User: brett.spurrier

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Posts by brett.spurrier

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Answer: A: How can I align a generated ligand (from SMILES) to a ligand in a PDB?
... I think I hav found an answer using OpenBabel. obfit "Oc1ccc(cc1O)C1Nc2cccc3cccc(N1)c23" fixed.pdb moving.pdb > new_aligned.pdb Where the smiles pattern matches my moving.pdb (which is where my generated conformers came from). ...
written 5 weeks ago by brett.spurrier0
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Comment: C: Ligand alignment to a fragment of a protein structure
... This looks like it might work if the number of atoms is the same between the two molecules, and the original post said this is **not** the case. In other words, `ref_atoms` and `samples_atoms` needs to be identical in length. Am I wrong here? ...
written 5 weeks ago by brett.spurrier0
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How can I align a generated ligand (from SMILES) to a ligand in a PDB?
... I have a ligand that exists in its own PDB (*reference PDB*). I have then generated another (structurally similar, but not exact) ligand from SMILES, and written that to a PDB. I am trying to find out how to superimpose the generated ligand onto the reference PDB, but I am having trouble finding a ...
pdb assembly superimpose ligands rdkit written 5 weeks ago by brett.spurrier0

Latest awards to brett.spurrier

Scholar 5 weeks ago, created an answer that has been accepted. For A: How can I align a generated ligand (from SMILES) to a ligand in a PDB?

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