Miscellaneous compounds
| 3DMET | Maeda 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 |
| AfroDB | Ntie-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 Repository | Malde 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 |
| BARD | Howe 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 |
| BIOFACQUIM | 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, Article No 31. Abstract |
| Cancer Odor Database | Janfaza 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 |
| CARLSBAD | Mathias 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 Chemistry | Jacobs 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 |
| CFam | Zhang 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 |
| ChEBI | Degtyarenko 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 |
| ChemBank | Seiler 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.cn | Provider: Shanghai Zhihua ChemTech Inc. |
| ChEMBL | Zdrazil B., Felix E., Hunter F., Manners E. J., Blackshaw J., Corbett S., de Veij M., Ioannidis H., Mendez Lopez D., Mosquera J. F., Magarinos M. P., Bosc N., Arcila R., Kizilören T., Gaulton A., Bento A. P., Adasme M. F., Monecke P., Landrum G. A., Leach A. R., The ChEMBL Database in 2023: a drug discovery platform spanning multiple bioactivity data types and time periods. Nucleic Acids Research, 2024, 52, D1180–D1192. Abstract |
| ChemDB | Chen 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 |
| ChemFOnt | Wishart D. S., Girod S., Peters H., Oler E., Jovel J., Budinski Z., Milford R., Lui V. W., Sayeeda Z., Mah R., Wei W., Badran H., Lo E., Yamamoto M., Djoumbou-Feunang Y., Karu N., Gautam V., ChemFOnt: the chemical functional ontology resource. Nucleic Acids Research, 2023, 51, D1220–D1229. Abstract |
| Chemical Checker | Duran-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 |
| ChemIDplus | Tomasulo P., ChemIDplus-super source for chemical and drug information. Medical Reference Services Quarterly, 2002, 21, 53-59. Abstract |
| cheML.io | Zhumagambetov 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 |
| ChemSpace Atlas | Zabolotna Y., Bonachera F., Horvath D., Lin A., Marcou G., Klimchuk O., Varnek A., Chemspace Atlas: multiscale chemography of ultralarge libraries for drug discovery. Journal of Chemical Information and Modeling, 2022, 62, 4537–4548. Abstract |
| ChemSpider | Pence 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 |
| ClassyFire | Djoumbou 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 |
| CMNPD | Lyu 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 |
| COCONUT | Sorokina 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 Database | Borysov 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 |
| ECHA | Provider: European Chemicals Agency |
| EMSL Basis Set Exchange | Schuchardt 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 SRS | Provider: Food and Drug Administration |
| FDB-17 | Visini R., Awale M., Reymond J.-L., Fragment database FDB-17. Journal of Chemical Information and Modeling, 2017, 57, 700–709. Abstract |
| Figshare | Thelwall M., Kousha K., Figshare: A universal repository for academic resource sharing? Online Information Review, 2016, 40, 333–346. Abstract |
| FilTer BaSe | Kolte 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 |
| FragmentStore | Ahmed 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 ChemWebRDF | Galgonek J., Vondrášek J., IDSM ChemWebRDF: SPARQLing small‑molecule datasets. Journal of Cheminformatics, 2021, 13, Article No 38. Abstract |
| J-Global | Provider: Japan Science and Technology Agency |
| KEGG compound | Kanehisa M., Furumichi M., Sato Y., Kawashima M., Ishiguro-Watanabe M., KEGG for taxonomy-based analysis of pathways and genomes. Nucleic Acids Research, 2023, 51, D587–D592. Abstract |
| Ligandbook | Domański 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 |
| LINCS | Provider: National Institutes of Health |
| MarkerDB | Wishart 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 |
| MeSH | Sayers E. W., Bolton E. E., Brister J. R., Canese K., Chan J., Comeau D. C., Farrell C. M., Feldgarden M., Fine A. M., Funk K., Hatcher E., Kannan S., Kelly C., Kim S., Klimke W., Landrum M. J., Lathrop S., Lu Z., Madden T. L., Malheiro A., Marchler-Bauer A., Murphy T. D., Phan L., Pujar S., Rangwala S. H., Schneider V. A., Tse T., Wang J., Ye J., Trawick B. W., Pruitt K. D., Sherry S. T., Database resources of the National Center for Biotechnology Information in 2023. Nucleic Acids Research, 2023, 51, D29–D38. Abstract |
| MMsINC | Masciocchi 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 demo | Haider N., Functionality pattern matching as an efficient complementary structure/reaction search tool: an open-source approach. Molecules, 2010, 15, 5079-5092. Abstract |
| NANPDB | Ntie-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 |
| NikkajiWeb | Provider: Japan Science and Technology Agency |
| NLM | Provider: US Department of Health & Human Services |
| NMRShiftDB | Steinbeck C., Kuhn S., NMRShiftDB – compound identification and structure elucidation support through a free community-built web database. Phytochemistry, 2004, 65, 2711–2717. Abstract |
| NPAtlas | van 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 |
| NUBBEDB | Valli 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 |
| OLS | Jupp 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 |
| OLSVis | Vercruysse S., Venkatesan A., Kuiper M., OLSVis: an animated, interactive visual browser for bio-ontologies. BMC Bioinformatics, 2012, 13, Article No 116. Abstract |
| Phytochemica | Pathania S., Ramakrishnan S. M., Bagler G., Phytochemica: a platform to explore phytochemicals of medicinal plants. Database, 2015, Article No bav075. Abstract |
| PubChem | Bolton 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 2023 update. Nucleic Acids Research, 2023, 51, D1373–D1380. Abstract |
| QsarDB | Ruusmann 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 |
| SANCDB | Diallo 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 |
| SCUBIDOO | Chevillard 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 |
| SigMol | Rajput A., Kaur K., Kumar M., SigMol: repertoire of quorum sensing signaling molecules in prokaryotes. Nucleic Acids Research, 2016, 44, D634–D639. Abstract |
| Springer Materials | Provider: Springer |
| SuperNatural | Gallo K., Kemmler E., Goede A., Becker F., Dunkel M., Preissner R., Banerjee P., SuperNatural 3.0-a database of natural products and natural product-based derivatives. Nucleic Acids Research, 2023, 51, D654–D659. Abstract |
| SureChEMBL | Papadatos 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 Products | Provider: The State University of Feriera De Santana, Bahia, Brazil |
| UniChem | Chambers 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 |
| UNIIQUIM | Gómez-García A., Medina-Franco J. L., Progress and impact of Latin American natural product databases. Biomolecules 2022, 12, Article No 1202. Abstract |
| UNPD | Gu 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 |
| VIETHERB | Nguyen-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 |
| ZINC | Irwin 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 15 | Sterling T., Irwin J. J., ZINC 15 – ligand discovery for everyone. Journal of Chemical Information and Modeling, 2015, 55, 2324–2337. Abstract |
| ZINC 20 | Irwin 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 |
| ZINC 22 | Tingle B. I., Tang K. G., Castanon M., Gutierrez J. J., Khurelbaatar M., Dandarchuluun C., Moroz Y. S., Irwin J. J., ZINC-22-A free multi-billion-scale database of tangible compounds for ligand discovery. Journal of Chemical Information and Modeling, 2023, 63, 1166−1176. Abstract |
Last Updated on 12-02-2024 by Piotr Minkiewicz