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 occuring 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.
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 CENEPT Navigator tool (a database of databases) for more resources in your subject 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 representitives 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.
Have you noticed the "Plot on Global" button on some of the pages? If you run a search and then click this button, it will project your search results onto the global view, allowing you to see how your selected compounds relate to all chemical space in the Atlas.
Q: Why does the NP Atlas not include full taxonomic assignments for producing organisms?
A: This is an important detail, and an area we aim to address in the next version of the Atlas.
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 aim to provide both old and current taxonomic names in the next Atlas release for cases where strains have been subject to taxonomic revision. We use the data from Mycobank in order to verify and validate genus names for all fungal metabolites.
Q: I tried to use the author dashboard, but it doesn't show all my papers. Why not?
A: There could be two reasons for this. We use the ORCID site to obtain the doi's of all the paper associated with each author. Make sure your ORCID profile is up to date. Alternatively, some of your papers may not be in the Atlas yet. Try searching for compounds from the missing papers. If they are not available, consider depositing the paper in our Deposit section.
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 imformation on the Contact page.