Ask for help from the community and get access to some deals from generous donors.
To get help or seek opinions from others, please open a new topic with a request in this category!
If you need computational resources / licenses, we also have some made aware of some generous offers:
BioSolveIT is offering a free 30 day license on their SeeSAR technology to help with designs. Please use the relevant request form on their site and mention “PostEra-COVID”
If you need computational resources, we can likely get you some. So feel please free to ask here. However, we have also found that if you mention you are working on COVID, companies/universities are sometimes kind enough to help with resources.
Due to the high demand, BioSolveIT decided to support the community with licenses for our Chemical Space search technology.
There are several ways to use it…
For the people who like an app:
The tool is called infiniSee. Download it from the website and follow the help to get it running.
For the hard-core users:
Download and install the machinery, which is behind infiniSee, named FeatureTrees. Download the space you want to search, put it in the same folder as FTrees and your license. Open the comandline and start with
FTrees.exe -h
which will show you all your search options.
For the KNIME-rs:
Install the nodes as described here. Use the “Chemical Space Search with FTrees” node and feed it with you favorite space.
The matching license…
Can be obtained like for SeeSAR using the request form. We will do the same 30 day thing.
Spaces!
There are several. Whilst the interest so far was in the REAL Space (13 bio compounds, purchasable from Enamine), I’d like to mention that there are as well the GalaXi (1.7 bio compounds, purchasable from WuXi) and the KnowledgeSpace (3 * 10^14 molecules, not purchasable), all can be downloaded and searched as described above.
Hi Franca, we are using SeeSAR… I have faced one problem regarding 6lu7 in SeeSAR, the SeeSAR was unable to show the co-crystal ligand (N3, peptide inhibitor) in the protein window as ligand. I thought that as it is a peptide, because of that may be the software unable to show it as ligand. So is there any way to solve this problem out?
Hi Neeluptal!
Funny that you ask, because yesterday SeeSAR 10.1 came out, which is able to solve that problem. Please download this version from our website (the license you got will remain valid), then follow this workflow:
go to the protein editor mode first
download your pdb file
to to the chains-tab in the sequence view
right-click on the little peptide (chain c in your case) and “classify chain as ligand”
store the protein in the table (with the green arrow)
right-click on your “new” protein in the table and “add to protein mode”
Please download this version from our website (the license you got will remain valid), then follow this workflow: