From owner-chemistry@ccl.net Sun May 20 01:56:00 2012 From: "Anurag Passi anuragpassibioinfo,gmail.com" To: CCL Subject: CCL: In Silico Compound Library Search Message-Id: <-46939-120520015123-6749-EmlQljclorNDOsyaeQrt3A()server.ccl.net> X-Original-From: Anurag Passi Content-Type: multipart/alternative; boundary=f46d044306869af0d004c0715ff7 Date: Sun, 20 May 2012 11:21:14 +0530 MIME-Version: 1.0 Sent to CCL by: Anurag Passi [anuragpassibioinfo-.-gmail.com] --f46d044306869af0d004c0715ff7 Content-Type: text/plain; charset=ISO-8859-1 Hey Nancy, you can use the advanced search option in PubChem only. It gives you the option to search the compounds based on the parameters you choose. This can include all the parameters you described. Here is the link for the same: http://www.ncbi.nlm.nih.gov/sites/entrez?db=pccompound&TabCmd=Limits Regards, Anurag On Sun, May 20, 2012 at 6:41 AM, Nancy nancy5villa[a]gmail.com < owner-chemistry]-[ccl.net> wrote: > Hi All, > > Does anyone know of a free cheminformatic service from which it's possible > to narrow down a search for molecules by inputting limits on their > molecular parameters, such as molecular weight or the number of hydrogen > bond donors, etc? Such a resource would be of great help. > > Thanks in advance, > Nancy > > > > -- Anurag Passi Sr. Project Fellow OSDD, CSIR 00-91-9899767938 skype: anurag.passi --f46d044306869af0d004c0715ff7 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hey Nancy,

you can use the advanced search option in PubChem only. I= t gives you the option to search the compounds based on the parameters you = choose. This can include all the parameters you described. Here is the link= for the same: http://www.ncbi.nlm.nih.gov/sites/entrez?db=3D= pccompound&TabCmd=3DLimits

Regards,
Anurag

On Sun, May 20, 20= 12 at 6:41 AM, Nancy nancy5villa[a]gmail.com <owner-chemistry]-[ccl.net> wrote:
Hi All,

Does anyone know of a free ch= eminformatic service from which it's possible to narrow down a search f= or molecules by inputting limits on their molecular parameters, such as mol= ecular weight or the number of hydrogen bond donors, etc?=A0 Such a resourc= e would be of great help.

Thanks in advance,
Nancy






--
Anurag Passi
Sr. Pro= ject Fellow
OSDD, CSIR
00-91-9899767938
skype: anurag.passi
--f46d044306869af0d004c0715ff7-- From owner-chemistry@ccl.net Sun May 20 11:01:00 2012 From: "Bruno Villoutreix bruno.villoutreix===gmail.com" To: CCL Subject: CCL: In Silico Compound Library Search Message-Id: <-46940-120520050135-26515-GsyM0a05gkrt1AbOzjm9Zw : server.ccl.net> X-Original-From: Bruno Villoutreix Content-Type: multipart/alternative; boundary=000e0ce02526e2de5504c0740652 Date: Sun, 20 May 2012 11:01:11 +0200 MIME-Version: 1.0 Sent to CCL by: Bruno Villoutreix [bruno.villoutreix : gmail.com] --000e0ce02526e2de5504c0740652 Content-Type: text/plain; charset=ISO-8859-1 FAF-drugs2 can do it online, this is free BV On Sun, May 20, 2012 at 3:11 AM, Nancy nancy5villa[a]gmail.com < owner-chemistry(0)ccl.net> wrote: > Hi All, > > Does anyone know of a free cheminformatic service from which it's possible > to narrow down a search for molecules by inputting limits on their > molecular parameters, such as molecular weight or the number of hydrogen > bond donors, etc? Such a resource would be of great help. > > Thanks in advance, > Nancy > > > > -- Dr. Bruno Villoutreix Director Inserm-Paris 7 Unit U973 Bioinformatics-Chemoinformatics --000e0ce02526e2de5504c0740652 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable FAF-drugs2 can do it online, this is free
BV

On Sun, May 20, 2012 at 3:11 AM, Nancy nancy5villa[a]gmail.com <owner-chemistry(0)ccl.net> = wrote:
Hi All,

Does anyone know of a free ch= eminformatic service from which it's possible to narrow down a search f= or molecules by inputting limits on their molecular parameters, such as mol= ecular weight or the number of hydrogen bond donors, etc?=A0 Such a resourc= e would be of great help.

Thanks in advance,
Nancy






--
Dr. Bruno Villoutreix <= br>Director Inserm-Paris 7 Unit U973
Bioinformatics-Chemoinformatics=A0 = =A0 =A0 =A0 =A0 =A0=A0


--000e0ce02526e2de5504c0740652-- From owner-chemistry@ccl.net Sun May 20 11:36:01 2012 From: "Felipe Pineda pideca^-^hotmail.com" To: CCL Subject: CCL: Lipid membrane modeling tool Message-Id: <-46941-120520093712-16447-cIJXanajna8XTEPZRTYTjQ(0)server.ccl.net> X-Original-From: "Felipe Pineda" Date: Sun, 20 May 2012 09:37:09 -0400 Sent to CCL by: "Felipe Pineda" [pideca:+:hotmail.com] Dear CCLers! I'd greatly appreciate any pointer to state-of-the-art, non-commercial molecular modeling tools for mono- and bilayer lipid membranes. I searched the CCL archive, but couldn't find any useful information. Many thanks in advance, Felipe Computational Chemistry and Biochemistry Lab Linnaeus University Kalmar, Sweden From owner-chemistry@ccl.net Sun May 20 12:11:01 2012 From: "Luis Felipe Pineda De Castro fpineda-x-uni-bonn.de" To: CCL Subject: CCL: [CCL] Lipid membrane modeling tool Message-Id: <-46942-120520104340-8428-pGsd2pgpbaA3R05bgL1yXg~~server.ccl.net> X-Original-From: "Luis Felipe Pineda De Castro" Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1; format="flowed" Date: Sun, 20 May 2012 16:43:31 +0200 MIME-Version: 1.0 Sent to CCL by: "Luis Felipe Pineda De Castro" [fpineda . uni-bonn.de] Dear CCLers! I'd greatly appreciate any pointer to state-of-the-art, non-commercial molecular modeling tools for mono- and bilayer lipid membranes. I searched the CCL archive, but couldn't find any useful information. Many thanks in advance, Felipe Computational Chemistry and Biochemistry Lab Linnaeus University Kalmar, Sweden From owner-chemistry@ccl.net Sun May 20 14:16:00 2012 From: "Venable, Richard (NIH/NHLBI) E venabler]-[nhlbi.nih.gov" To: CCL Subject: CCL: [CCL] Lipid membrane modeling tool Message-Id: <-46943-120520141412-5523-NjyXNhFisoZ4mj4bzaBm8w : server.ccl.net> X-Original-From: "Venable, Richard (NIH/NHLBI) [E]" Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Sun, 20 May 2012 14:13:40 -0400 MIME-Version: 1.0 Sent to CCL by: "Venable, Richard (NIH/NHLBI) [E]" [venabler * nhlbi.nih.gov] For building bilayer models with CHARMM FF suitable for use with CHARMM or NAMD, I suggest www.charmm-gui.org In CHARMM, converting a bilayer model into a symmetric dual leaflet monolayer system is fairly easy; a thicker water layer is strongly advised. -- Rick Venable 5635 FL/T906 Membrane Biophysics Section NIH/NHLBI Lab. of Computational Biology Bethesda, MD 20892-9314 U.S.A. (301) 496-1905 venabler AT nhlbi*nih*gov On 5/20/12 10:43 AM, "Luis Felipe Pineda De Castro fpineda-x-uni-bonn.de" wrote: > >Sent to CCL by: "Luis Felipe Pineda De Castro" [fpineda . uni-bonn.de] >Dear CCLers! > >I'd greatly appreciate any pointer to state-of-the-art, >non-commercial molecular modeling tools for mono- and >bilayer lipid membranes. I searched the CCL archive, but >couldn't find any useful information. > >Many thanks in advance, > >Felipe >Computational Chemistry and Biochemistry Lab >Linnaeus University >Kalmar, Sweden> > From owner-chemistry@ccl.net Sun May 20 15:00:00 2012 From: "Andreas Klamt klamt/./cosmologic.de" To: CCL Subject: CCL: Lipid membrane modeling tool Message-Id: <-46944-120520130152-14344-HdX8MIWNneCoXK+O0thGxA/a\server.ccl.net> X-Original-From: Andreas Klamt Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=UTF-8; format=flowed Date: Sun, 20 May 2012 19:01:42 +0200 MIME-Version: 1.0 Sent to CCL by: Andreas Klamt [klamt^cosmologic.de] Hi Felipe, we do have the COSMOmic extension of COSMotherm, which calculates the distribution of molecules in micellar systems, incl. biomembranes. See: COSMOmic: A Mechanistic Approach to the Calculation of Membrane−Water Partition Coefficients and Internal Distributions within Membranes and Micelles by: Andreas Klamt, Uwe Huniar, Simon Spycher, Jörg Keldenich The Journal of Physical Chemistry B, Vol. 112, No. 38. (25 September 2008), pp. 12148-12157, doi:10.1021/jp801736k But it is not free, though our academic prices are quite moderate. Best regards Andreas Am 20.05.2012 15:37, schrieb Felipe Pineda pideca^-^hotmail.com: > Sent to CCL by: "Felipe Pineda" [pideca:+:hotmail.com] > Dear CCLers! > > I'd greatly appreciate any pointer to state-of-the-art, non-commercial molecular modeling tools for mono- and bilayer lipid membranes. I searched the CCL archive, but couldn't find any useful information. > > Many thanks in advance, > > Felipe > Computational Chemistry and Biochemistry Lab > Linnaeus University > Kalmar, Sweden> > > -- Prof. Dr. Andreas Klamt CEO / Geschäftsführer COSMOlogic GmbH& Co. KG Burscheider Strasse 515 D-51381 Leverkusen, Germany phone +49-2171-731681 fax +49-2171-731689 e-mail klamt=-=cosmologic.de web www.cosmologic.de [University address: Inst. of Physical and Theoretical Chemistry, University of Regensburg] Join us at the 4th-COSMO-RS-Symposium April 2013 Details at www.cosmologic.de/symposium2013 HRA 20653 Amtsgericht Koeln, GF: Prof. Dr. Andreas Klamt Komplementaer: COSMOlogic Verwaltungs GmbH HRB 49501 Amtsgericht Koeln, GF: Prof. Dr. Andreas Klamt