Miscellaneous compounds

3DMETMaeda M. H., Kondo K., Three-dimensional structure database of natural metabolites (3DMET): A novel database of curated 3D structures. Journal of Chemical Information and Modeling, 2013, 53, 527–533. Abstract
AfroDBNtie-Kang F., Zofou D., Babiaka S. B., Meudom R., Scharfe M., Lifongo L. L., Mbah J. A., Mbaze L. M., Sippl W., Efange S. M. N. AfroDb: A select highly potent and diverse natural product library from African medicinal plants. PLOS One, 2013, 8, Article No e78085. Abstract
ATB RepositoryMalde A. K., Zuo L., Breeze M., Stroet M., Poger D., Nair P. C., Oostenbrink C., Mark A. E., An Automated Force Field Topology Builder (ATB) and repository: version 1.0. Journal of Chemical Theory and Computation, 2011, 7, 4026–4037. Abstract
BARDHowe E. A., de Souza A., Lahr D. L., Chatwin S., Montgomery P., Alexander B. R., Nguyen D.-T., Cruz Y., Stonich D. A., Walzer G., Rose J. T., Picard S. C., Liu Z., Rose J. N., Xiang X., Asiedu J., Durkin D., Levine J., Yang J. J., Schürer S. C., Braisted J. C., Southall N., Southern M. R., Chung T. D. Y., Brudz S., Tanega C., Schreiber S. L., Bittker J. A., Guha R., Clemons P. A., BioAssay Research Database (BARD): chemical biology and probe-development enabled by structured metadata and result types. Nucleic Acids Research, 2015, 43, D1163–D1170. Abstract
BIOFACQUIMPilón-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, Article No 31. Abstract
Cancer Odor DatabaseJanfaza S., Nojavani M. B., Khorsand B., Nikkhah M., Zahiri J., Cancer Odor Database (COD): a critical databank for cancer diagnosis research. Database, 2017, Article No bax055. Abstract
CARLSBADMathias S. L., Hines-Kay J., Yang J. J., Zahoransky-Kohalmi G., Bologa C. G., Ursu O., Oprea T. I., The CARLSBAD database: a confederated database of chemical bioactivities. Database, 2013, Article No bat044. Abstract
CAS Common ChemistryJacobs A., Williams D., Hickey K., Patrick N., Williams A. J., Chalk S., McEwen L., Willighagen E., Walker M., Bolton E., Sinclair G., Sanford A., CAS Common Chemistry in 2021: expanding access to trusted chemical information for the scientific community. Journal of Chemical Information and Modeling, 2022, 62, 2737–2743. Abstract
CFamZhang C., Tao L., Qin C., Zhang P., Chen S., Zeng X., Xu F., Chen Z., Yang S. Y., Chen Y. Z., CFam: a chemical families database based on iterative selection of functional seeds and seed-directed compound clustering. Nucleic Acids Research, 2015, 43, D558–D565. Abstract
ChEBIDegtyarenko K., De Matos P., Ennis M., Hastings J., Zbinden M., McNaught A., Alcántara R., Darsow M., Guedj M., Ashburner M., ChEBI: A database and ontology for chemical entities of biological interest. Nucleic Acids Research, 2008, 36, D344-D350. Abstract

Hastings J., Owen G., Dekker A., Ennis M., Kale N., Muthukrishnan V., Turner S., Swainston N., Mendes P., Steinbeck C., ChEBI in 2016: Improved services and an expanding collection of metabolites. Nucleic Acids Research, 2016, 44, D1214–D1219. Abstract
ChemBankSeiler K. P., George G. A., Happ M. P., Bodycombe N. E., Carrinski H. A., Norton S., Brudz S., Sullivan J. P., Muhlich J., Serrano M., Ferraiolo P., Tolliday N. J., Schreiber S. L., Clemons P. A., ChemBank: A small-molecule screening and cheminformatics resource database. Nucleic Acids Research, 2008, 36, D351-D359.  Abstract
Chembase.cnProvider: Shanghai Zhihua ChemTech Inc.
ChEMBLMendez D., Gaulton A., Bento P., Chambers J., De Veij M., Félix E., Magariños M. P., Mosquera J. F., Mutowo P., Nowotka M., Gordillo-Marañón M., Hunter F., Junco L., Mugumbate G., Rodriguez-Lopez M., Atkinson F., Bosc N., Radoux C. J., Segura-Cabrera A., Hersey A., Leach A. R., ChEMBL: towards direct deposition of bioassay data. Nucleic Acids Research, 2019, 47, D930-D940.  Abstract
ChemDBChen J. H., Linstead E., Swamidass S. J., Wang D., Baldi P., ChemDB update-full-text search and virtual chemical space. Bioinformatics, 2007, 23, 2348-2351. Abstract
Chemical CheckerDuran-Frigola M., Pauls E., Guitart-Pla O., Bertoni M., Alcalde V., Amat D., Juan-Blanco T., Aloy P., Extending the small-molecule similarity principle to all levels of biology with the Chemical Checker. Nature Biotechnology, 2020, 38, 1087-1096. Abstract
ChemIDplusTomasulo P., ChemIDplus-super source for chemical and drug information. Medical Reference Services Quarterly, 2002, 21, 53-59. Abstract
cheML.ioZhumagambetov R., Kazbek D., Shakipov M., Maksut D., Peshkov V. A., Fazli S., cheML.io: an online database of ML-generated molecules. RSC Advances, 2020, 10, 45189-45198. Abstract
ChemSpiderPence H. E., Williams A., Chemspider: An online chemical information resource. Journal of Chemical Education, 2010, 87, 1123–1124.  Abstract 

Williams A., Tkachenko V., The Royal Society of Chemistry and the delivery of chemistry data repositories for the community. Journal of Computer Aided Molecular Design, 2014, 28, 1023–1030. Abstract
ClassyFireDjoumbou Feunang Y., Eisner R., Knox C., Chepelev L., Hastings J., Owen G., Fahy E., Steinbeck C., Subramanian S., Bolton E., Greiner R., Wishart D. S., ClassyFire: automated chemical classification with a comprehensive, computable taxonomy. Journal of Cheminformatics, 2016, 8, Article No 61.  Abstract
CMNPDLyu C., Chen T., Qiang B., Liu N., Wang H., Zhang L., Liu Z., CMNPD: a comprehensive marine natural products database towards facilitating drug discovery from the ocean. Nucleic Acids Research, 2021, 49, D509–D515. Abstract
COCONUTSorokina M., Merseburger P., Rajan K., Yirik M. A., Steinbeck C., COCONUT online: Collection of Open Natural Products database. Journal of Cheminformatics, 2021, 13, Article No 2. Abstract
Crystallography Open DatabaseBorysov S. S., Geilhufe R. M., Balatsky A. V., Organic materials database: An open-access online database for data mining. PLoS ONE, 2017, 12, Article No 0171501. Abstract
ECHAProvider: European Chemicals Agency
EMSL Basis Set ExchangeSchuchardt K. L., Didier B. T., Elsethagen T., Sun L., Gurumoorthi V., Chase J., Li J., Windus, T. L., Basis Set Exchange: a community database for computational sciences. Journal of Chemical Information and Modeling, 2007, 47, 1045-1052. Abstract
FDA SRSProvider: Food and Drug Administration
FDB-17Visini R., Awale M., Reymond J.-L., Fragment database FDB-17. Journal of Chemical Information and Modeling, 2017, 57, 700–709.  Abstract
FilTer BaSeKolte B. S., Londhe S. R., Solanki B. R., Gacche R. N., Meshram R. J., FilTer BaSe: A web accessible chemical database for small compound libraries. Journal of Molecular Graphics and Modelling, 2018, 80, 95–103. Abstract
FragmentStoreAhmed J., Worth C. L., Thaben P., Matzig C., Blasse C., Dunkel M., Preissner R., FragmentStore-a comprehensive database of fragments linking metabolites, toxic molecules and drugs. Nucleic Acids Research, 2011, 39, D1049-D1054. Abstract
GDB-13 MQN
GDB-13 SMIfp
Blum L. C., Reymond J.-L., 970 million druglike small molecules for virtual screening in the chemical universe database GDB-13. Journal of American Chemical Society, 2009, 131, 8732–8733. Abstract

Reymond J.-L., The chemical space project. Accounts of Chemical Research, 2015, 48, 722–730. Abstract
GDB-17 Apfp
GDB-17 MQN
GDB-17 SMIfp
GDB-17 Xfp
Ruddigkeit L., Blum L. C., Reymond J.-L., Visualization and virtual screening of the chemical universe database GDB-17. Journal of Chemical Information and Modeling, 2013, 53, 56–65. Abstract

Reymond J.-L., The chemical space project. Accounts of Chemical Research, 2015, 48, 722–730. Abstract
ISDM ChemWebRDFGalgonek J., Vondrášek J., IDSM ChemWebRDF: SPARQLing small‑molecule datasets. Journal of Cheminformatics, 2021, 13, Article No 38. Abstract
J-GlobalProvider: Japan Science and Technology Agency
KEGG compoundKanehisa M., Furumichi M., Sato Y., Ishiguro-Watanabe M., Tanabe M., KEGG: integrating viruses and cellular organisms. Nucleic Acids Research, 2021, 49, D545–D551. Abstract
LigandbookDomański J., Beckstein O., Iorga B. I., Ligandbook: an online repository for small and drug-like molecule force field parameters. Bioinformatics, 2017, 33, 1747-1749.  Abstract
LINCSProvider: National Institutes of Health
MarkerDBWishart D. S., Bartok B., Oler E., Liang K. Y. H., Budinski Z., Berjanskii M., Guo A., Cao X., Wilson M., MarkerDB: an online database of molecular biomarkers. Nucleic Acids Research, 2021, 49, D1259–D1267. Abstract
MeSHSayers E. W., Bolton E. E., Brister J. R., Canese K., Chan J., Comeau D. C., Connor R., Funk K., Kelly C., Kim S., Madej T., Marchler-Bauer A., Lanczycki C., Lathrop S., Lu Z., Thibaud-Nissen F., Murphy T., Phan L., Skripchenko Y., Tse T., Wang J., Williams R., Trawick B. W., Pruitt K. D., Sherry S. T., Database resources of the National Center for Biotechnology Information. Nucleic Acids Research, 2022, 50, D20–D26. Abstract
MMsINCMasciocchi J., Frau G., Fanton M., Sturlese M., Floris M., Pireddu L., Palla P., Cedrati F., Rodriguez-Tomé P., Moro S., MMsINC: A large-scale chemoinformatics database. Nucleic Acids Research, 2009, 37, D284-D290. Abstract
MolDB5R demoHaider N., Functionality pattern matching as an efficient complementary structure/reaction search tool: an open-source approach. Molecules, 2010, 15, 5079-5092. Abstract
NANPDBNtie-Kang F., Telukunta K. K., Döring K., Simoben C. V., Moumbock A. F. A., Malange Y. I., Njume L. E., Yong J. N., Sippl W., Günther S., NANPDB: a resource for natural products from northern African sources. Journal of Natural Products, 2017, 80, 2067–2076. Abstract
NikkajiWebProvider: Japan Science and Technology Agency
NLMProvider: US Department of Health & Human Services
NMRShiftDBSteinbeck C., Kuhn S., NMRShiftDB – compound identification and structure elucidation support through a free community-built web database. Phytochemistry, 2004, 65, 2711–2717. Abstract
NPAtlasvan Santen J. A., Poynton E. F., Iskakova D., McMann E., Alsup T. A., Clark T. N., Claire H. Fergusson C. H., Fewer D. P., Hughes A. H., McCadden C. A., Parra J., Soldatou S., Rudolf J. D., Janssen E. M.-L., Duncan K. R., Linington R. G., The Natural Products Atlas 2.0: a database of microbially-derived natural products. Nucleic Acids Research, 2022, 50, D1317–D1323. Abstract
NUBBEDBValli M., dos Santos R. N., Figueira L. D., Nakajima C. H., Castro-Gamboa I., Andricopulo A. D., Bolzani V. S., Development of a natural products database from the biodiversity of Brazil. Journal of Natural Products, 2013, 76, 439–444. Abstract
OLSJupp S., Burdett T., Malone J., Leroy C., Pearce M., McMurry J., Parkinson H., A new ontology lookup service at EMBL-EBI. CEUR Workshop Proceedings, 2015, 1546, 118-119. Abstract
OLSVisVercruysse S., Venkatesan A., Kuiper M., OLSVis: an animated, interactive visual browser for bio-ontologies. BMC Bioinformatics, 2012, 13, Article No 116. Abstract
PhytochemicaPathania S., Ramakrishnan S. M., Bagler G., Phytochemica: a platform to explore phytochemicals of medicinal plants. Database, 2015, Article No bav075. Abstract
PubChemBolton E.E., Wang Y., Thiessen P.A., Bryant S.H., PubChem: integrated platform of small molecules and biological activities. Annual Reports in Computational Chemistry, 2008, 4, 217-241. Abstract 

Kim S., Chen J., Cheng T., Gindulyte A., He J., He S., Li Q., Shoemaker B. A., Thiessen P. A., Yu B., Zaslavsky L., Zhang J., Bolton E. E., PubChem in 2021: new data content and improved web interfaces. Nucleic Acids Research, 2021, 49, D1388–D1395. Abstract
QsarDBRuusmann V., Sild S., Maran U., QSAR DataBank repository: open and linked qualitative and quantitative structure–activity relationship models. Journal of Cheminformatics, 2015, 7, Article No 32. Abstract
SANCDBDiallo B. N., Glenister M., Musyoka T. M., Lobb K., Bishop Ö. T., SANCDB: an update on South African natural compounds and their readily available analogs. Journal of Cheminformatics, 2021, 13, Article No 37. Abstract
SCUBIDOOChevillard F., Kolb P., SCUBIDOO: A large yet screenable and easily searchable database of computationally created chemical compounds optimized toward high likelihood of synthetic tractability. Journal of Chemical Information and Modeling, 2015, 55, 1824–1835. Abstract
SigMolRajput A., Kaur K., Kumar M., SigMol: repertoire of quorum sensing signaling molecules in prokaryotes. Nucleic Acids Research, 2016, 44, D634–D639. Abstract
Springer MaterialsProvider: Springer
SuperNaturalBanerjee P., Erehman J., Gohlke B.-O., Wilhelm T., Preissner R., Dunkel M., Super Natural II-a database of natural products. Nucleic Acids Research, 2015, 43, D935–D939. Abstract
SureChEMBLPapadatos G., Davies M., Dedman N., Chambers J., Gaulton A., Siddle J., Koks R., Irvine S. A., Pettersson J., Goncharoff N., Hersey A., Overington J. P., SureChEMBL: a large-scale, chemically annotated patent document database. Nucleic Acids Research, 2016, 44, D1220–D1228. Abstract
UEFS Natural ProductsProvider: The State University of Feriera De Santana, Bahia, Brazil
UniChemChambers J., Davies M., Gaulton A., Hersey A., Velankar S., Petryszak R., Hastings J., Bellis L., McGlinchey S., Overington J. P., UniChem: a unified chemical structure cross-referencing and identifier tracking system. Journal of Cheminformatics, 2013, 5, Article No 3. Abstract
UNIIQUIMProvider: Universidad Nacional Autonoma de Mexico
UNPDGu J., Gui Y., Chen L., Yuan G., Lu H.-Z., Xu X. Use of natural products as chemical library for drug discovery and network pharmacology. PLoS ONE. 2013, 8, e62839. Abstract
VIETHERBNguyen-Vo T.-H., Le T., Pham D., Nguyen T., Le P., Nguyen A., Nguyen T., Nguyen T.-N., Nguyen V., Do H., Trinh K., Duong H. T., Le L., VIETHERB: a database for Vietnamese herbal species. Journal of Chemical Information and Modeling, 2019, 59, 1–9. Abstract
ZINCIrwin J. J., Sterling T., Mysinger M. M., Bolstad E. S., Coleman R. G., ZINC: A free tool to discover chemistry for biology. Journal of Chemical Information and Modeling, 2012, 52, 1757–1768. Abstract
ZINC 15Sterling T., Irwin J. J., ZINC 15 – ligand discovery for everyone. Journal of Chemical Information and Modeling, 2015, 55, 2324–2337. Abstract
ZINC 20Irwin J. J., Tang K. G., Young J., Dandarchuluun C., Wong B. R., Khurelbaatar M., Moroz Y. S., Mayfield J., Sayle R. A., ZINC20—A free ultralarge-scale chemical database for ligand discovery. Journal of Chemical Information and Modeling, 2020, 60, 6065-6073. Abstract