From owner-chemistry %-% at %-% ccl.net Tue May 19 17:44:00 2020 From: "Pavel Polishchuk pavel_polishchuk]-[ukr.net" To: CCL Subject: CCL: Pharmacophore flexible search tool Message-Id: <-54069-200519162922-19846-Us7R0CXd3lpQLrU1UgPG8Q*o*server.ccl.net> X-Original-From: Pavel Polishchuk Content-Language: en-US Content-Type: multipart/alternative; boundary="------------5EC06F94B77D5DC7C6C51D6A" Date: Tue, 19 May 2020 22:29:13 +0200 MIME-Version: 1.0 Sent to CCL by: Pavel Polishchuk [pavel_polishchuk(_)ukr.net] This is a multi-part message in MIME format. --------------5EC06F94B77D5DC7C6C51D6A Content-Type: text/plain; charset=UTF-8; format=flowed Content-Transfer-Encoding: 8bit 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 > > ------------------------------------------------------------------------------------------ > Dr. Douglas R. Houston > Senior Lecturer in Computational Biochemistry > Institute of Quantitative Biology, Biochemistry and Biotechnology > Room 2.12,Waddington 1 Building > King's Buildings > University of Edinburgh > Edinburgh,EH9 3BF, UK > Tel. 07986875743 > > The University of Edinburgh is a charitable body, registered in > Scotland, with registration number SC005336. -- Dr. Pavel Polishchuk senior researcher Institute of Molecular and Translational Medicine Faculty of Medicine and Dentistry Palacky University Hněvotínská 1333/5 779 00 Olomouc Czech Republic +420 585632298 --------------5EC06F94B77D5DC7C6C51D6A Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: 8bit 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

------------------------------------------------------------------------------------------

Dr. Douglas R. Houston

Senior Lecturer in Computational Biochemistry

Institute of Quantitative Biology, Biochemistry and Biotechnology

Room 2.12, Waddington 1 Building

King's Buildings

University of Edinburgh

Edinburgh, EH9 3BF, UK

Tel. 07986875743

The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

-- 
Dr. Pavel Polishchuk
senior researcher
Institute of Molecular and Translational Medicine
Faculty of Medicine and Dentistry
Palacky University
Hněvotínská 1333/5 
779 00 Olomouc
Czech Republic
+420 585632298

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