Question: Cluster Ligand Database And Extract Fragments
3
gravatar for Flow
2.2 years ago by
Flow1.4k
Flow1.4k wrote:

We have a database of 5000 mol2 ligand structures from ZINC database. We wonder what could be the best approach for performing this;

a) process database and get ligand clusters in terms of similarity, and also after flexible alignment

b) after a), extract the mol2 files of the most common fragments

Thanks

ADD COMMENTlink modified 7 months ago by Biostar ♦♦ 0 • written 2.2 years ago by Flow1.4k
2
gravatar for dimkal
2.1 years ago by
dimkal650
dimkal650 wrote:

Both points that you're describing are very easy to do with Canvas (by Schrodinger). Not sure if you have access to it, perhaps you can get an evaluation copy. Here's a link to the Canvas product page.

ADD COMMENTlink written 2.1 years ago by dimkal650
1

if you want, i have access to Canvas. send it to me I'll do it for you.

ADD REPLYlink written 2.1 years ago by dimkal650

I had a quick look but they do not seem to be free

ADD REPLYlink written 2.1 years ago by Flow1.4k

thanks a lot for your offer, but I am in the situation that I need to do this on a regular basis

ADD REPLYlink written 2.1 years ago by Flow1.4k
2
gravatar for Rajarshi Guha
2.1 years ago by
Rajarshi Guha750
Rajarshi Guha750 wrote:

There are a number of free tools to perform the clustering and the fragment based analysis for small molecules. You could use the CDK to evaluate numerical descriptors or binary fingerprints and use that data to perform clustering (R, WEKA, Matlab, Python, ....). Other options include RDKit or OpenBabel

For fragmentation, you could also use the CDK, RDKit or a tool from NCGC to generate molecular fragments. R is particularly handy for fragment based analysis, and works directly with the CDK (see slides 158-169, though the API has been updated to be easier to use)

And given you're working with just 5000 molecules, the whole thing could be quite straightforward within R (assuming a decent amount of RAM), but of course other environments such as PipelinePilot and KNIME are also pretty straihgtforward

ADD COMMENTlink written 2.1 years ago by Rajarshi Guha750
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