From owner-chemistry@ccl.net Wed Mar 26 18:16:01 2014 From: "Andrew Voronkov drugdesign-,-yandex.ru" To: CCL Subject: CCL: Similarity exclusion filters Message-Id: <-49871-140326181502-4894-wlj79LMFI3trGquUo5V6aQ*_*server.ccl.net> X-Original-From: Andrew Voronkov Content-Transfer-Encoding: 7bit Content-Type: text/plain Date: Thu, 27 Mar 2014 02:14:53 +0400 MIME-Version: 1.0 Sent to CCL by: Andrew Voronkov [drugdesign[a]yandex.ru] Dear CCL users, are you aware of any scripts or programs, which can be used for filtering out similar compounds. Let s say there is a set of known compounds for the biotarget. Then I make a screening of certain dataset through this biotarget. After screening, I would like to filter out all compounds, which are similar to the already known dataset, which I provide let s say as smiles file. It would be nice to have some script, where I can setup that for example compounds with 80-95% similarity to already known compounds are filtered out. Are you aware of such software, scripts? Maybe there is someone, who can consult me about writing such script? Maybe something like OpenBabel etc. can be used for that? Best regards, Andrey From owner-chemistry@ccl.net Wed Mar 26 22:13:00 2014 From: "=?ISO-8859-1?Q?Jos=E9_Fernando_Ruggiero_Bachega?= ferbachega[#]gmail.com" To: CCL Subject: CCL: GTKDynamo: A PyMOL Plug-In for QC/MM Hybrid Potential Simulations Message-Id: <-49872-140326195250-5944-HZHMHsY6NHAH+/AI/td7DQ:-:server.ccl.net> X-Original-From: =?ISO-8859-1?Q?Jos=E9_Fernando_Ruggiero_Bachega?= Content-Type: multipart/alternative; boundary=001a1136be723cdb6504f58b2a82 Date: Wed, 26 Mar 2014 20:52:44 -0300 MIME-Version: 1.0 Sent to CCL by: =?ISO-8859-1?Q?Jos=E9_Fernando_Ruggiero_Bachega?= [ferbachega**gmail.com] --001a1136be723cdb6504f58b2a82 Content-Type: text/plain; charset=ISO-8859-1 Dear CCL members; I'd like to announce that a new version of GTKDynamo program is now available on our home page: https://sites.google.com/site/gtkdynamo/home GTKDynamo is free/open source software which, together with pDynamo, transforms PyMOL into a powerful interface for molecular modeling. The interface has been designed to facilitate determining reaction pathways in biological systems, specially using hybrid QC/MM (or QM/MM) methods. Best regards Fernando Bachega --001a1136be723cdb6504f58b2a82 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
=09 =09 =09

Dear CCL members;

I'd like to announce that a new version of GTKDynamo program is now available on our home page:=A0 https://sites.goog= le.com/site/gtkdynamo/home

GTKDynamo is free/open source software which, together with pDynamo, transforms PyMOL into a powerful interface for molecular modeling. The interface has been designed to facilitate determining reaction pathways in biological systems, specially using hybrid QC/MM (or QM/MM) methods.


Best regards

Fernando Bachega

--001a1136be723cdb6504f58b2a82-- From owner-chemistry@ccl.net Wed Mar 26 22:48:00 2014 From: "Nicolas Cheron nicolas.cheron.boulot * gmail.com" To: CCL Subject: CCL: Similarity exclusion filters Message-Id: <-49873-140326195257-5980-Nd2edlBP1n3X3QyUKPqU4g^server.ccl.net> X-Original-From: Nicolas Cheron Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Wed, 26 Mar 2014 19:52:11 -0400 MIME-Version: 1.0 Sent to CCL by: Nicolas Cheron [nicolas.cheron.boulot|*|gmail.com] Hi, You can do it with jcsearch from ChemAxon: * jcsearch -q "${Smiles_String}" DatabaseInWhichYouSearch.smi -t:i:0.2 (0.2 is the treshold: 0=very similar, 1=very different) You can also do it with OpenBabel: * obabel SmilesFile.smi DatabaseInWhichYouSearch.smi -ofpt This will give you the list of the Tanimoto scores with the names of the molecules with which you have compared your query. Nicolas 2014-03-26 18:14 GMT-04:00 Andrew Voronkov drugdesign-,-yandex.ru : > > Sent to CCL by: Andrew Voronkov [drugdesign[a]yandex.ru] > Dear CCL users, are you aware of any scripts or programs, which can be used for filtering out similar compounds. > Let s say there is a set of known compounds for the biotarget. Then I make a screening of certain dataset through this biotarget. After screening, I would like to filter out all compounds, which are similar to the already known dataset, which I provide let s say as smiles file. > It would be nice to have some script, where I can setup that for example compounds with 80-95% similarity to already known compounds are filtered out. > > Are you aware of such software, scripts? Maybe there is someone, who can consult me about writing such script? Maybe something like OpenBabel etc. can be used for that? > > Best regards, > Andrey> >