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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 nameNP typeEstimated size (number of NP molecules with correct structures)Number of unique molecules in COCONUTPercentage of molecules with stereochemistryIs open (data can be freely browsed)Recquires a registrationIs maintained (2019)Is updated
AfroCancertm, plants, africa39036569.76%YesNANANo
AfroDBtm, plants, africa95487470.73%YesNoNoNo
AfroMalariaDBtm, plants, africa26525270.93%yesNANAno
Afrotryptm, plants, drug-like, africa321xxUnknownNANANo
Alkamid databaseplants, structure300xxyesnoyesno
Ambinter-Greenpharma natural compound library (GPNCL)Generalistic, industrial> 150,000xxNoYesYesYes
AnalytiCon Discovery MEGxbacteria, plants, industrial5147490844.15%YesYesYesYes
AntiBasedrug-like> 40,000xxNoNoYesNo
AntiMarinMarine, drug-like> 60,000xxNoUnknownNoNo
ATBD (Animal Toxin Database)toxins1000xxUnknownUnknownNoUnknown
Ayurvedatm, asia950xxNoYesYesUnknown
Berdy’s Bioactive Natural Products DatabaseGeneralisticxxxNoUnknownNoNo
Binding DBDrug-likexxxYesNoYesNo
BIOFAQUIMPlant, fungi, america42040059.05%YesNoYesYes
BioPhytMolDrug-like, plants, asia633xxYesNoYesYes
CamMedNPtm, plants, africa> 2500xxYes, but proprietary formatNoNANo
Carotenoids DatabaseStructure117499157.63%YesNoYesYes
CAS registry/SciFinderChemicals> 300,000xxNoYesYesYes
CEMTDD - Chinese Ethnic Minority Traditional Drug Databasetm, plants, asia4060xxYesNoYesNo
CHDD (Chinese Traditional Medicinal Herbs database)tm, plants, asia> 30,000xxUnknownUnknownNoNo
Chem-TCMPlants, tm, asia> 12,000xxNoYesYesNo
ChemBridge diversity datasetsGeneralistic, industrialxxxNoYesNoNo
ChemDBPlants, asia> 1000xxUnknownUnknownNoNo
ChemIDplusDrug-like, toxins9042xxYesNoYesYes
CHMIS-CPlants, tm, asia> 8000xxYesNoNoNo
CNPD (Chinese Natural Products Database)Generalistic> 57,000xxUnknownUnknownNoNo
ConMedNPPlants, tm, africa3118250469.59%YesNANANA
CSLS/NCI (Chemical Structure Lookup Service)MetabolitesxxxYesNoYesNo
Database of Indonesian Medicinal PlantsPlants, tm, asia6776xxYesNoYesNo
DESMSCI (Dragon Exploration System on Marin Sponge Compounds Interactions)MarinexxxYesNoNoNo
DFC (Dictionary of Food COmpounds)Food> 41,000xxNoYesYesYes
DMNP (Dictionary of Marine Natural Products)Marine> 30,000xxNoYesYesYes
DNP (Dictionary of Natural Products) by Chapman and Hall (also known as CHEMnetBase)Generalistic> 230,000xxNoYesYesYes
Drugbank NPsDrug-like2617261751.32%YesNoYesYes
eBasisFood xxNoYesYesYes
ETCM (Encyclopedia of Traditional Chinese Medicine)tm, asia7274xxYesNoYesYes
ETM-DBtm, plants, africa1795165340.46%YesNoYesYes
HIM (Herbal Ingridients in-vivo Metabolism database)Drug-like, tm, plants126196241.62%YesNoNoNo
HIT (Herbal Ingridients Targets)Drug-like, tm, plants52447244.03%YesNoNoNo
IMPPATtm, plants, asia9596xxYesNoYesYes
Indofine Chemical Company Inc. natural productsGeneralistic, industrial564651.06%YesNoYes 
InPACdbDrug-like, plants, asia12412162.10%YesNoNoNo
InterBioScreen Ltd (IBS)Generalistic, industrial68,35067,29242.17%YesYesYesYes
iSMARTtm, plants, asiaxxxYesNoYesYes
Lichen DatabaseFungi24915626.67%YesNoYesNo
LOPAC1280 by MerckDrug-like1280xxNoYesYesYes
MAPS databasePlants, asiaxxxUnknownUnknownNoNo
Marine Compound Database (MCDB)Marine182xxYesNoNoNo
Marine Natural Product Database (MNPD)Marine6000xxYesNoNoNo
MarineLitMarine> 29,000xxNoYesYesYes
MedPServerPlants, tm, asia, drug-like1124xxYesNoYesYes
Mitishamba databasePlants, africa1102101023.84%YesNoYesNo
NADItm, plants3000xxNoYesYesUnknown
NANPDBPlants, africa6832391375.02%YesNoYesYes
NaprAlertGeneralistic> 15,5000xxNoYesYesYes
NAPROC-13Dereplication> 18,000xxYesNoYesYes
NCI DTP dataDrug-like41840436.76%YesNoYesNo
NeMedPlanttm, plants, asia100xxYesNoYesNo
Novel Antibiotics databaseDrug-like5430xxYesNoYesNo
NPACTPlants, drug-like1573145377.53%YesNoYesYes
NPASSPlants, bacteria, metazoa, fungi30,85827,47971.58%YesNoYesYes
NPAtlasBacteria, fungi20,03518,95967.03%YesNoYesYes
NPCAREPlants, marine, bacteria, drug-like137013640%YesNoYes (server fails sometimes)Yes
NPL (library)Plants, drug-like814xxNoNANANA
NuBBEDBPlants, insects, america2215202258.34%YesNoYes 
Open Source MalariaDrug-like842xxYesNoYesYes
p-ANAPL (Pan-African Natural Product Library )Plants, africa5384670.86%YesNoNA 
PAMDBMetabolites, bacteriaxxxYesNoYesYes
PhytochemicaPlants, tm, asia571xxYesNoNoNo
PhytoHubFood, plants1200xxYesNoYesYes
Pi Chemicals System Natural ProductsGeneralistic, industrial405xxYesNoYesYes
PrestwickPlants, industrial320xxNoYesYesYes
ProCarDBStructure, bacteria304xxYesNoYesNo
REAXYSChemicals> 220,000xxNoYesYes 
SANCDBPlants, africa62359282.28%YesNoYesYes
Seaweed Metabolite Database (SWMD)Marine111042378.53%YesNoYesNo
Specs Natural ProductsGeneralistic, industrial74574553.02%YesYesYesNo
Spektraris NMRDereplication24824291.53%YesNoYesNo
Super Natural IIGeneralistic320,670235,43683.55%YesNoYesNo
Super ScentOther2100xxYesNoYesNo
Super SweetFood, metabolites15,000xxYesNoYesNo
TargetMol Natural Compound LibraryGeneralistic, industrial1680xxNoYesYesYes
TC-MCtm, asia, plants> 20,000xxYesNoYesYes
TCMDB@Taiwantm, asia, plants58,35150,89190.38%YesNoYes (server fails sometimes)Yes
TCMIDtm, asia, plants12,54910,5720%YesNoYesNo
TCMSPtm, asia, plants29,384xxYesNoNoNo
TIMtm, asia, plants1829xxNoUnknownNoNo
TIPdbAsia, plants, drug-like8656775277.10%YesNoYesNo
TMDBPlants, metabolites1393xxYesNoNoNo
TPPTPlants, toxins, europe1583148676.84%YesNoYesNo
UEFSPlants, america50348168.93%YesNoNoNo
UNPD (Universal Natural Products Database)Generalistic213,100156,98412.62%YesNoNoNo
VIETHERBPlants, asia10,887xxYesUnknownNoNo
Yeast Metabolome DatabaseMetabolites, dereplication16,042xxYesNoYesYes
YaTCMtm, asia, plants47,696xxYesNoYesYes
ZINC natural products catalogueGeneralistic85,198673,3690.49%YesNoYesYes
Database nameNP typeEstimated size (number of NP molecules with correct structures)Is commercialMolecule structures easily retrievable (download link, data packed in one file, bulk download option)Has extensive metadata (organism, tissue, geo info, …)Has cross-refsMost recent publication (citation)Most recent publication (DOI)
3DMETGeneralistic18248NoNoNoYesMaeda 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. Epub 2013 Mar 7. PubMed PMID: 23293959.
AfroCancertm, plants, africa390NoNANoNoFidele 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
AfroDBtm, plants, africa954NoYesNoNoNtie-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.
AfroMalariaDBtm, plants, africa265noNAnonoOnguéné, 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.
Afrotryptm, plants, drug-like, africa321NoNAUnknownUnknownIbezim, 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.
Alkamid databaseplants, structure300nonoyesnoBoonen, 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
Ambinter-Greenpharma natural compound library (GPNCL)Generalistic, industrial> 150,000YesNoUnknownUnknownxx
AnalytiCon Discovery MEGxbacteria, plants, industrial5147NoYesNoNoxx
AntiBasedrug-like> 40,000YesYesUnknownUnknownLaatsch H (2012) Antibase Version 4.0—The natural compound identifier. Wiley-VCH Verlag GmbH & Co. KGaAx
AntiMarinMarine, drug-like> 60,000YesUnknownUnknownUnknownBlunt, J., Munro, M. & Laatsch, H. Antimarin database. University of Canterbury; Christchurch, New Zealand: University of Gottingen; Gottingen, Germany, (2007).x
ATBD (Animal Toxin Database)toxins1000NoUnknownUnknownUnknownHe QY, He QZ, Deng XC, et al. ATDB: a uni-database platform for animal toxins. Nucleic Acids Res. 2008;36(Database issue):D293–D297.
Ayurvedatm, asia950UnknownUnknownUnknownUnknownLagunin 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. Russian. PubMed PMID:25978395.
Berdy’s Bioactive Natural Products DatabaseGeneralisticxYesUnknownUnknownUnknownBerdy J., Kertesz M. (1989) Bioactive natural products database: an aid for natural products identification. In: Collier H.R. (eds) Chemical Information. Springer, Berlin, Heidelberg
BiGGMetabolites7339NoNAYesYesKing 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.
Binding DBDrug-likexNoYesYesYesGilson 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.
BIOFAQUIMPlant, fungi, america420NoYesYesNoPilón-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
BioPhytMolDrug-like, plants, asia633NoNoYesNoSharma 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.
BitterDBFood654NoNoYesYesAyana 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.
BRENDAMetabolitesxNoYesYesYesJeske 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
CamMedNPtm, plants, africa> 2500NoYes, but proprietary format (MDB readable by MOE)UnknownUnknownNtie-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
Carotenoids DatabaseStructure1174NoYesYesYesJunko Yabuzaki, Carotenoids Database: structures, chemical fingerprints and distribution among organisms, Database, Volume 2017, 2017, bax004
CAS registry/SciFinderChemicals> 300,000YesUnknownUnknownUnknownGabrielson SW. SciFinder. J Med Libr Assoc. 2018;106(4):588–590. doi:10.5195/jmla.2018.515
CEMTDD - Chinese Ethnic Minority Traditional Drug Databasetm, plants, asia4060NoNoYesNoHuang 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
CHDD (Chinese Traditional Medicinal Herbs database)tm, plants, asia> 30,000UnknownUnknownUnknownUnknownXuebin 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
ChEBIChemicals15,736NoYesYesYesJanna 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
Chem-TCMPlants, tm, asia> 12,000YesUnknownUnknownUnknownEhrman, 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
ChemBankChemicalsxNoUnknownUnknownUnknownPetri 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. Review. PubMed PMID: 18551413.
ChEMBLChemicals1899NoYesNoYesAnna 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
ChemBridge diversity datasetsGeneralistic, industrialxNoUnknownUnknownUnknownxx
ChemDBPlants, asia> 1000NoUnknownUnknownUnknownMirza 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.
ChemIDplusDrug-like, toxins9042NoNoNoYesPatricia Tomasulo (2002) ChemIDplus-Super Source for Chemical and Drug Information, Medical Reference Services Quarterly, 21:1, 53–59
ChemSpiderChemicals9732NoYesNoYesHarry E. Pence, Antony Williams, “ChemSpider: An Online Chemical Information Resource”, J. Chem. Educ.201087111123-1124
CHMIS-CPlants, tm, asia> 8000NoUnknownUnknownUnknownXueliang Fang, Lei Shao, Hui Zhang, Shaomeng Wang, “CHMIS-C:  A Comprehensive Herbal Medicine Information System for Cancer”, J. Med. Chem.20054851481-1488
CMAUPPlants47,645NoYesYesYesXian 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
CNPD (Chinese Natural Products Database)Generalistic> 57,000UnknownUnknownUnknownUnknownShen, 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)
ConMedNPPlants, tm, africa3118NANANoNoFidele 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
CSLS/NCI (Chemical Structure Lookup Service)MetabolitesxNoYesNoYesM. 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
Database of Indonesian Medicinal PlantsPlants, tm, asia6776NoNoNoNoYanuar 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.
DESMSCI (Dragon Exploration System on Marin Sponge Compounds Interactions)MarinexNoNoUnknownUnknownSagar S, Kaur M, Radovanovic A, Bajic VB. Dragon exploration system on marine sponge compounds interactions. J Cheminform. 2013 Feb 16;5(1):11. PubMed PMID: 23415072; PubMed Central PMCID: PMC3608955.”
DFC (Dictionary of Food COmpounds)Food> 41,000YesYesUnknownUnknownxx
DMNP (Dictionary of Marine Natural Products)Marine> 30,000YesYesUnknownUnknownxx
DNP (Dictionary of Natural Products) by Chapman and Hall (also known as CHEMnetBase)Generalistic> 230,000YesYesUnknownUnknownxx
Drugbank NPsDrug-like2617NoYesYesYesDavid 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
eBasisFood YesUnknownUnknownUnknownJ. 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
ETCM (Encyclopedia of Traditional Chinese Medicine)tm, asia7274NoNoYesNoXu 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.
ETM-DBtm, plants, africa1795NoNoYesYesBultum 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. PubMed PMID: 31412866; PubMed Central PMCID: PMC6692943.
GNPSDereplication7619NoYesNoNoWant 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)
HIM (Herbal Ingridients in-vivo Metabolism database)Drug-like, tm, plants1261NoUnknownUnknownUnknownKang 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. PubMed PMID: 23721660; PubMed Central PMCID: PMC3679852.
HIT (Herbal Ingridients Targets)Drug-like, tm, plants524NoUnknownUnknownUnknownHao 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
HMDBDereplicationxNoYesYesYesWishart 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. PubMed PMID: 29140435; PubMed Central PMCID: PMC5753273.
IMPPATtm, plants, asia9596NoNoYesYesMohanraj 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. PubMed PMID: 29531263; PubMed Central PMCID: PMC5847565.
InflamNatDrug-like552NAYesYesNoZhang 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. Epub 2018 Dec 20.
Indofine Chemical Company Inc. natural productsGeneralistic, industrial56NoYesNoNoxx
InPACdbDrug-like, plants, asia124NoYesUnknownUnknownVetrivel U, Subramanian N, Pilla K. InPACdb--Indian plant anticancer compounds database. Bioinformation. 2009;4(2):71–74. Published 2009 Sep 5.
InterBioScreen Ltd (IBS)Generalistic, industrial68,350NoYesNoNoxx
iSMARTtm, plants, asiaxNoNoNoYesKai-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
KEGGMetabolitesxNoNoNoYesMinoru 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
KNApSaCKPlants10,265NoNoYesNoKensuke 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,
Lichen DatabaseFungi249NoYesYesYesxx
LOPAC1280 by MerckDrug-like1280UnknownUnknownUnknownUnknownxx
MAPS databasePlants, asiaxNoUnknownUnknownUnknownAshfaq 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.
Marine Compound Database (MCDB)Marine182NoUnknownUnknownUnknownBabu 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.
Marine Natural Product Database (MNPD)Marine6000UnknownUnknownUnknownUnknownLei J, Zhou J. A marine natural product database. J Chem Inf Comput Sci. 2002 May-Jun;42(3):742-8. PubMed PMID: 12086536.
MarineLitMarine> 29,000YesYesUnknownUnknownBlunt 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.
MassbankDereplicationxNoNoNoYesHorai 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. PubMed PMID: 20623627.
MedPServerPlants, tm, asia, drug-like1124NoNoYesYesPotshangbam 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. Epub 2018 Nov 28. PubMed PMID:30381914.
MetaCycMetabolitesxNoYesYesYesRon 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
METLINDereplicationxNoNoNoYesGuijas 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. Epub 2018 Feb 9. PubMed PMID: 29381867; PubMed Central PMCID: PMC5933435.
Mitishamba databasePlants, africa1102NoNoYesNoxx
NADItm, plants3000YesUnknownUnknownUnknownIkram 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. Epub 2015 Jan 29. PubMed PMID: 25555059; PubMed Central PMCID: PMC4340357.
NANPDBPlants, africa6832NoYesNoNoNtie-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. Epub 2017 Jun 22. PubMed PMID: 28641017.
NaprAlertGeneralistic> 15,5000YesUnknownYesUnknownLoub 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-13Dereplication> 18,000NoNoNoNo (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
NCI DTP dataDrug-like418NoYesNoNoxx
NeMedPlanttm, plants, asia100NoNoYesNoMeetei 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.
NMRShiftDBDereplication1875NoYesNoNoKuhn 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. Epub 2015 May 21. PubMed PMID: 25998807.
Novel Antibiotics databaseDrug-like5430YesNoYesUnknownxx
NPACTPlants, drug-like1573NoYesNoYesManu 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
NPASSPlants, bacteria, metazoa, fungi30,858NoYesYesYesXian 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
NPAtlasBacteria, fungi20,035NoYesYesNoxx
NPCAREPlants, marine, bacteria, drug-like1370NoYesNo but contains impact of nps on different cancer tissues and associated genesYesChoi 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.
NPEdiaGeneralistic18,016NoNoYesYesTakeshi 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)
NPL (library)Plants, drug-like814NANAUnknownUnknownRonald 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
NuBBEDBPlants, insects, america2215NoYesNoNoPilon 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
Open Source MalariaDrug-like842NoYesNoYesWilliamson 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.
p-ANAPL (Pan-African Natural Product Library )Plants, africa538NoNANoNoNtie-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.
PAMDBMetabolites, bacteriaxNoYesYesYesWeiliang 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
Phenol-explorerFood862NoYesYesYesJoseph 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
PhytochemicaPlants, tm, asia571NoNoYesSupposedlyPathania,S., Ramakrishnan,S.M., and Bagler,G. Phytochemica: a platform to explore phytochemicals of medicinal plants. Database (2015) Vol. 2015: article ID bav075;
PhytoHubFood, plants1200NoNoYesYesxx
Pi Chemicals System Natural ProductsGeneralistic, industrial405NoNoNoNoxx
PrestwickPlants, industrial320YesUnknwnUnknownUnknownxx
ProCarDBStructure, bacteria304NoNoYesYesNupur, Vats A, Dhanda SK, Raghava GPS, Pinnaka A, Kumar A (2016):”ProCarDB: a database of bacterial carotenoids”; BMC Microbiology 16(96)
PubChemChemicals3529NoYesNoYesSunghwan 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
REAXYSChemicals> 220,000YesUnknownUnknownUnknownxx
ReSpectDereplication4767NoYesYesYesSawada 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. Epub 2012 Aug 4. PubMed PMID: 22867903
SANCDBPlants, africa623NoNoYesYesHatherley 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. eCollection 2015. PubMed PMID: 26097510; PubMed Central PMCID: PMC4471313
Seaweed Metabolite Database (SWMD)Marine1110NoYesYesNoDavis 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.
Specs Natural ProductsGeneralistic, industrial745NoUnknwonNoNoxx
Spektraris NMRDereplication248NoYesNoYesFischedick 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. Epub 2014 Dec 19. PubMed PMID: 25534952; PubMed Central PMCID: PMC4441555
StreptomeDBBacteria6415NoNoYesNoDennis 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
Super Natural IIGeneralistic320,670NoNoNoTo supplyers onlyPriyanka 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
Super ScentOther2100NoNoNoYesMathias 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
Super SweetFood, metabolites15,000NoNoNoYesJessica 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
TargetMol Natural Compound LibraryGeneralistic, industrial1680YesNoUnkownUnknownxx
TC-MCtm, asia, plants> 20,000NoNoYesYesKim 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. PubMed PMID: 26156871; PubMed Central PMCID: PMC4495939.
TCMDB@Taiwantm, asia, plants58,351NoYesNoNoChen 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. PubMed PMID: 21253603; PubMed Central PMCID: PMC3017089
TCMIDtm, asia, plants12,549NoNoYes (but difficutl to extract)Yes 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. Epub 2012 Nov 29. PubMed PMID: 23203875; PubMed Central PMCID: PMC3531123.
TCMSPtm, asia, plants29,384NoUnknownUnknownUnknownRu 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.
TIMtm, asia, plants1829NoNoUnknownUnknownPolur 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. Epub 2011 Feb 10
TIPdbAsia, plants, drug-like8656NoYesNoNoChun-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
TMDBPlants, metabolites1393NoUnknownYesYesYue 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.
TPPTPlants, toxins, europe1583NoYesYesYesGünthardt 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. Epub 2018 Jul 16. PubMed PMID: 29944838.
TriForCPlants266NoNoYesYesKarel 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
UEFSPlants, america503NoYesNoNoxx
UNPD (Universal Natural Products Database)Generalistic213,100NoYesNoNoGu 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. Print 2013. PubMed PMID: 23638153; PubMed Central PMCID: PMC3636197
VIETHERBPlants, asia10,887NoUnknownUnknownUnknownNguyen-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. Epub 2018 Dec 3. PubMed PMID: 30407009.
Yeast Metabolome DatabaseMetabolites, dereplication16,042NoYesYesYesRamirez-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.
YaTCMtm, asia, plants47,696NoNoNoNoLi 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. eCollection 2018. PubMed PMID: 30546860; PubMed Central PMCID: PMC6280608.
ZINC natural products catalogueGeneralistic85,198NoYesNoNoSterling T, Irwin JJ. ZINC 15--Ligand Discovery for Everyone. J Chem Inf Model. 2015;55(11):2324–2337.