If you use any of these files, please cite:
Zani CL & Carroll AR. Database for Rapid Dereplication of Known Natural Products Using Data from MS and Fast NMR Experiments. J Nat Prod 80(6):1758-1766, 2017. DOI: 10.1021/acs.jnatprod.6b01093
https://www.dropbox.com/sh/xbklrj25gxp8vtg/AAC6wwPrnay_mWdGHcAOM-eBa?dl=0
June 21, 2021 DEREP-NP-COCONUT was added. We used the COlleCtion of Open NatUral producTs (COCONUT), a database with about 400,000 unique compounds. Duplicate compounds, as per the DataWarrior algorithm, were removed from the SDF file downloaded from https://coconut.naturalproducts.net/ on june 6th, 2021)
15/06/2017 We are thankfull to Prof. John Blunt, Professor Emeritus at School of Physical and Chemical Sciences, University of Canterbury, NEW ZEALAND, for this nice version of DEREP-NP for ChemFinder users. If your ChemFinder version is newer than 5 you will be asked if you want to upgrade the files. No problems with that.
Quick Tips to Use the Database in DataWarrior
- When you open the DataWarrior file you downloaded, close all graphics windows and leave only the Table and Structures windows open.
- Delete all search criteria on the right pane, if any.
- In the EDIT menu select NEW FILTER. Use text filters and the appropriate options in the dropdown box (starts with, contains, equals). To search ranges, use the SLIDER filter format when selecting the new filter and then in the right pane select the min and max values by double-clicking on the numbers at the ends of the slider.
- If you could deduce a partial structure from the NMR data, include it in the search: In the EDIT menu select NEW FILTER and then Structure [Structure List, SSS]. On the filters pane, right click in the white part of the filter and choose ADD and draw the substructure. Note that when you hover over an atom a blue dot appears and if click Q, you can define various atom properties. If you draw two substructures in the same filter it will work as OR Boolean. To create an AND query, you need set two Structure [Structure List, SSS] filters. To do this, create a new filter and select SHOW DUPLICATE FILTERS check box. Now, both SS must be present in the same structure. Note, however, that using this procedure you are not counting number of the SS, just their presence.
- The yin-yang bouton in each search means a NOT Boolean and can be used to omit structures that comply to the query.
- For other functionalities read DataWarrior help.
Modifications in v2
Date Issue status Req/Sugg_by
17/Jul/17 UNPD InChI and InChIKeys substituted using INDIGO2 InChi Node (KNIME) Done Prof. John Blunt
17/Jul/17 8541 duplicated structures (using DW) removed Zani
14/Jul/17 Manually correct 40 structures with wrong charges Done Zani
14/Jul/17 Included Indigo2 Standardizer node to correct wrong charges Done Zani
5/Jul/17 Cq sp in DEREP is not giving the correct counts. It is currently including a terminal alkyne as 2 Fixed Prof. John Blunt
5/Jul/17 Cq sp is missing CN and C=C=C Fixed Prof. John Blunt
5/Jul/17 it would be more logical to have CH3 singlet as arising from CH3-C to be consistent with CH3 doublet and triplet. The count of CH3 All - CH3 singlet would reveal other CH3s on O or N or S. Fixed Prof. John Blunt
5/Jul/17 There is currently no count of acetyl groups on N - quite a common feature. Count of amides would also be very useful. Included Prof. John Blunt
5/Jul/17 it is very useful to have counts of 1,1 and 1,2 disub alkenes, trisub alkenes and vinyl groups. Another useful count is fully substituted benzenes Included Prof. John Blunt
Jun17 CH-O(all) is counting CH anomeric (O-CH-O) twice Fixed Prof. A. Carroll