FAQ
General
Q: What is the Natural Products Atlas?
A: The Natural Products Atlas is a database of all small molecules discovered from bacteria and fungi. It is
designed to provide a central repository for all naturally occurring microbial compounds as a resource for
researchers in the area of natural products science.
Q: How do I use it?
A: Simple! Head to the Basic Search page, and start exploring. It's free. The Search section allows you to
find compounds with specific attributes (e.g. name, molecular weight, origin species). The Explore section
provides several different viewpoints on chemical space occupied by natural products, and helps to put
individual compounds in context with other entries in the database. The Discover section is an evolving set
of dashboards that allow you to look at the dataset from other viewpoints. We encourage you to deposit new
compounds through the Deposit page, and to let us known about
Additions and Corrections. If you use either of these tools you will need to register using our simple
login system.
Compound Structures
Q: Why is my compound missing from the Atlas?
A: There could be several reasons for this. Have a look at the About
section to see if your compound fits our criteria. If it does, then please let us know by filling in a
couple of details in the Additions and Corrections section.
Q: Why don't you include compounds for plants?
A: This area is just too huge. There are some good existing commercial resources that cover this set of
compounds, as well as some nice academic efforts on this subject. Check out the LOTUS resource or the COCONUT database for more information in
this area.
Q: The stereochemistry for one of compounds in the Atlas is incomplete/ wrong. What should I do?
A: Check the list of reassignment papers in the
Compounds page to make sure you are looking at the most recent paper about the structure. If this list
is incomplete and we don't have the latest structure correct, please help us out by submitting the correct
structure and the reference that defined this structure reassignment in the Additions and Corrections section.
Q: Why is the picture of the structure so badly overlapped?
A: We use an automated tool to draw structures, and it can't always cope well with structures with complex
ring systems. You can easily manipulate the layout in any chemistry drawing package by copying either the
Inchi or SMILES from the Compounds page and then
'Paste special' in your favourite drawing tool. Alternatively, you can download the mol file from the compound
page and open this in any structure drawing package.
The Explore Section
Q: What is the significance of clusters? How are they defined?
A: Clusters are groups of compounds in the Atlas that share very high structural similarity. It is a way to
quickly find out which other compounds are known that relate closely to a given compound of interest.
Clusters are created by using Morgan fingerprinting (radius = 2) and Dice similarity scoring in RDkit, with
a similarity cutoff of 0.75. These clusters are not based on whether compounds were published in the same
paper, or if they have the same common name, but rather on whether they share substantial similarities in
structural features.
Q: What about nodes? How do they differ from clusters?
A: Nodes are groups of clusters that share more general structural features. in essence you can think of
clusters as your immediate family, and nodes as your broader family tree. Nodes are calculated by finding
the most interconnected compound in each cluster, and using these compounds as representatives for each
cluster to calculate structure similarities. This calculation differs from cluster similarities in both the
fingerprinting method (Atom pairs) and the similarity scoring method (Dice, 0.7 cutoff).
Q: What does the Global view show me?
A: The global view presents all of the nodes in the NP Atlas, arrayed as a spherical plot. The distribution
of nodes in this spherical plot is defined based on their C:H, C:O and C:N ratios. C:H defines the polar
angle (the radial value in the xy plane). C:O defines the azimuth value (the angle in the z axis) and the
C:N ratio sets the radius (distance from the origin). Therefore, nodes containing similar types of compounds
should be in similar places in the global plot. This coordinate system is dependent on physical properties
of the compounds in the sample set, so the positions of existing nodes will not change with the addition of
new data to the Atlas over time.
Taxonomy
Q: Why does the NP Atlas not include full taxonomic assignments for producing organisms?
A: It does! You can search at any taxonomic rank on the Basic Search page. You can get all the taxonomic
details for each compound from the json files in the Zenodo repository. You can also explore the taxonomic
distributions using the Taxonomy dashboard in the Discover section.
Q: The genus name listed for a producing organism is not on the list of currently accepted genus names
in LPSN/ Mycobank. Why is that?
A: Genus names are provided as reported in the original isolation paper. We use the data from
LPSN to verify and validate genus names for all
bacterial metabolites and Mycobank to
verify and validate genus names for all fungal metabolites.
Discover Section
Q: What is SNAP-MS?
A: SNAP-MS is a tool for annotation compound family assignments based on grouping of molecules in the Atlas
and grouping of MS/MS spectra from your metabolomics data. You can read about the platform in this paper:
10.1038/s41467-022-35734-z.
If you have trouble you can access the documentation for SNAP-MS
here.
Q: I can't do the kind of search I want easily. Can you help?
A: We accept suggestions and requests for new dashboards in the Discover section. If enough people ask for
the same kind of data display, we will implement it. Send us your thoughts via the contact information on
the Contact page.
