Question: Small Molecule Superposition Tool
3
gravatar for Nir London
7.8 years ago by
Nir London220
Nir London220 wrote:

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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ADD COMMENTlink written 7.8 years ago by Nir London220

can you clarify, when you say "databse of conformations" do you mean same molecule or all different molecule.

ADD REPLYlink written 7.8 years ago by dimkal730
1
gravatar for Egon Willighagen
7.8 years ago by
Maastricht
Egon Willighagen5.2k wrote:

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.

ADD COMMENTlink written 7.8 years ago by Egon Willighagen5.2k
0
gravatar for Flow
7.8 years ago by
Flow1.5k
Flow1.5k wrote:

I would recommend you chemaxon tools or also open eyes tools

ADD COMMENTlink written 7.8 years ago by Flow1.5k

Do you know of a specific tool or API command? or generally assume they have one?

ADD REPLYlink written 7.8 years ago by Nir London220

I was in several conferences and they were always there talking about their products for this purpose. Can not remember details. I encorauge you to visit their websites, good luck!

ADD REPLYlink written 7.8 years ago by Flow1.5k

Chemaxon tools are free btw!

ADD REPLYlink written 7.8 years ago by Flow1.5k
0
gravatar for Alastair Kerr
7.8 years ago by
Alastair Kerr5.2k
The University of Edinburgh, UK
Alastair Kerr5.2k wrote:

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++. [?]

ADD COMMENTlink written 7.8 years ago by Alastair Kerr5.2k
0
gravatar for Woa
7.8 years ago by
Woa2.7k
United States
Woa2.7k wrote:

FlexS (commercial, scriptable)

ADD COMMENTlink written 7.8 years ago by Woa2.7k
0
gravatar for dimkal
7.8 years ago by
dimkal730
United States
dimkal730 wrote:

I'm know that Schrodinger has such tools like substructure search and small molecule fingerprints. Small molecule matching is not a trivial thing, and in my opinion Schrodinger tools do the best, not free though.

ADD COMMENTlink written 7.8 years ago by dimkal730
0
gravatar for mikmaksi
7.8 years ago by
mikmaksi60
mikmaksi60 wrote:

I'll recommend Visual Molecular Dynamics, since no one has mentioned it yet. It's definitely command-line scriptable.

ADD COMMENTlink written 7.8 years ago by mikmaksi60

vmd cannot automatically alight a ligand. You need to specify corresponding atoms to VMD. also it's not trivial to align ligands with different chemistry

ADD REPLYlink written 7.8 years ago by dimkal730
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