093/nar/gkw1074
ChemBridge diversity datasets	Generalistic, industrial	x	No	Unknown	Unknown	Unknown	x	x
ChemDB	Plants, asia	> 1000	No	Unknown	Unknown	Unknown	Mirza SB, Bokhari H, Fatmi MQ. Exploring Natural Products from the Biodiversity of Pakistan for Computational Drug Discovery Studies: Collection, Optimization, Design and Development of A Chemical Database (ChemDP). Curr Comput Aided Drug Des. 2015;11(2):102–9. PubMed PMID: 26343150.	https://doi.org/10.2174/157340991102150904101740
ChemIDplus	Drug-like, toxins	9042	No	No	No	Yes	Patricia Tomasulo (2002) ChemIDplus-Super Source for Chemical and Drug Information, Medical Reference Services Quarterly, 21:1, 53–59	https://doi.org/10.1300/J115v21n01_04
ChemSpider	Chemicals	9732	No	Yes	No	Yes	Harry E. Pence, Antony Williams, “ChemSpider: An Online Chemical Information Resource”, J. Chem. Educ.201087111123-1124	https://doi.org/10.1021/ed100697w
CHMIS-C	Plants, tm, asia	> 8000	No	Unknown	Unknown	Unknown	Xueliang Fang, Lei Shao, Hui Zhang, Shaomeng Wang, “CHMIS-C: A Comprehensive Herbal Medicine Information System for Cancer”, J. Med. Chem.20054851481-1488	https://doi.org/10.1021/jm049838d
CMAUP	Plants	47,645	No	Yes	Yes	Yes	Xian Zeng, Peng Zhang, Yali Wang, et al. CMAUP: a database of collective molecular activities of useful plants. Nucleic Acids Research 2019; 47(D1): D1118-D1127	https://doi.org/10.1093/nar/gky965
CNPD (Chinese Natural Products Database)	Generalistic	> 57,000	Unknown	Unknown	Unknown	Unknown	Shen, Jianhua; Xu, Xiaoying; Cheng, Feng; Liu, Hong; Luo, Xiaomin; Shen, Jingkang; Chen, Kaixian; Zhao, Weimin; Shen, Xu; Jiang, Hualiang, “Virtual Screening on Natural Products for Discovering Active Compounds and Target Information”, Current Medicinal Chemistry, Volume 10, Number 21, 2003, pp. 2327–2342(16)	https://doi.org/10.2174/0929867033456729
ConMedNP	Plants, tm, africa	3118	NA	NA	No	No	Fidele Ntie-Kang, Pascal Amoa Onguéné, Michael Scharfe, Luc C. Owono Owono, Eugene Megnassan, Luc Meva’a Mbaze, Wolfgang Sippl, Simon M. N. Efange, “ConMedNP: a natural product library from Central African medicinal plants for drug discovery”, RSC Adv., 2014, 4, 409–419	https://doi.org/10.1039/C3RA43754J
CSLS/NCI (Chemical Structure Lookup Service)	Metabolites	x	No	Yes	No	Yes	M. Sitzmann, I.V. Filippov & M.C. Nicklaus (2008) Internet resources integrating many small-molecule databases1,SAR and QSAR in Environmental Research, 19:1–2, 1–9	https://doi.org/10.1080/10629360701843540
Database of Indonesian Medicinal Plants	Plants, tm, asia	6776	No	No	No	No	Yanuar A, Mun’im A, Lagho ABA, Syahdi RR, Rahmat M, Suhartanto H. Medicinal plants database and three dimensional structure of the chemical compounds from medicinal plants in Indonesia. Int J Comput Sci. 2011;8:180–3.	https://arxiv.org/abs/1111.7183
DESMSCI (Dragon Exploration System on Marin Sponge Compounds Interactions)	Marine	x	No	No	Unknown	Unknown	Sagar S, Kaur M, Radovanovic A, Bajic VB. Dragon exploration system on marine sponge compounds interactions. J Cheminform. 2013 Feb 16;5(1):11. https://doi.org/10.1186/1758-2946-5-11. PubMed PMID: 23415072; PubMed Central PMCID: PMC3608955.”https://doi.org/10.1186/1758-2946-5-11	https://doi.org/10.1186/1758-2946-5-11
DFC (Dictionary of Food COmpounds)	Food	> 41,000	Yes	Yes	Unknown	Unknown	x	x
DMNP (Dictionary of Marine Natural Products)	Marine	> 30,000	Yes	Yes	Unknown	Unknown	x	x
DNP (Dictionary of Natural Products) by Chapman and Hall (also known as CHEMnetBase)	Generalistic	> 230,000	Yes	Yes	Unknown	Unknown	x	x
Drugbank NPs	Drug-like	2617	No	Yes	Yes	Yes	David S Wishart, Yannick D Feunang, An C Guo, Elvis J Lo, Ana Marcu, Jason R Grant, Tanvir Sajed, Daniel Johnson, Carin Li, Zinat Sayeeda, Nazanin Assempour, Ithayavani Iynkkaran, Yifeng Liu, Adam Maciejewski, Nicola Gale, Alex Wilson, Lucy Chin, Ryan Cummings, Diana Le, Allison Pon, Craig Knox, Michael Wilson, DrugBank 5.0: a major update to the DrugBank database for 2018, Nucleic Acids Research, Volume 46, Issue D1, 4 January 2018, Pages D1074–D1082	https://doi.org/10.1093/nar/gkx1037
eBasis	Food		Yes	Unknown	Unknown	Unknown	J. Plumb, S. Pigat, F Bompola, M, Cushen, H Pinchen, E Nørby, S Astley, J Lyons, M Kiely and P Finglas. eBASIS (Bioactive Substances in Food Information Systems) and Bioactive Intakes: Major Updates of the Bioactive Compound Composition and Beneficial Bioeffects Database and the Development of a Probabilistic Model to Assess Intakes in Europe. Nutrients 2017, 9(4), 320	https://doi.org/10.3390/nu9040320
ETCM (Encyclopedia of Traditional Chinese Medicine)	tm, asia	7274	No	No	Yes	No	Xu HY, Zhang YQ, Liu ZM, Chen T, Lv CY, Tang SH, Zhang XB, Zhang W, Li ZY, Zhou RR, Yang HJ, Wang XJ, Huang LQ. ETCM: an encyclopaedia of traditional Chinese medicine. Nucleic Acids Res. 2018 Oct 26.	https://doi.org/10.1093/nar/gky987
ETM-DB	tm, plants, africa	1795	No	No	Yes	Yes	Bultum LE, Woyessa AM, Lee D. ETM-DB: integrated Ethiopian traditional herbal medicine and phytochemicals database. BMC Complement Altern Med. 2019 Aug 14;19(1):212. https://doi.org/10.1186/s12906-019-2634-1. PubMed PMID: 31412866; PubMed Central PMCID: PMC6692943.	https://doi.org/10.1186/s12906-019-2634-1
FooDB	Food	24,215	No	Yes	Yes	Yes	x	x
GNPS	Dereplication	7619	No	Yes	No	No	Want et al. “Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking”, Nature Biotechnology volume 34, pages 828–837 (2016)	https://doi.org/10.1038/nbt.3597
HIM (Herbal Ingridients in-vivo Metabolism database)	Drug-like, tm, plants	1261	No	Unknown	Unknown	Unknown	Kang H, Tang K, Liu Q, Sun Y, Huang Q, Zhu R, Gao J, Zhang D, Huang C, Cao Z. HIM-herbal ingredients in-vivo metabolism database. J Cheminform. 2013 May 31;5(1):28. https://doi.org/10.1186/1758-2946-5-28. PubMed PMID: 23721660; PubMed Central PMCID: PMC3679852.	https://doi.org/10.1186/1758-2946-5-28
HIT (Herbal Ingridients Targets)	Drug-like, tm, plants	524	No	Unknown	Unknown	Unknown	Hao Ye, Li Ye, Hong Kang, Duanfeng Zhang, Lin Tao, Kailin Tang, Xueping Liu, Ruixin Zhu, Qi Liu, Y. Z. Chen, Yixue Li, Zhiwei Cao, HIT: linking herbal active ingredients to targets, Nucleic Acids Research, Volume 39, Issue suppl_1, 1 January 2011, Pages D1055–D1059	https://doi.org/10.1093/nar/gkq1165
HMDB	Dereplication	x	No	Yes	Yes	Yes	Wishart DS, Feunang YD, Marcu A, Guo AC, Liang K, Vázquez-Fresno R, Sajed T, Johnson D, Li C, Karu N, Sayeeda Z, Lo E, Assempour N, Berjanskii M, Singhal S, Arndt D, Liang Y, Badran H, Grant J, Serra-Cayuela A, Liu Y, Mandal R, Neveu V, Pon A, Knox C, Wilson M, Manach C, Scalbert A. HMDB 4.0: the human metabolome database for 2018. Nucleic Acids Res. 2018 Jan 4;46(D1):D608-D617. https://doi.org/10.1093/nar/gkx1089. PubMed PMID: 29140435; PubMed Central PMCID: PMC5753273.	https://doi.org/10.1093/nar/gkx1089
IMPPAT	tm, plants, asia	9596	No	No	Yes	Yes	Mohanraj K, Karthikeyan BS, Vivek-Ananth RP, Chand RPB, Aparna SR, Mangalapandi P, Samal A. IMPPAT: A curated database of Indian Medicinal Plants, Phytochemistry And Therapeutics. Sci Rep. 2018 Mar 12;8(1):4329. https://doi.org/10.1038/s41598-018-22631-z. PubMed PMID: 29531263; PubMed Central PMCID: PMC5847565.	https://doi.org/10.1038/s41598-018-22631-z
InflamNat	Drug-like	552	NA	Yes	Yes	No	Zhang R, Lin J, Zou Y, Zhang XJ, Xiao WL. Chemical Space and Biological Target Network of Anti-Inflammatory Natural Products. J Chem Inf Model. 2019 Jan 28;59(1):66–73. https://doi.org/10.1021/acs.jcim.8b00560. Epub 2018 Dec 20.	https://doi.org/10.1021/acs.jcim.8b00560
Indofine Chemical Company Inc. natural products	Generalistic, industrial	56	No	Yes	No	No	x	x
InPACdb	Drug-like, plants, asia	124	No	Yes	Unknown	Unknown	Vetrivel U, Subramanian N, Pilla K. InPACdb--Indian plant anticancer compounds database. Bioinformation. 2009;4(2):71–74. Published 2009 Sep 5.	https://doi.org/10.6026/97320630004071
InterBioScreen Ltd (IBS)	Generalistic, industrial	68,350	No	Yes	No	No	x	x
iSMART	tm, plants, asia	x	No	No	No	Yes	Kai-Wei Chang, Tsung-Ying Tsai, Kuan-Chung Chen, Shun-Chieh Yang, Hung-Jin Huang, Tung-Ti Chang, Mao-Feng Sun, Hsin-Yi Chen, Fuu-Jen Tsai & Calvin Yu-Chian Chen (2011) iSMART: An Integrated Cloud Computing Web Server for Traditional Chinese Medicine for Online Virtual Screening, de novo Evolution and Drug Design, Journal of Biomolecular Structure and Dynamics, 29:1, 243–25	https://doi.org/10.1080/073911011010524988
KEGG	Metabolites	x	No	No	No	Yes	Minoru Kanehisa, Miho Furumichi, Mao Tanabe, Yoko Sato, Kanae Morishima, KEGG: new perspectives on genomes, pathways, diseases and drugs, Nucleic Acids Research, Volume 45, Issue D1, January 2017, Pages D353–D361	https://doi.org/10.1093/nar/gkw1092
KNApSaCK	Plants	10,265	No	No	Yes	No	Kensuke Nakamura, Naoki Shimura, Yuuki Otabe, Aki Hirai-Morita, Yukiko Nakamura, Naoaki Ono, Md Altaf Ul-Amin, Shigehiko Kanaya, KNApSAcK-3D: A Three-Dimensional Structure Database of Plant Metabolites, Plant and Cell Physiology, Volume 54, Issue 2, February 2013, Page e4,	https://doi.org/10.1093/pcp/pcs186
Lichen Database	Fungi	249	No	Yes	Yes	Yes	x	x
LOPAC1280 by Merck	Drug-like	1280	Unknown	Unknown	Unknown	Unknown	x	x
MAPS database	Plants, asia	x	No	Unknown	Unknown	Unknown	Ashfaq UA, Mumtaz A, Qamar TU, Fatima T. MAPS Database: Medicinal plant Activities, Phytochemical and Structural Database. Bioinformation. 2013;9(19):993–995. Published 2013 Dec 6.	https://doi.org/10.6026/97320630009993
Marine Compound Database (MCDB)	Marine	182	No	Unknown	Unknown	Unknown	Babu PA, Puppala SS, Aswini SL, Vani MR, Kumar CN, Prasanna T. A database of natural products and chemical entities from marine habitat. Bioinformation. 2008;3(3):142–143.	https://doi.org/10.6026/97320630003142
Marine Natural Product Database (MNPD)	Marine	6000	Unknown	Unknown	Unknown	Unknown	Lei J, Zhou J. A marine natural product database. J Chem Inf Comput Sci. 2002 May-Jun;42(3):742-8. PubMed PMID: 12086536.	https://doi.org/10.1021/ci010111x
MarineLit	Marine	> 29,000	Yes	Yes	Unknown	Unknown	Blunt JW, Carroll AR, Copp BR, Davis RA, Keyzers RA, Prinsep MR. Marine natural products. Nat Prod Rep. 2018 Jan 16;35(1):8–53. Review. PubMed PMID: 29335692.	https://doi.org/10.1039/c7np00052a
Massbank	Dereplication	x	No	No	No	Yes	Horai H, Arita M, Kanaya S, Nihei Y, Ikeda T, Suwa K, Ojima Y, Tanaka K, Tanaka S, Aoshima K, Oda Y, Kakazu Y, Kusano M, Tohge T, Matsuda F, Sawada Y, Hirai MY, Nakanishi H, Ikeda K, Akimoto N, Maoka T, Takahashi H, Ara T, Sakurai N, Suzuki H, Shibata D, Neumann S, Iida T, Tanaka K, Funatsu K, Matsuura F, Soga T, Taguchi R, Saito K, Nishioka T. MassBank: a public repository for sharing massspectral data for life sciences. J Mass Spectrom. 2010 Jul;45(7):703–14. https://doi.org/10.1002/jms.1777. PubMed PMID: 20623627.	https://doi.org/10.1002/jms.1777
MedPServer	Plants, tm, asia, drug-like	1124	No	No	Yes	Yes	Potshangbam AM, Polavarapu R, Rathore RS, Naresh D, Prabhu NP, Potshangbam N, Kumar P, Vindal V. MedPServer: A database for identification of therapeutic targets and novel leads pertaining to natural products. Chem Biol Drug Des. 2019 Apr;93(4):438–446. https://doi.org/10.1111/cbdd.13430. Epub 2018 Nov 28. PubMed PMID:30381914.	https://doi.org/10.1111/cbdd.13430
MetaCyc	Metabolites	x	No	Yes	Yes	Yes	Ron Caspi, Richard Billington, Carol A Fulcher, Ingrid M Keseler, Anamika Kothari, Markus Krummenacker, Mario Latendresse, Peter E Midford, Quang Ong, Wai Kit Ong, Suzanne Paley, Pallavi Subhraveti, Peter D Karp, The MetaCyc database of metabolic pathways and enzymes, Nucleic Acids Research, Volume 46, Issue D1, 4 January 2018, Pages D633–D639	https://doi.org/10.1093/nar/gkx935
METLIN	Dereplication	x	No	No	No	Yes	Guijas C, Montenegro-Burke JR, Domingo-Almenara X, Palermo A, Warth B, Hermann G, Koellensperger G, Huan T, Uritboonthai W, Aisporna AE, Wolan DW, Spilker ME, Benton HP, Siuzdak G. METLIN: A Technology Platform for Identifying Knowns and Unknowns. Anal Chem. 2018 Mar 6;90(5):3156–3164. https://doi.org/10.1021/acs.analchem.7b04424. Epub 2018 Feb 9. PubMed PMID: 29381867; PubMed Central PMCID: PMC5933435.	https://doi.org/10.1021/acs.analchem.7b04424
Mitishamba database	Plants, africa	1102	No	No	Yes	No	x	x
NADI	tm, plants	3000	Yes	Unknown	Unknown	Unknown	Ikram NK, Durrant JD, Muchtaridi M, Zalaludin AS, Purwitasari N, Mohamed N, Rahim AS, Lam CK, Normi YM, Rahman NA, Amaro RE, Wahab HA. A virtual screening approach for identifying plants with anti H5N1 neuraminidase activity. J Chem Inf Model. 2015 Feb 23;55(2):308–16. https://doi.org/10.1021/ci500405g. Epub 2015 Jan 29. PubMed PMID: 25555059; PubMed Central PMCID: PMC4340357.	https://doi.org/10.1021/ci500405g
NANPDB	Plants, africa	6832	No	Yes	No	No	Ntie-Kang F, Telukunta KK, Döring K, Simoben CV, A Moumbock AF, Malange YI, Njume LE, Yong JN, Sippl W, Günther S. NANPDB: A Resource for Natural Products from Northern African Sources. J Nat Prod. 2017 Jul 28;80(7):2067–2076. https://doi.org/10.1021/acs.jnatprod.7b00283. Epub 2017 Jun 22. PubMed PMID: 28641017.	https://doi.org/10.1021/acs.jnatprod.7b00283
NaprAlert	Generalistic	> 15,5000	Yes	Unknown	Yes	Unknown	Loub WD, Farnsworth NR, Soejarto DD, Quinn ML. NAPRALERT: computer handling of natural product research data. J Chem Inf Comput Sci. 1985 May;25(2):99–103. PubMed PMID: 4008538.	x
NAPROC-13	Dereplication	> 18,000	No	No	No	No (but has bibliographic references)	José Luis López-Pérez, Roberto Therón, Esther del Olmo, David Díaz, NAPROC-13: a database for the dereplication of natural product mixtures in bioassay-guided protocols, Bioinformatics, Volume 23, Issue 23, 1 December 2007, Pages 3256–3257	https://doi.org/10.1093/bioinformatics/btm516
NCI DTP data	Drug-like	418	No	Yes	No	No	x	x
NeMedPlant	tm, plants, asia	100	No	No	Yes	No	Meetei PA, Singh P, Nongdam P, Prabhu NP, Rathore R, Vindal V. NeMedPlant: a database of therapeutic applications and chemical constituents of medicinal plants from north-east region of India. Bioinformation. 2012;8(4):209–211.	https://doi.org/10.6026/97320630008209
NIST	Chemicals	x	Yes	Yes	Unknown	Unknown	x	x
NMRDATA	Dereplication	x	Unknown	Unknown	Unknown	Unknown	x	x
NMRShiftDB	Dereplication	1875	No	Yes	No	No	Kuhn S, Schlörer NE. Facilitating quality control for spectra assignments of small organic molecules: nmrshiftdb2--a free in-house NMR database with integrated LIMS for academic service laboratories. Magn Reson Chem. 2015 Aug;53(8):582–9. https://doi.org/10.1002/mrc.4263. Epub 2015 May 21. PubMed PMID: 25998807.	https://doi.org/10.1002/mrc.4263
Novel Antibiotics database	Drug-like	5430	Yes	No	Yes	Unknown	x	x
NPACT	Plants, drug-like	1573	No	Yes	No	Yes	Manu Mangal, Parul Sagar, Harinder Singh, Gajendra P. S. Raghava, Subhash M. Agarwal, NPACT: Naturally Occurring Plant-based Anti-cancer Compound-Activity-Target database, Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D1124–D1129	https://doi.org/10.1093/nar/gks1047
NPASS	Plants, bacteria, metazoa, fungi	30,858	No	Yes	Yes	Yes	Xian Zeng, Peng Zhang, Weidong He, Chu Qin, Shangying Chen, Lin Tao, Yali Wang, Ying Tan, Dan Gao, Bohua Wang, Zhe Chen, Weiping Chen, Yu Yang Jiang, Yu Zong Chen, NPASS: natural product activity and species source database for natural product research, discovery and tool development, Nucleic Acids Research, Volume 46, Issue D1, 4 January 2018, Pages D1217–D1222	https://doi.org/10.1093/nar/gkx1026
NPAtlas	Bacteria, fungi	20,035	No	Yes	Yes	No	x	x
NPCARE	Plants, marine, bacteria, drug-like	1370	No	Yes	No but contains impact of nps on different cancer tissues and associated genes	Yes	Choi H, Cho SY, Pak HJ, et al. NPCARE: database of natural products and fractional extracts for cancer regulation. J Cheminform. 2017;9:2. Published 2017 Jan 5.	https://doi.org/10.1186/s13321-016-0188-5
NPEdia	Generalistic	18,016	No	No	Yes	Yes	Takeshi Tomikia, Tamio Saitoa, Masashi Uekia, Hideaki Konnoa,Takeo Asaokab, Ryuichiro Suzukia, Masakazu Uramotoa, Hideaki, Kakeyaa, and Hiroyuki Osada. RIKEN Natural Products Encyclopedia (RIKEN NPEdia),a Chemical Database of RIKEN Natural Products Depository(RIKEN NPDepo). Journal of Computer Aided Chemistry , Vol.7, 157–162 (2006)	https://doi.org/10.2751/jcac.7.157
NPL (library)	Plants, drug-like	814	NA	NA	Unknown	Unknown	Ronald J. Quinn, Anthony R. Carroll, Ngoc B. Pham, Paul Baron, Meredith E. Palframan, Lekha Suraweera, Gregory K. Pierens, Sorel Muresan. Developing a Drug-like Natural Product Library. J. Nat. Prod.2008713464-468 Publication Date:February 8, 2008	https://doi.org/10.1021/np070526y
NuBBEDB	Plants, insects, america	2215	No	Yes	No	No	Pilon AC, Valli M, Dametto AC, et al. NuBBEDB: an updated database to uncover chemical and biological information from Brazilian biodiversity. Sci Rep. 2017;7(1):7215. Published 2017 Aug 3	https://doi.org/10.1038/s41598-017-07451-x
Open Source Malaria	Drug-like	842	No	Yes	No	Yes	Williamson et al. Open Source Drug Discovery: Highly Potent Antimalarial Compounds Derived from the Tres Cantos Arylpyrroles. ACS Cent Sci. 2016 Oct 26;2(10):687–701. Epub 2016 Sep 14.	https://doi.org/10.1021/acscentsci.6b00086
p-ANAPL (Pan-African Natural Product Library )	Plants, africa	538	No	NA	No	No	Ntie-Kang F, Amoa Onguéné P, Fotso GW, et al. Virtualizing the p-ANAPL library: a step towards drug discovery from African medicinal plants. PLoS One. 2014;9(3):e90655. Published 2014 Mar 5.	https://doi.org/10.1371/journal.pone.0090655
PAMDB	Metabolites, bacteria	x	No	Yes	Yes	Yes	Weiliang Huang, Luke K Brewer, Jace W Jones, Angela T Nguyen, Ana Marcu, David S Wishart, Amanda G Oglesby-Sherrouse, Maureen A Kane, Angela Wilks, PAMDB: a comprehensive Pseudomonas aeruginosa metabolome database, Nucleic Acids Research, Volume 46, Issue D1, 4 January 2018, Pages D575–D580	https://doi.org/10.1093/nar/gkx1061
Phenol-explorer	Food	862	No	Yes	Yes	Yes	Joseph A. Rothwell, Jara Perez-Jimenez, Vanessa Neveu, Alexander Medina-Remón, Nouha M’Hiri, Paula García-Lobato, Claudine Manach, Craig Knox, Roman Eisner, David S. Wishart, Augustin Scalbert, Phenol-Explorer 3.0: a major update of the Phenol-Explorer database to incorporate data on the effects of food processing on polyphenol content, Database, Volume 2013, 2013, bat070	https://doi.org/10.1093/database/bat070
Phytochemica	Plants, tm, asia	571	No	No	Yes	Supposedly	Pathania,S., Ramakrishnan,S.M., and Bagler,G. Phytochemica: a platform to explore phytochemicals of medicinal plants. Database (2015) Vol. 2015: article ID bav075;	https://doi.org/10.1093/database/bav075
PhytoHub	Food, plants	1200	No	No	Yes	Yes	x	x
Pi Chemicals System Natural Products	Generalistic, industrial	405	No	No	No	No	x	x
Prestwick	Plants, industrial	320	Yes	Unknwn	Unknown	Unknown	x	x
ProCarDB	Structure, bacteria	304	No	No	Yes	Yes	Nupur, Vats A, Dhanda SK, Raghava GPS, Pinnaka A, Kumar A (2016):”ProCarDB: a database of bacterial carotenoids”; BMC Microbiology 16(96)	https://doi.org/10.1186/s12866-016-0715-6
PubChem	Chemicals	3529	No	Yes	No	Yes	Sunghwan Kim, Paul A. Thiessen, Evan E. Bolton, Jie Chen, Gang Fu, Asta Gindulyte, Lianyi Han, Jane He, Siqian He, Benjamin A. Shoemaker, Jiyao Wang, Bo Yu, Jian Zhang, Stephen H. Bryant, PubChem Substance and Compound databases, Nucleic Acids Research, Volume 44, Issue D1, 4 January 2016, Pages D1202–D1213	https://doi.org/10.1093/nar/gkv951
REAXYS	Chemicals	> 220,000	Yes	Unknown	Unknown	Unknown	x	x
ReSpect	Dereplication	4767	No	Yes	Yes	Yes	Sawada Y, Nakabayashi R, Yamada Y, Suzuki M, Sato M, Sakata A, Akiyama K, Sakurai T, Matsuda F, Aoki T, Hirai MY, Saito K. RIKEN tandem mass spectral database (ReSpect) for phytochemicals: a plant-specific MS/MS-based data resource and database. Phytochemistry. 2012 Oct;82:38–45. https://doi.org/10.1016/j.phytochem.2012.07.007. Epub 2012 Aug 4. PubMed PMID: 22867903	https://doi.org/10.1016/j.phytochem.2012.07.007
SANCDB	Plants, africa	623	No	No	Yes	Yes	Hatherley R, Brown DK, Musyoka TM, Penkler DL, Faya N, Lobb KA, Tastan Bishop Ö. SANCDB: a South African natural compound database. J Cheminform. 2015 Jun 19;7:29. https://doi.org/10.1186/s13321-015-0080-8. eCollection 2015. PubMed PMID: 26097510; PubMed Central PMCID: PMC4471313	https://doi.org/10.1186/s13321-015-0080-8
Seaweed Metabolite Database (SWMD)	Marine	1110	No	Yes	Yes	No	Davis GD, Vasanthi AH. Seaweed metabolite database (SWMD): A database of natural compounds from marine algae. Bioinformation. 2011;5(8):361–364. Published 2011 Jan 22.	https://doi.org/10.6026/97320630005361
Specs Natural Products	Generalistic, industrial	745	No	Unknwon	No	No	x	x
Spektraris NMR	Dereplication	248	No	Yes	No	Yes	Fischedick JT, Johnson SR, Ketchum RE, Croteau RB, Lange BM. NMR spectroscopic search module for Spektraris, an online resource for plant natural product identification--Taxane diterpenoids from Taxus × media cell suspension cultures as a case study. Phytochemistry. 2015 May;113:87–95. https://doi.org/10.1016/j.phytochem.2014.11.020. Epub 2014 Dec 19. PubMed PMID: 25534952; PubMed Central PMCID: PMC4441555	https://doi.org/10.1016/j.phytochem.2014.11.020
StreptomeDB	Bacteria	6415	No	No	Yes	No	Dennis Klementz, Kersten Döring, Xavier Lucas, Kiran K. Telukunta, Anika Erxleben, Denise Deubel, Astrid Erber, Irene Santillana, Oliver S. Thomas, Andreas Bechthold, Stefan Günther, StreptomeDB 2.0—an extended resource of natural products produced by streptomycetes, Nucleic Acids Research, Volume 44, Issue D1, 4 January 2016, Pages D509–D514	https://doi.org/10.1093/nar/gkv1319
Super Natural II	Generalistic	320,670	No	No	No	To supplyers only	Priyanka Banerjee, Jevgeni Erehman, Björn-Oliver Gohlke, Thomas Wilhelm, Robert Preissner, Mathias Dunkel, Super Natural II—a database of natural products, Nucleic Acids Research, Volume 43, Issue D1, 28 January 2015, Pages D935–D939	https://doi.org/10.1093/nar/gku886
Super Scent	Other	2100	No	No	No	Yes	Mathias Dunkel, Ulrike Schmidt, Swantje Struck, Lena Berger, Bjoern Gruening, Julia Hossbach, Ines S. Jaeger, Uta Effmert, Birgit Piechulla, Roger Eriksson, Jette Knudsen, Robert Preissner, SuperScent—a database of flavors and scents, Nucleic Acids Research, Volume 37, Issue suppl_1, 1 January 2009, Pages D291–D294	https://doi.org/10.1093/nar/gkn695
Super Sweet	Food, metabolites	15,000	No	No	No	Yes	Jessica Ahmed, Saskia Preissner, Mathias Dunkel, Catherine L. Worth, Andreas Eckert, Robert Preissner, SuperSweet—a resource on natural and artificial sweetening agents, Nucleic Acids Research, Volume 39, Issue suppl_1, 1 January 2011, Pages D377–D382	https://doi.org/10.1093/nar/gkq917
TargetMol Natural Compound Library	Generalistic, industrial	1680	Yes	No	Unkown	Unknown	x	x
TC-MC	tm, asia, plants	> 20,000	No	No	Yes	Yes	Kim SK, Nam S, Jang H, Kim A, Lee JJ. TM-MC: a database of medicinal materials and chemical compounds in Northeast Asian traditional medicine. BMC Complement Altern Med. 2015 Jul 9;15:218. https://doi.org/10.1186/s12906-015-0758-5. PubMed PMID: 26156871; PubMed Central PMCID: PMC4495939.	https://doi.org/10.1186/s12906-015-0758-5
TCMDB@Taiwan	tm, asia, plants	58,351	No	Yes	No	No	Chen CY. TCM Database@Taiwan: the world’s largest traditional Chinese medicine database for drug screening in silico. PLoS One. 2011 Jan 6;6(1):e15939. https://doi.org/10.1371/journal.pone.0015939. PubMed PMID: 21253603; PubMed Central PMCID: PMC3017089	https://doi.org/10.1371/journal.pone.0015939
TCMID	tm, asia, plants	12,549	No	No	Yes (but difficutl to extract)	Yes	https://doi.org/10.1093/nar/gks1100Xue R, Fang Z, Zhang M, Yi Z, Wen C, Shi T. TCMID: Traditional Chinese Medicine integrative database for herb molecular mechanism analysis. Nucleic Acids Res. 2013 Jan;41(Database issue):D1089–95. https://doi.org/10.1093/nar/gks1100. Epub 2012 Nov 29. PubMed PMID: 23203875; PubMed Central PMCID: PMC3531123.	https://doi.org/10.1093/nar/gks1100
TCMSP	tm, asia, plants	29,384	No	Unknown	Unknown	Unknown	Ru J, Li P, Wang J, et al. TCMSP: a database of systems pharmacology for drug discovery from herbal medicines. J Cheminform. 2014;6(1):13. Published 2014 Apr 16.	https://doi.org/10.1186/1758-2946-6-13
TIM	tm, asia, plants	1829	No	No	Unknown	Unknown	Polur H, Joshi T, Workman CT, Lavekar G, Kouskoumvekaki I. Back to the Roots: Prediction of Biologically Active Natural Products from Ayurveda Traditional Medicine. Mol Inform. 2011 Mar 14;30(2–3):181–7. https://doi.org/10.1002/minf.201000163. Epub 2011 Feb 10	https://doi.org/10.1002/minf.201000163
TIPdb	Asia, plants, drug-like	8656	No	Yes	No	No	Chun-Wei Tung, Ying-Chi Lin, Hsun-Shuo Chang, Chia-Chi Wang, Ih-Sheng Chen, Jhao-Liang Jheng, Jih-Heng Li, TIPdb-3D: the three-dimensional structure database of phytochemicals from Taiwan indigenous plants, Database, Volume 2014, 2014, bau055	https://doi.org/10.1093/database/bau055
TMDB	Plants, metabolites	1393	No	Unknown	Yes	Yes	Yue Y, Chu GX, Liu XS, et al. TMDB: a literature-curated database for small molecular compounds found from tea. BMC Plant Biol. 2014;14:243. Published 2014 Sep 16. https://doi.org/10.1186/s12870-014-0243-1	https://doi.org/10.1186/s12870-014-0243-1
TPPT	Plants, toxins, europe	1583	No	Yes	Yes	Yes	Günthardt BF, Hollender J, Hungerbühler K, Scheringer M, Bucheli TD. Comprehensive Toxic Plants-Phytotoxins Database and Its Application in Assessing Aquatic Micropollution Potential. J Agric Food Chem. 2018 Jul 25;66(29):7577–7588. https://doi.org/10.1021/acs.jafc.8b01639. Epub 2018 Jul 16. PubMed PMID: 29944838.	https://doi.org/10.1021/acs.jafc.8b01639
TriForC	Plants	266	No	No	Yes	Yes	Karel Miettinen, Sabrina Iñigo, Lukasz Kreft, Jacob Pollier, Christof De Bo, Alexander Botzki, Frederik Coppens, Søren Bak, Alain Goossens, The TriForC database: a comprehensive up-to-date resource of plant triterpene biosynthesis, Nucleic Acids Research, Volume 46, Issue D1, 4 January 2018, Pages D586–D594	https://doi.org/10.1093/nar/gkx925
UEFS	Plants, america	503	No	Yes	No	No	x	x
UNPD (Universal Natural Products Database)	Generalistic	213,100	No	Yes	No	No	Gu J, Gui Y, Chen L, Yuan G, Lu HZ, Xu X. Use of natural products as chemical library for drug discovery and network pharmacology. PLoS One. 2013 Apr 25;8(4):e62839. https://doi.org/10.1371/journal.pone.0062839. Print 2013. PubMed PMID: 23638153; PubMed Central PMCID: PMC3636197	https://doi.org/10.1371/journal.pone.0062839
VIETHERB	Plants, asia	10,887	No	Unknown	Unknown	Unknown	Nguyen-Vo TH, Le T, Pham D, Nguyen T, Le P, Nguyen A, Nguyen T, Nguyen TN, Nguyen V, Do H, Trinh K, Duong HT, Le L. VIETHERB: A Database for Vietnamese Herbal Species. J Chem Inf Model. 2019 Jan 28;59(1):1–9. https://doi.org/10.1021/acs.jcim.8b00399. Epub 2018 Dec 3. PubMed PMID: 30407009.	https://doi.org/10.1021/acs.jcim.8b00399
Yeast Metabolome Database	Metabolites, dereplication	16,042	No	Yes	Yes	Yes	Ramirez-Gaona M, Marcu A, Pon A, et al. YMDB 2.0: a significantly expanded version of the yeast metabolome database. Nucleic Acids Res. 2017;45(D1):D440–D445. https://doi.org/10.1093/nar/gkw1058	https://doi.org/10.1093/nar/gkw1058
YaTCM	tm, asia, plants	47,696	No	No	No	No	Li B, Ma C, Zhao X, Hu Z, Du T, Xu X, Wang Z, Lin J. YaTCM: Yet another Traditional Chinese Medicine Database for Drug Discovery. Comput Struct Biotechnol J. 2018 Nov 23;16:600–610. https://doi.org/10.1016/j.csbj.2018.11.002. eCollection 2018. PubMed PMID: 30546860; PubMed Central PMCID: PMC6280608.	https://doi.org/10.1016/j.csbj.2018.11.002
ZINC natural products catalogue	Generalistic	85,198	No	Yes	No	No	Sterling T, Irwin JJ. ZINC 15--Ligand Discovery for Everyone. J Chem Inf Model. 2015;55(11):2324–2337. https://doi.org/10.1021/acs.jcim.5b00559	https://doi.org/10.1021/acs.jcim.5b00559

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