From owner-chemistry@ccl.net Fri Dec 16 10:08:00 2011 From: "Trinh Tran tranductrinh],[gmail.com" To: CCL Subject: CCL:G: Normal mode analysis Message-Id: <-46047-111216020356-24325-fCXFnLaGUOcxVY3OwlqzjQ|server.ccl.net> X-Original-From: "Trinh Tran" Date: Fri, 16 Dec 2011 02:03:54 -0500 Sent to CCL by: "Trinh Tran" [tranductrinh|*|gmail.com] Hello all, I am in search of the program REDONG developed by Allouche A. Allouche and J. Pourcin, Spectrochim. Acta 49A (1993) to do the normal mode analysis from the output of gaussian calculation. But so far, no luck in finding it. Could any of you point me at the right direction or show me the suitable program to do the same thing. I want to transform the force matrix to have the force constant. I appreciate your help, Regards, From owner-chemistry@ccl.net Fri Dec 16 10:43:00 2011 From: "Alex Allardyce aa]![chemaxon.hu" To: CCL Subject: CCL: Call for papers: ChemAxon 2012 EUGM, May 22-23, Budapest, Hungary. Message-Id: <-46048-111216034647-10673-P4RThcxMw2gmP3S6rwjwkA__server.ccl.net> X-Original-From: Alex Allardyce Content-Type: multipart/alternative; boundary="------------080906090502030704050605" Date: Fri, 16 Dec 2011 09:46:38 +0100 MIME-Version: 1.0 Sent to CCL by: Alex Allardyce [aa]-[chemaxon.hu] This is a multi-part message in MIME format. --------------080906090502030704050605 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 8bit Excuse cross postings. We are calling for papers for ChemAxon's 2012 European User Group Meeting, to be held on Tuesday and Wednesday, May 22-23 at the Hotel Budapest Centrum, in downtown Budapest, Hungary. The meeting will feature presentations from ChemAxon users, a 1-2-1 session, lightning presentations/exhibition from ChemAxon Partners and the latest updates on product developments, as well as discussion shaping future product development. Oral abstract submission deadline is *February 13th*, 2012 and for poster abstracts, May 1st. To find out more visit the meeting page and to submit an abstract please register . To review the archives of previous meetings, including original presentations (slides and video) and meeting reports from Wendy Warr and Yvonne Martin visit this page . We look forward to seeing you there. BR of the season Alex *UGM Satellite meetings:* /(May 21st afternoon and May 24th 29th)/ /Markush Forum - Monday May 21st, afternoon/ Preceding the UGM we have the third European meeting of the Markush Forum, an afternoon for interested organizations to participate in the development of ChemAxon's tools for Markush structure enumeration and search. This meeting is open to users, content developers should contact us to confirm their participation. Find out more here: http://www.chemaxon.com/events/ugm-budapest-2012/#markush /Developer and End user training - Thursday May 24th/ Following the UGM will be a 2 track developer and end user Training Day. For developers we have a tutorial/code session and for end users we have 2 tracks to focus on different products with hands-on training. Find out more about the Application Focus (End user) Training here: http://www.chemaxon.com/events/ugm-budapest-2012/#appfocus Find out more about the Developer Training here: http://www.chemaxon.com/events/ugm-budapest-2012/#developer ##################### *Review: Speakers and topics from 2011 European and US User Group Meetings *US UGM - Sept, 2011 Keynote: Surviving the whitewater of R&D Informatics: How can we best support science in an everchanging world Sarah Blendermann, Alex Drijver (Pfizer, ChemAxon) ZINC-12: A tool for the discovery, prioritization and acquisition of commercially available small molecule reagents for biology John Irwin (University of California San Francisco) A Novel Approach to Pharmaceutical Registration - Registration as a Service Charles Wilkins (GlaxoSmithKline) Implementation of an Integrated Cheminformatics System at RTI Danni Harris (RTI International) The Evolution of the Broad Chemical Biology Informatics Platform Benjamin Alexander (Broad Institute) Development and Deployment of Reagent Logistics Solution Using JChem Base/Cartridge Matthew Pustelnik (Takeda) Centralizing data for drug discovery in a multi-group academic setting with ChemAxon Erin Bolstad (University of Montana) Enterprise Deployment of JChem for Excel (JC4XL) Matthew Pustelnik (Takeda) Deploying Instant JChem on an Enterprise Scale Brett Hiemenz (GlaxoSmithKline) Excel as a Cheminformatics Interface Yingyao Zhou (Genomics Institute of the Novartis Research Foundation) Efficient simultaneous matching of multiple SMARTS using the ChemAxon toolkits Roger Sayle (NextMove Software) Advanced searching chemical structures in patents Steve Hajkowski (Thomson Reuters) Tools for Analyzing Exemplified and Markush Structures in Chemical Patents Christopher Kibbey (Pfizer) Reaction scheme: Capture, Iterator, and Parser Zhenbin Li (Boehringer Ingelheim Pharmaceuticals Inc.) Screen3D: a new high-throughput flexible alignment method Oleg Ursu (University of New Mexico) Smashing Molecules - How Molecular Fragments Allow us to Explore Large Chemical Spaces Rajarshi Guha (NIH Chemical Genomics Center) Mining promiscuous chemotypes in PubChem Oleg Ursu (University of New Mexico) Text mining for chemical information: the ChiKEL project David Milward, Daniel Bonniot de Ruisselet (Linguamatics, ChemAxon) EUGM - May 2011 The challenges facing the modern large pharma R&D manager, an exchange of views Ashley George, Alex Drijver (GlaxoSmithKline, ChemAxon) Migrating to ChemAxon : the good, the bad & the ugly Catherine Reisser (Evotec) Benchmarking ChemAxon's Name-to-Structure batch tool on patent text Andrew Hinton (Digital Science (MacMillan Publisher Ltd)) Automated spelling correction to improve recall rates of name-to-structure tools for chemical text mining Sorel Muresan (AstraZeneca) Analyzing search hits with ChemAxon's Markush Enumeration tool Guy de Weck (F. Hoffmann-La Roche AG) Perspiration, Inspiration, and Happenstance in Scientific Discoveries Yvonne Martin (Martin Consulting) DrugPredict: Online drug discovery service using polypharmacology-based interaction profiling Zoltán Simon (Delta Informatika, Eötvös Loránd University) Blobs of hope and other flights of fancy Steve Muchmore (Abbott Laboratories) Computational toxicology : in silico assessment of the hERG channel inhibition potential for the early drug cardiotoxicity testing Aleksander Mendyk (Jagiellonian University) SAR Analyzer - intuitive access to SAR information Lisa Peltason (F. Hoffmann-La Roche AG) Cheminformatics in SharePoint Ian Berry (Evotec) Interactive structure standardization Dragos Horváth (CNRS-Université de Strasbourg) Using Knime to provide desktop tools to chemists Bob Marmon (Evotec) SAR analysis in Excel using Helium and JChem Karen Worsfold (GlaxoSmithKline) 7 Years of ChemAxon at Evotec : choices and possibilities Ian Berry (Evotec) Marvin 5.4 : A new generation of structure indexing at Elsevier Heike Nau (Elsevier) Utilizing Marvin in rich internet applications using Microsoft Silverlight Hans Jürgen Himmler (AKos GmbH) -- --------------080906090502030704050605 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Excuse cross postings.

We are calling for papers for ChemAxon's 2012 European User Group Meeting, to be held on Tuesday and Wednesday, May 22-23 at the Hotel Budapest Centrum, in downtown Budapest, Hungary.

The meeting will feature presentations from ChemAxon users, a 1-2-1 session, lightning presentations/exhibition from ChemAxon Partners and the latest updates on product developments, as well as discussion shaping future product development.

Oral abstract submission deadline is February 13th, 2012 and for poster abstracts, May 1st. To find out more visit the meeting page and to submit an abstract please register.

To review the archives of previous meetings, including original presentations (slides and video) and meeting reports from Wendy Warr and Yvonne Martin visit this page.

We look forward to seeing you there.

BR of the season
Alex

UGM Satellite meetings: (May 21st afternoon and May 24th 29th)

Markush Forum - Monday May 21st, afternoon
Preceding the UGM we have the third European meeting of the Markush Forum, an afternoon for interested organizations to participate in the development of ChemAxon's tools for Markush structure enumeration and search. This meeting is open to users, content developers should contact us to confirm their participation.  Find out more here: http://www.chemaxon.com/events/ugm-budapest-2012/#markush

Developer and End user training - Thursday May 24th
Following the UGM will be a 2 track developer and end user Training Day. For developers we have a tutorial/code session and for end users we have 2 tracks to focus on different products with hands-on training.
Find out more about the Application Focus (End user) Training here: http://www.chemaxon.com/events/ugm-budapest-2012/#appfocus
Find out more about the Developer Training here: http://www.chemaxon.com/events/ugm-budapest-2012/#developer

#####################
Review: Speakers and topics from 2011 European and US User Group Meetings
US UGM - Sept, 2011
Keynote: Surviving the whitewater of R&D Informatics: How can we best support science in an everchanging world
Sarah Blendermann, Alex Drijver (Pfizer, ChemAxon)

ZINC-12: A tool for the discovery, prioritization and acquisition of commercially available small molecule reagents for biology
John Irwin (University of California San Francisco)

A Novel Approach to Pharmaceutical Registration - Registration as a Service
Charles Wilkins (GlaxoSmithKline)

Implementation of an Integrated Cheminformatics System at RTI
Danni Harris (RTI International)

The Evolution of the Broad Chemical Biology Informatics Platform
Benjamin Alexander (Broad Institute)

Development and Deployment of Reagent Logistics Solution Using JChem Base/Cartridge
Matthew Pustelnik (Takeda)

Centralizing data for drug discovery in a multi-group academic setting with ChemAxon
Erin Bolstad (University of Montana)

Enterprise Deployment of JChem for Excel (JC4XL)
Matthew Pustelnik (Takeda)

Deploying Instant JChem on an Enterprise Scale
Brett Hiemenz (GlaxoSmithKline)

Excel as a Cheminformatics Interface
Yingyao Zhou (Genomics Institute of the Novartis Research Foundation)

Efficient simultaneous matching of multiple SMARTS using the ChemAxon toolkits
Roger Sayle (NextMove Software)

Advanced searching chemical structures in patents
Steve Hajkowski (Thomson Reuters)

Tools for Analyzing Exemplified and Markush Structures in Chemical Patents
Christopher Kibbey (Pfizer)

Reaction scheme: Capture, Iterator, and Parser
Zhenbin Li (Boehringer Ingelheim Pharmaceuticals Inc.)

Screen3D: a new high-throughput flexible alignment method
Oleg Ursu (University of New Mexico)

Smashing Molecules - How Molecular Fragments Allow us to Explore Large Chemical Spaces
Rajarshi Guha (NIH Chemical Genomics Center)

Mining promiscuous chemotypes in PubChem
Oleg Ursu (University of New Mexico)

Text mining for chemical information: the ChiKEL project
David Milward, Daniel Bonniot de Ruisselet (Linguamatics, ChemAxon)

EUGM - May 2011
The challenges facing the modern large pharma R&D manager, an exchange of views
Ashley George, Alex Drijver (GlaxoSmithKline, ChemAxon)

Migrating to ChemAxon : the good, the bad & the ugly
Catherine Reisser (Evotec)

Benchmarking ChemAxon’s Name-to-Structure batch tool on patent text
Andrew Hinton (Digital Science (MacMillan Publisher Ltd))

Automated spelling correction to improve recall rates of name-to-structure tools for chemical text mining
Sorel Muresan (AstraZeneca)

Analyzing search hits with ChemAxon's Markush Enumeration tool
Guy de Weck (F. Hoffmann-La Roche AG)

Perspiration, Inspiration, and Happenstance in Scientific Discoveries
Yvonne Martin (Martin Consulting)

DrugPredict: Online drug discovery service using polypharmacology-based interaction profiling
Zoltán Simon (Delta Informatika, Eötvös Loránd University)

Blobs of hope and other flights of fancy
Steve Muchmore (Abbott Laboratories)

Computational toxicology : in silico assessment of the hERG channel inhibition potential for the early drug cardiotoxicity testing
Aleksander Mendyk (Jagiellonian University)

SAR Analyzer - intuitive access to SAR information
Lisa Peltason (F. Hoffmann-La Roche AG)

Cheminformatics in SharePoint
Ian Berry (Evotec)

Interactive structure standardization
Dragos Horváth (CNRS-Université de Strasbourg)

Using Knime to provide desktop tools to chemists
Bob Marmon (Evotec)

SAR analysis in Excel using Helium and JChem
Karen Worsfold (GlaxoSmithKline)

7 Years of ChemAxon at Evotec : choices and possibilities
Ian Berry (Evotec)

Marvin 5.4 : A new generation of structure indexing at Elsevier
Heike Nau (Elsevier)

Utilizing Marvin in rich internet applications using Microsoft  Silverlight
Hans Jürgen Himmler (AKos GmbH)
--

--------------080906090502030704050605-- From owner-chemistry@ccl.net Fri Dec 16 13:46:00 2011 From: "Andrew Voronkov drugdesign[a]yandex.ru" To: CCL Subject: CCL: =?koi8-r?B?8NLJx8zB28HAINcg8c7ExcvTLvDP3tTV?= Message-Id: <-46049-111216134304-23851-mj8JHQVcTn/Wa/0d9T2G6A .. server.ccl.net> X-Original-From: Andrew Voronkov Content-Transfer-Encoding: base64 Content-Type: text/html; charset=utf-8 Date: Fri, 16 Dec 2011 22:42:58 +0400 MIME-Version: 1.0 Sent to CCL by: Andrew Voronkov [drugdesign(-)yandex.ru] PHA+0J/RgNC40LLQtdGCITwvcD4gIDxwPtCvINC/0L7Qu9GM0LfRg9GO0YHRjCDQr9C90LTQtdC6 0YEu0J/QvtGH0YLQvtC5LCDQuCDQvNC90LUg0LfQtNC10YHRjCDQvdGA0LDQstC40YLRgdGPLiAg 0JfQtNC10YHRjCDQvdC1INCx0YvQstCw0LXRgiDRgdC/0LDQvNCwLCDQuCDQstGB0LUg0L/QuNGB 0YzQvNCwINC/0YDQvtCy0LXRgNGP0Y7RgtGB0Y8g0L3QsCDQstC40YDRg9GB0YsuINCX0LTQtdGB 0Ywg0L3QtSDQvtCz0YDQsNC90LjRh9C10L0g0YDQsNC30LzQtdGAINC/0L7Rh9GC0L7QstC+0LPQ viDRj9GJ0LjQutCwLCDQsCDRgtC10LzRiyDQvtGE0L7RgNC80LvQtdC90LjRjyDQvNC+0LbQvdC+ INC80LXQvdGP0YLRjCDRhdC+0YLRjCDQutCw0LbQtNGL0Lkg0LTQtdC90YwuPC9wPiAgPHA+0J/Q tdGA0LXQtdGF0LDRgtGMINCyINCv0L3QtNC10LrRgS7Qn9C+0YfRgtGDINC+0YfQtdC90Ywg0L/R gNC+0YHRgtC+LiDQn9GA0Lgg0Y3RgtC+0Lwg0LLRgdC1INC/0LjRgdGM0LzQsCDRgdC+INGB0YLQ sNGA0L7Qs9C+INGP0YnQuNC60LAg0LDQstGC0L7QvNCw0YLQuNGH0LXRgdC60Lgg0L/QtdGA0LXQ tdC00YPRgiDQvdCwINC90L7QstGL0Lkg0LDQtNGA0LXRgSwg0LAg0YHQvtC+0LHRidCw0YLRjCDQ stGB0LXQvCDQtNGA0YPQt9GM0Y/QvCDQuCDQt9C90LDQutC+0LzRi9C8INC90L7QstGL0Lkg0LDQ tNGA0LXRgSDQvdC1INC/0YDQuNC00ZHRgtGB0Y8g4oCUINC/0LjRgdGM0LzQsCwg0L7RgtC/0YDQ sNCy0LvQtdC90L3Ri9C1INC90LAg0YHRgtCw0YDRi9C5INGP0YnQuNC6LCDQsdGD0LTRg9GCINC/ 0YDQuNGF0L7QtNC40YLRjCDQsiDQr9C90LTQtdC60YEu0J/QvtGH0YLRgy48L3A+ICA8cD7QmCDQ tdGJ0ZEg0L7QtNC40L0g0L/RgNC40Y/RgtC90YvQuSDQvNC+0LzQtdC90YIg4oCUINCyINCv0L3Q tNC10LrRgS7Qn9C+0YfRgtC1INGDINC60LDQttC00L7Qs9C+INC10YHRgtGMINC60LDQuiDQtNC7 0LjQvdC90YvQuSDQsNC00YDQtdGBIEB5YW5kZXgucnUg0LjQu9C4IEB5YW5kZXguY29tLCDRgtCw 0Log0Lgg0LrQvtGA0L7RgtC60LjQuSDigJQgQHlhLnJ1LjwvcD48cD48YSBocmVmPSJodHRwOi8v cGFzc3BvcnQueWFuZGV4LnJ1L3Bhc3Nwb3J0P21vZGU9c2ltcGxlcmVnJmFtcDtmcm9tPW1haWwm YW1wO2xvZ2luPWNoZW1pc3RyeSZhbXA7cmV0cGF0aD1odHRwJTNBJTJGJTJGbWFpbC55YW5kZXgu cnUlMkZuZW8yJTJGY29sbGVjdCUyRiUzRmludml0ZSUyNmxvZ2luJTNEY2hlbWlzdHJ5JTQwY2Ns Lm5ldCIgc3R5bGU9ImJhY2tncm91bmQ6IzRkODVkOTtwYWRkaW5nOjVweCAxMHB4IDVweCAxMHB4 O2NvbG9yOiNmZmY7Ij7Qn9GA0LjQvdGP0YLRjCDQv9GA0LjQs9C70LDRiNC10L3QuNC1PC9hPjwv cD4= From owner-chemistry@ccl.net Fri Dec 16 14:21:00 2011 From: "Andrew Voronkov drugdesign],[yandex.ru" To: CCL Subject: CCL: chemical databases search using multiple substructures, is it available somehwere? Message-Id: <-46050-111216135553-3808-7es7j06aK/6xlSNqrj/dug|,|server.ccl.net> X-Original-From: Andrew Voronkov Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=koi8-r Date: Fri, 16 Dec 2011 22:55:44 +0400 MIME-Version: 1.0 Sent to CCL by: Andrew Voronkov [drugdesign=-=yandex.ru] Dear CCL users, I am regularly using PubChem to mine databases using Substructure search, when as substructure I usually use key pharmacophore containing fragment. Is that possible to use two or several fragments not connected into one structure? There are software štools like in BioSolve IT or OpenEye for bioisosteric linker search between two fragments, I have somehow similar task, I need to enter two pharmacophore containing fragments and find in databases of catalog compounds all the structures which contain both of these fragments. Can anyone recommend me what can I use for such multiple-substructure search through chemical databases? Best regards, Andrew From owner-chemistry@ccl.net Fri Dec 16 17:41:01 2011 From: "Benjamin Stein benjamin.w.stein,,gmail.com" To: CCL Subject: CCL:G: Normal mode analysis Message-Id: <-46051-111216173928-32704-9PRp6emWPp1CAbvUpSKCKg..server.ccl.net> X-Original-From: Benjamin Stein Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=us-ascii Date: Fri, 16 Dec 2011 15:39:18 -0700 Mime-Version: 1.0 (Apple Message framework v1251.1) Sent to CCL by: Benjamin Stein [benjamin.w.stein:+:gmail.com] Hi Trinh, I think Gaussian already calculates what you're looking for. Here's an excerpt from a G03 output: 1 A Frequencies -- 19.1401 Red. masses -- 3.5907 Frc consts -- 0.0008 IR Inten -- 0.2305 Raman Activ -- 0.4498 Depolar (P) -- 0.7500 Depolar (U) -- 0.8571 Also see: http://www.gaussian.com/g_whitepap/vib.htm Best, Ben On Dec 16, 2011, at 12:03 AM, Trinh Tran tranductrinh],[gmail.com wrote: > > Sent to CCL by: "Trinh Tran" [tranductrinh|*|gmail.com] > Hello all, > I am in search of the program REDONG developed by Allouche > A. Allouche and J. Pourcin, Spectrochim. Acta 49A (1993) > to do the normal mode analysis from the output of gaussian calculation. But so far, no luck in finding it. Could any of you point me at the right direction or show me the suitable program to do the same thing. I want to transform the force matrix to have the force constant. > > I appreciate your help, > Regards,> > From owner-chemistry@ccl.net Fri Dec 16 18:16:00 2011 From: "Wolf Ihlenfeldt wdi!=!xemistry.com" To: CCL Subject: CCL: chemical databases search using multiple substructures, is it available somehwere? Message-Id: <-46052-111216173221-31985-/vR4robuXdGjEygBcI0W0Q*_*server.ccl.net> X-Original-From: Wolf Ihlenfeldt Content-Type: multipart/alternative; boundary=20cf3074b6a839b65d04b43d2c10 Date: Fri, 16 Dec 2011 23:32:14 +0100 MIME-Version: 1.0 Sent to CCL by: Wolf Ihlenfeldt [wdi!A!xemistry.com] --20cf3074b6a839b65d04b43d2c10 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable I think that should actually work in PubChem, if they have not changed the defaults of the structure match engine. Just enter multiple fragments in one record. Reported matches contain both fragments, without overlap . If this is not the case, the defaults were changed. PubChem, in order to keep the user interface manageable, only exposes a small fraction of the engine capabilities, so the desired behaviour may not be accessible via this path. If you need more control on the match process, you can download the Cactvs toolkit (www.xemistry.com/academic for academic/educational use, commercial users need a license). This is the match engine behind PubChem. With the full scriptable matcher, there are many additional facilities to control the match process on your own data files (and/or/xor of multiple fragments, fragment overlap control, etc.). Matches can be performed with identical syntax both on standard data files (SDF,SMILES, InChI, MOL2, albeit slow) or optimized query files (cbs or bdb formats, invest time once to compute screens, etc, but after that, queries are much quicker) On Fri, Dec 16, 2011 at 7:55 PM, Andrew Voronkov drugdesign],[yandex.ru < owner-chemistry.:.ccl.net> wrote: > > Sent to CCL by: Andrew Voronkov [drugdesign=3D-=3Dyandex.ru] > Dear CCL users, > I am regularly using PubChem to mine databases using Substructure search, > when as substructure I usually use key pharmacophore containing fragment. > Is that possible to use two or several fragments not connected into one > structure? > There are software tools like in BioSolve IT or OpenEye for bioisosteric > linker search between two fragments, I have somehow similar task, I need = to > enter two pharmacophore containing fragments and find in databases of > catalog compounds all the structures which contain both of these fragment= s. > > Can anyone recommend me what can I use for such multiple-substructure > search through chemical databases? > > Best regards, > Andrew > > > > -=3D This is automatically added to each message by the mailing script = =3D-> > > --=20 Wolf-D. Ihlenfeldt - Xemistry GmbH - wdi.:.xemistry.com Phone: +49 6174 201455 - Fax +49 6174 209665 --- xemistry gmbh =E2=80=93 Gesch=C3=A4ftsf=C3=BChrer/Managing Director: Dr. W.= D. Ihlenfeldt Address: Hainholzweg 11, D-61462 K=C3=B6nigstein, Germany HR K=C3=B6nigstein B7522 : Ust/VAT ID DE215316329 : DUNS 34-400-1719 --20cf3074b6a839b65d04b43d2c10 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
I think that should actually work in PubChem, if they have not changed = the defaults of the structure match engine.

Just enter multiple frag= ments in one record. Reported matches contain both fragments, without overl= ap . If this is not the case, the defaults were changed. PubChem, in order = to keep the user interface manageable, only exposes a small fraction of the= engine capabilities, so the desired behaviour may not be accessible via th= is path.

If you need more control on the match process, you can download the Cac= tvs toolkit (www.xemistry.com/= academic for academic/educational use, commercial users need a license)= . This is the match engine behind PubChem. With the full scriptable matcher= , there are many additional facilities to control the match process on your= own data files (and/or/xor of multiple fragments, fragment overlap control= , etc.). Matches can be performed with identical syntax both on standard da= ta files (SDF,SMILES, InChI, MOL2, albeit slow) or optimized query files (c= bs or bdb formats, invest time once to compute screens, etc, but after that= , queries are much quicker)

=C2=A0
On Fri, Dec 16, 2011 at 7:55 PM, A= ndrew Voronkov drugdesign],[yandex.ru <owner-chemistr= y.:.ccl.net> wrote:

Sent to CCL by: Andrew Voronkov [drugdesign=3D-=3Dyandex.ru]
Dear CCL users,
I am regularly using PubChem to mine databases using Substructure search, w= hen as substructure I usually use key pharmacophore containing fragment. Is that possible to use two or several fragments not connected into one str= ucture?
There are software =C2=A0tools like in BioSolve IT or OpenEye for bioisoste= ric linker search between two fragments, I have somehow similar task, I nee= d to enter two pharmacophore containing fragments and find in databases of = catalog compounds all the structures which contain both of these fragments.=

Can anyone recommend me what can I use for such multiple-substructure searc= h through chemical databases?

Best regards,
Andrew



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Phone: +49 6174 201455 - Fax +49 6174 209665
---<= br>xemistry gmbh =E2=80=93 Gesch=C3=A4ftsf=C3=BChrer/Managing Director: Dr.= W. D. Ihlenfeldt
Address: Hainholzweg 11, D-61462 K=C3=B6nigstein, Germany
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