About
Poynton, E. F.; van Santen, J. A.; Pin, M.; Contreras, M. M.; McMann, E.; Parra, J.; Showalter,B.; Zaroubi, L.; Duncan, K. R.; Linington, R. G.* "The Natural Products Atlas 3.0: Extending the Database of Microbially-Derived Natural Products", Nucleic Acids Research, 2024, gkae1093. 10.1093/nar/gkae1093
van Santen, J. A.; Poynton, E. F.; Iskakova, D.; McMann, E.; Alsup, T. A.; Clark, T. N.; Fergusson, C. H.; Fewer, D. P.; Hughes, A. H.; McCadden, C. A.; Parra Villalobos, 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, D1, 11, D1317-D1323. 10.1093/nar/gkab941
van Santen, J. A.; Jacob, G.; Leen Singh, A.; Aniebok, V.; Balunas, M. J.; Bunsko, D.; Carnevale Neto, F.; Castaño-Espriu, L.; Chang, C.; Clark, T. N.; Cleary Little, J. L.; Delgadillo, D. A.; Dorrestein, P. C.; Duncan, K. R.; Egan, J. M.; Galey, M. M.; Haeckl, F. P. J.; Hua, A.; Hughes, A. H.; Iskakova, D.; Khadilkar, A.; Lee, J.-H.; Lee, S.; LeGrow, N.; Liu, D. Y.; Macho, J. M.; McCaughey, C. S.; Medema, M. H.; Neupane, R. P.; O'Donnell, T. J.; Paula, J. S.; Sanchez, L. M.; Shaikh, A. F.; Soldatou, S.; Terlouw, B. R.; Tran, T. A.; Valentine, M.; van der Hooft, J. J. J.; Vo, D. A.; Wang, M.; Wilson, D.; Zink, K. E.; Linington, R. G.* "The Natural Products Atlas: An Open Access Knowledge Base for Microbial Natural Products Discovery”, ACS Central Science, 2019, 5, 11, 1824-1833. 10.1021/acscentsci.9b00806
Users are encouraged to cite these publications if the Atlas was used in the course of their study.
The NP Atlas Team
The Natural Products Atlas is created by a consortium of data curators from around the world, and is maintained by researchers in the Linington Research Group in the Department of Chemistry at Simon Fraser University in Vancouver, Canada.
Current curators include: Ella Poynton, Jeffrey van Santen, Matthew Pin, Marla Macias Contreras, Emily McMann, Jonathan Parra, Brandon Showalter, Liana Zaroubi, Katherine Duncan and Roger G. Linington
Previous curators include: Tyler Alsup, Victor Aniebok, Marcy Balunas, Derek Bunsko, Fausto Carnevale-Neto, Laia Castano-Espriu, Chen Chang, Trevor Clark, Jessica Cleary Little, David Delgadillo, Joseph Egan, Claire Fergusson, David Fewer, Melissa Galey, Jake Haeckl, Alex Hua, Alison Hughes, Dasha Iskakova, Grégoire Jacob, Elisabeth Janssen, Aswad Khadilkar, Jeongho Lee, Sanghoon Lee, Nicole LeGrow, Dennis Liu, Jocelyn Macho, Caitlin McCadden, Catherine McCaughey, Marnix Medema, Ram Neupane, Timothy O’Donnell, Jasmine Paula, Jeffrey Rudolf, Laura Sanchez, Anam Shaikh, Amrit Leen Singh, Sylvia Soldatou, Barbara Terlouw, Tuan Anh Tran, Mercia Valentine, Justin van der Hooft, Duy Vo, Darryl Wilson, Katherine Zink.
Compound Scope
The Natural Products Atlas is designed to cover all microbially-derived natural products published in the peer-reviewed primary scientific literature. This encompasses bacterial, fungal and cyanobacterial compounds, but does not include compounds from plants, invertebrates or other higher organisms unless these compounds have also been explicitly identified from a microbial source. Compounds from lichens and mushrooms and other higher fungi are included. Compounds from marine macro algae and diatoms are excluded.
Compounds reported exclusively in conference proceedings, M.Sc. and Ph.D. theses, personal communications or the popular press are not included. Currently, the Natural Products Atlas does not include compounds from the patent literature.
In general compounds are only included if they were published with sufficient analytical data to permit their unambiguous structural assignment. In rare cases, structures have been included on the basis of mass spectral data alone (e.g. large families of peptidic natural products), but typically only in cases where one or more family members in the isolation paper were subject to full structural characterization.
We have excluded primary metabolites, as defined by the primary metabolite compound list curated by KEGG. We have also excluded biomolecules (enzymes, proteins etc), but have retained large amino acid-based structures if they derive from secondary metabolite biosynthesis (NRPS or RIPPs). The upper molecular weight cutoff is 3000 Da.
Configurational Assignment
Compounds are reported with the highest level of available configurational assignment. If compounds are subject to configurational assignment or revision after the initial publication the currently accepted structure is presented, with the original isolation reference listed first, and all subsequent updates to the structure provided in the reassignment reference list. If structures are subject to structural revision through synthesis or re-isolation then the correct structure is presented, with prior structures listed in the reassignment reference table. In the rare cases where published compounds are reassigned to previously published structures the name of the incorrect compound is added to the list of synonyms for the correct structure, the deprecated entry in the Atlas is retired, and the reason for deprecation provided to users who visit this now-defunct page.
Biosynthetic Engineering
The Atlas is designed to include all naturally occurring compounds, but excludes 'non-natural' natural products derived from feeding synthetic precursors, biosynthetic engineering, semi-synthesis, biotransformation and other derivatization and diversification methods. This area is complicated, and includes a number of edge cases that are difficult to categorize. Currently compounds discovered using heterologous expression are included, provided that the entire natural gene cluster is expressed. Compounds from recombination of modules from different gene clusters are excluded. Compounds discovered by manipulating regulatory proteins are included, but those created by gene knockout/ inactivation to make shunt products are not. Compounds produced by feeding naturally occurring feedstocks (e.g. proteinogenic amino acids) are included, those from feeding non-natural feedstocks (e.g. fluorotyrosine) are excluded. In short, if it is plausible that this compound could be found in nature it is included, otherwise we have excluded it.
