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Question: Question: How to superpose ligands ?

pinke
1099 days ago

Question: How to superpose ligands ?

Could anyone please tell me, how to superpose ligands to compare ?

Answers
0

Hi Pinke,

Try FLEXS http://pubs.acs.org/doi/abs/10.1021/jm981037l?journalCode=jmcmar Method for Fast Flexible Ligand Superposition. ProFit and SuperPose protein superposition server are also good for this.

Thanks

0

Hi Pinke,

As per my vivid knowledge of molecular docking, I guess there are an option to run ligand_alignment.py in PyMol http://compbio.cs.toronto.edu/ligalign/tutorial.html

If you believe in trying and testing new algorithms for the same then optAlign from the Kabsch code http://www.pymolwiki.org/index.php/Kabsch is a simply an algorithm to find the optimal superposition of two coordinate sets.  Another one is CEAlign http://www.pymolwiki.org/index.php/Cealign that could solve the problem entirely, but would need some modification to do so.

Thanks

0

@shikha and jit , Thank you veryy much for replying,

I just started learning bioinformatics tools. iam not much used to linux os, so please please kindly suggest me some tool which is free , user friendly and compatible with windows xp. Thank you.