Hi Everyone,
Does anyone knows of a good tool for the super-positioning of small molecules? Preferably from command-line/scriptable. The task it should solve e.g. is given one conformation for a small molecule, compare it to a large database of conformations and calculate RMSD. Optimally the molecules shouldn't even be identical or in the same frame of reference.
Your input is most appreciated!
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Nir London •
The Chemistry Development Kit can do this. It has a few algorithms for MCS to determine how two molecules should be aligned, as well as a RMSD-based algorithm to align two molecules via the shared MCS. This functionality is used in Bioclipse, and can be scripted as detailed in this blog post, and reproduced here:
var smileses = new Array("CC(C)C", "CCCN", "CCC=O");
var unaligned = cdk.createMoleculeList();
for (i=0; i<smileses.length; i++) {
mol = cdk.fromSMILES(smileses[i]);
mol = cdk.generate3dCoordinates(mol)
unaligned.add(mol);
}
var aligned = cdk.kabsch(unaligned)
jmol.load(aligned.get(0));
for (i=1; i<aligned.size(); i++) {
jmol.append(aligned.get(i));
}
The last code bit visualized the alignment in Jmol.
Since you are looking at conformers, it may be possible to take advantage of the fact that atom ordering is identical, allowing you to skip the MCS step, but that is harder to do with the current Bioclipse APIs.
Do you know of a specific tool or API command? or generally assume they have one?
The structural labs here use Lidaeus
LIDAEUS (LIgand Discovery At Edinburgh UniverSity) is a high throughput in-silicon screening program written by Dr Paul Taylor of the Institute of Structural and Molecular Biology, University of Edinburgh. LIDAEUS is a highly adaptable and modular rigid body docking in-silicon screening code written in C++. [?]
I'll recommend Visual Molecular Dynamics, since no one has mentioned it yet. It's definitely command-line scriptable.
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can you clarify, when you say "databse of conformations" do you mean same molecule or all different molecule.