CCL: Pharmacophore flexible search tool



Hi Douglas,

  I recommend pharmit tool as it seems most relevant to your task - https://sourceforge.net/p/pharmit/code/ci/master/tree/src/
  It can generate a pharmacophore query for a single reference conformer and a conformer library for your dataset and it can screen the database against the query.
  Database generation will take relatively long time but screening will be very fast.

  Alternatively you may use a tool which is developed in my group - psearch https://github.com/meddwl/psearch/tree/dev2 (recommend to use this branch, it was tested but not yet merged to master)
  It can generate a database of conformers and screen it against a pharmacophore query.
  The tool has some limitations and drawbacks:
  1) it uses undirected features only (H-bond donors/acceptors and aromatic).
  2) it can generate ligand-based models for a training data set but to generate a pharmacophore for a single conformer you have to use pmapper - https://github.com/DrrDom/pmapper
  3) screening does not guarantee to find all matching compounds in a database, but for large datasets this can be acceptable
  But there are also some advantages, e.g. multicore support that speeds up all steps and easy installation
  If you will have questions regarding psearch/pmapper fill free to contact me.

Kind regards,
Pavel.
 

On 19/05/2020 20:00, HOUSTON Douglas DouglasR.Houston]![ed.ac.uk wrote:
Hi all,

Does anyone know of a free (for academics at least) chemical search tool, that will screen a large compound library (say an SDF of 100,000 molecules) against a reference pharmacophore/ligand, and treat the library compounds as flexible and not rigid?

I've asked this before but for some reason the formatting was so screwed up I don't think most people could read it!

Regards,
Doug

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Dr. Douglas R. Houston
Senior Lecturer in Computational Biochemistry
Institute of Quantitative Biology, Biochemistry and Biotechnology
Room 2.12, Waddington 1 Building
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--
 Dr. Pavel Polishchuk
 senior researcher
 Institute of Molecular and Translational Medicine
 Faculty of Medicine and Dentistry
 Palacky University
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