From owner-chemistry@ccl.net Tue Apr 17 00:38:01 2012 From: "Prashant Singh Rana psrana- -gmail.com" To: CCL Subject: CCL: Optimize the molecular descriptor in QSAR Message-Id: <-46711-120417003642-15261-pa7anqTfydlIpDF1z2N/dA[-]server.ccl.net> X-Original-From: Prashant Singh Rana Content-Type: multipart/alternative; boundary=f46d0442827a972ae304bdd87bd4 Date: Tue, 17 Apr 2012 10:06:30 +0530 MIME-Version: 1.0 Sent to CCL by: Prashant Singh Rana [psrana#%#gmail.com] --f46d0442827a972ae304bdd87bd4 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Thanks Dave for your valuable comments. more comment are needed:- 1. I am agree with you that Evolutionary Algorithms (EA) are not fast, but Evolutionary Algorithms (eg. Genetic Algorithms, PSO, DE, ACO, ABC, etc) are fair methods to explore and test the unknown sets. 2. In my point of view EA is more effective to solve the combinatorial problems . On Tue, Apr 17, 2012 at 4:52 AM, Dave Winkler Dave.Winkler..csiro.au < owner-chemistry#ccl.net> wrote: > See comments below > > Prof. Dave Winkler > Team Leader > Materials Science & Engineering > Bayview Ave, Clayton 3169 > Bag 10 Clayton South MDC 3169 > Phone: +61 3 9545 2477 > > > On 17/04/2012, at 4:05 AM, Prashant Singh Rana psrana]|[gmail.com wrote: > > Dear CCL subscribers > > 1. What are the tool you use to optimize the molecular descriptor in QSAR= Study ? > > A very efficient Bayesian method using and expectation maximisation (see > QSAR Comb Sci 2009 28, 1092 =E2=80=93 1097 and 28, 645-653 > > > 2. What are the highly molecular descriptors are need to be optimize ? > > This method allows you to take a very large pool of descriptors eg from > DRAGON, VolSurf, Adriana etc and optimally select the most relevant ones > for the problem. > > > I want to use Evolutionary Algorithms to optimize the molecular descripto= r in QSAR. > > I'm not convinced that some evolutionary selection methods are not just > fast ways to generate chance correlations (See Topliss' papers in J Med > Chem). It is very important that subsets of descriptors are chosen > appropriately from a larger pool or spurious models can result. > > These issues and common QSAR mistakes have been discussed in a recent Che= m > Rev paper (Le et al. Chem Rev 2012 ASAP) > > > Please Comment. > > > -- > Thanks & Regards > Prashant > > > > --=20 Thanks & Regards Prashant Singh Rana PhD Research Scholar Department of Information & Communication Technology ABV-Indian Institute of Information Technology & Management (IIITM), Gwalior, MP, India. Contact: +91-9098236997 +91-9313889932 Email : psrana#iiitm.ac.in psrana#gmail.com Web : www.psrana.com "Try to Fail, BUT Don't Fail to Try" --f46d0442827a972ae304bdd87bd4 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Thanks Da= ve for your valuable comments.

more comment are needed:-

1. I am agree with you that Evolution= ary Algorithms (EA) are not fast, but Evolutionary Algorithms (eg. Genetic = Algorithms, PSO, DE, ACO, ABC, etc) are fair methods to explore and test th= e unknown sets.

2. In my point of view EA is more effective to solve the combinatorial = problems .




On Tue, Apr 17, 20= 12 at 4:52 AM, Dave Winkler Dave.Winkler..csiro.au <owner-chemistry#ccl.net> wrote:
See comm= ents below

Prof. Dav= e Winkler
Team Leader
Materials Science & Engineering
Bayview Ave, Clayton = 3169
Bag 10 Clayton South MDC 3169
Phone: +61 3 9545 2477

On 17/04/2012, at 4:05 AM, Prashant Singh Rana psrana]|[gmail.com wrote:

Dear CCL subscribers

1. What are the tool you use to optimize the molecular descriptor in QSAR S=
tudy ?
A very efficient Bayesian method using = and expectation maximisation (see QSAR Comb Sci 2009=C2=A028,=C2=A01092 =E2= =80=93 1097 and=C2=A028, 645-653

2. What are the highly molecular descriptors are need to be =
optimize ?
This method allows you to take a very large pool = of descriptors eg from DRAGON, VolSurf, Adriana etc and optimally select th= e most relevant ones for the problem.

I want to use Evolutionary Algorithms to optimize the molecular descriptor =
in QSAR.
I'm not convinced that some evolutionary sele= ction methods are not just fast ways to generate chance correlations (See T= opliss' papers in J Med Chem). =C2=A0It is very important that subsets = of descriptors are chosen appropriately from a larger pool or spurious mode= ls can result.

These issues and common QSAR mistakes have been discuss= ed in a recent Chem Rev paper (Le et al. Chem Rev 2012 ASAP)

Please Comment.


--=20
Thanks & Regards
Prashant





--
Thanks & Regards

Prashant Singh Rana
PhD Research= Scholar
Department of Information & Communication Technology
ABV-Indian Institute of Information Technology & Management (IIITM), Gw= alior, MP, India.

Contact:=C2=A0 +91-9098236997
=C2=A0 =C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0=C2=A0 +91-9313889932
Email=C2=A0=C2=A0 := =C2=A0=C2=A0 psrana= #iiitm.ac.in
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 psrana#gmail.com
Web=C2=A0 =C2=A0= =C2=A0 :=C2=A0=C2=A0 ww= w.psrana.com

"Try to Fail, BUT Don't Fail to Try"<= br> --f46d0442827a972ae304bdd87bd4-- From owner-chemistry@ccl.net Tue Apr 17 08:30:01 2012 From: "Tamas Gunda tgunda2#,#puma.unideb.hu" To: CCL Subject: CCL: CAS number to Chemdraw Molecular Structures Message-Id: <-46712-120417082758-10528-CZncSMxwDil3ibb1JSYTmQ*o*server.ccl.net> X-Original-From: "Tamas Gunda" Content-Transfer-Encoding: 7bit Content-Type: text/plain; format=flowed; charset="iso-8859-1"; reply-type=original Date: Tue, 17 Apr 2012 14:27:45 +0200 MIME-Version: 1.0 Sent to CCL by: "Tamas Gunda" [tgunda2 * puma.unideb.hu] When using the Molgrabber module of ChemDoodle, on entering a CAS number you'll get back immediately the structure via Pubchem. You can save it as ChemDraw cdx file from within ChemDoodle (www.chemdoodle.com) Tamas Gunda ===================================================================== > From: Need47 need47..gmail.com Sent: Monday, April 16, 2012 22:35 PM To: Gunda, Gunda Subject: CCL: CAS number to Chemdraw Molecular Structures Hi, Not sure whether this would help by looking up CAS via the PubChem database: Given a CAS number, say 205692-63-3 Step 1: look up the compound identifier (CID) in the Compound database of the PubChem using http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=205692-63-3 . This would return an XML file (which is simple to parse) that contains the CID ( 5245728 in this case) if there was a successful retrieval. Step 2: with a single CID or a list of CIDs, you can use the Download tool (http://pubchem.ncbi.nlm.nih.gov/pc_fetch/pc_fetch.cgi) provided at PubChem to get various structure formats such as SDF at SMILES Step 3: write a script to batch it up. >Tiejun On Mon, Apr 16, 2012 at 2:09 PM, S SC lcqsigi]~[hotmail.com wrote: Sent to CCL by: "S SC" [lcqsigi/a\hotmail.com] Dear all, Is there a freeware that is able to convert CAS numbers into Chemdraw-like molecular structures. That is I am looking for a software that can translate CAS numbers into the chemical structures that are used in published papers (i.e., the 2D structures depicted by the pubchem database). Thanks,E-mail to subscribers: CHEMISTRY!=cl.net or use:E-mail to administrators: CHEMISTRY-REQUEST!=cl.net or usehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Tue Apr 17 11:51:01 2012 From: "Igor Filippov Contr filippovi(a)mail.nih.gov" To: CCL Subject: CCL: Optimization of molecular descriptor in QSAR Message-Id: <-46713-120417105056-2784-pWuOQY6hNzcEJYDSBVGa7g^server.ccl.net> X-Original-From: "Igor Filippov [Contr]" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="UTF-8" Date: Tue, 17 Apr 2012 10:49:40 -0400 MIME-Version: 1.0 Sent to CCL by: "Igor Filippov [Contr]" [filippovi[A]mail.nih.gov] I found chembench - http://chembench.mml.unc.edu/home - to be a good tool to experiment with different QSAR methods, free of charge. One of the methods it offers is kNN-ga (k-nearest neighbors with genetic algorithm for feature selection), perhaps this is what you're looking for in evolutionary algorithms? I rather disagree with the previous post that evolutionary algorithms generate chance correlations. IMHO these two things are completely orthogonal. EA does not guarantee correct result just by itself, but it should not lead to a wrong result if used properly. Igor On Mon, 2012-04-16 at 15:54 -0400, Prashant Singh Rana psrana^_^gmail.com wrote: > Sent to CCL by: "Prashant Singh Rana" [psrana(-)gmail.com] > Dear CCL subscribers > > 1. What are the tool you use to optimize the molecular descriptor in QSAR Study ? > > 2. What are the highly molecular descriptors are need to be optimize ? > > I want to use Evolutionary Algorithms to optimize the molecular descriptor in QSAR. > > Please Comment. > > From owner-chemistry@ccl.net Tue Apr 17 12:26:01 2012 From: "Alex Allardyce aallardyce]_[chemaxon.com" To: CCL Subject: CCL: CAS number to Chemdraw Molecular Structures Message-Id: <-46714-120417112326-25316-WAblihHHRp0J61iRYD+s6w::server.ccl.net> X-Original-From: Alex Allardyce Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=utf-8 Date: Tue, 17 Apr 2012 17:23:10 +0200 (CEST) MIME-Version: 1.0 Sent to CCL by: Alex Allardyce [aallardyce * chemaxon.com] Missed this. Yes our name to structure functionality handles this through webservice at CACTUS so you need to be online and confident of their data! For single structure you paste into our chem editor, MarvinSketch (free for all desktops) or import a list to MarvinView (again free). You can export the structure file or copy paste the image into MS Office/open office. If you want to run batch then you have a few choices - command line, API, KNIME or Pipeline Pilot nodes, etc etc in Marvin distributable. If you want batch in a desktop app then I think the easiest is JChem for Excel - just paste the list in a column then choose convert to structure (see user guide: http://www.chemaxon.com/jchem4excel/userguide/convert_from_iupac_name_to_str.html) will generate the structures. You can export from Excel to your favorite structure file format or copy paste the images. Batching out images can be tricky so I would suggest scripting for that. I will see about adding CAS number recognition to chemicalize.org, it should be straightforward - so long as the service is fast and we don't start trying to see CAS numbers in Singaporean telephone numbers... Lets see! Cheers Alex PS - all things are free for academic teaching and research ----- Original Message ----- > From: "S SC lcqsigi]~[hotmail.com" To: "Alex Allardyce " Sent: Monday, April 16, 2012 8:09:29 PM Subject: CCL: CAS number to Chemdraw Molecular Structures Sent to CCL by: "S SC" [lcqsigi/a\hotmail.com] Dear all, Is there a freeware that is able to convert CAS numbers into Chemdraw-like molecular structures. That is I am looking for a software that can translate CAS numbers into the chemical structures that are used in published papers (i.e., the 2D structures depicted by the pubchem database). Thanks,http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Tue Apr 17 17:38:01 2012 From: "Jesse Gordon jesse.gordon-*-dotmatics.com" To: CCL Subject: CCL: CAS number to Chemdraw Molecular Structures Message-Id: <-46715-120417100208-19300-DdNiNVF1h5ITXy3u3AFQxA~!~server.ccl.net> X-Original-From: Jesse Gordon Content-Type: multipart/alternative; boundary=f46d042c6c3f2ee5c804bde0609f Date: Tue, 17 Apr 2012 10:01:30 -0400 MIME-Version: 1.0 Sent to CCL by: Jesse Gordon [jesse.gordon(~)dotmatics.com] --f46d042c6c3f2ee5c804bde0609f Content-Type: text/plain; charset=ISO-8859-1 Here's a clean method: - Bring up http://www.chemspider.com in any browser (that's the Royal Society of Chemistry's ChemSpider site, very reliable and also free) - On the home page, put in any CAS#, such as 50-78-2 - Just under the 2D rendering is a "Save" button where you can save as MOL format. - Open the MOL file in any chemical drawing tool. - If you just want the image for publication, you can right-click on the molecular rendering in ChemSpider and "Save Picture As", then use the PNG directly in your paper. ===================================== Jesse Gordon Application Scientist Dotmatics Inc. 400 West Cummings Park #5450, Woburn MA 01801 T: +1 781-305-3114 M: +1-617-320-6989 Email: jesse.gordon##dotmatics.com Skype: jessegordon ====================================== See the latest in Dotmatics Suite of Solutions at: Booth # 11 CHI Drug Discovery Chemistry, April 17-19, 2012, Hilton San Diego Resort & Spa, San Diego, CA, www.drugdiscoverychemistry.com Booth # 323 Bio-IT World Conference, April 24-26, 2012, World Trade center, Boston, MA, www.bio-itworldexpo.com On 16 April 2012 14:09, S SC lcqsigi]~[hotmail.com wrote: > > Sent to CCL by: "S SC" [lcqsigi/a\hotmail.com] > Dear all, > > Is there a freeware that is able to convert CAS numbers into Chemdraw-like > molecular structures. > > That is I am looking for a software that can translate CAS numbers into > the chemical structures that are used in published papers (i.e., the 2D > structures depicted by the pubchem database). > > Thanks,> > > -- ===================================== Jesse Gordon Application Scientist Dotmatics Inc. 400 West Cummings Park #5450, Woburn MA 01801 T: +1 781-305-3114 M: +1-617-320-6989 Email: jesse.gordon##dotmatics.com Skype: jessegordon ====================================== See the latest in Dotmatics Suite of Solutions at: Booth # 11 CHI Drug Discovery Chemistry, April 17-19, 2012, Hilton San Diego Resort & Spa, San Diego, CA, www.drugdiscoverychemistry.com Booth # 323 Bio-IT World Conference, April 24-26, 2012, World Trade center, Boston, MA, www.bio-itworldexpo.com -- Disclaimer: This electronic mail and its attachments are intended solely for the person(s) to whom they are addressed and contain information which is confidential or otherwise protected from disclosure, except for the purpose for which they are intended. Dissemination, distribution, or reproduction by anyone other than the intended recipients is prohibited and may be illegal. If you are not an intended recipient, please immediately inform the sender and return the electronic mail and its attachments and destroy any copies which may be in your possession. Dotmatics Limited screens electronic mails for viruses but does not warrant that this electronic mail is free of any viruses. Dotmatics Limited accepts no liability for any damage caused by any virus transmitted by this electronic mail. Dotmatics Limited is registered in England & Wales No. 5614524 with offices at The Old Monastery, Windhill, Bishops Stortford, Herts, CM23 2ND, UK. --f46d042c6c3f2ee5c804bde0609f Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Here's a clean method:
- Bring up http://www.chemspider.com in any browser (that's th= e Royal Society of Chemistry's ChemSpider site, very reliable and also = free)
- On the home page, put in any CAS#, such as 50-78-2
- Just = under the 2D rendering is a "Save" button where you can save as M= OL format.
- Open the MOL file in any chemical drawing tool.
- If you just want the image for publication, you can right-click on t= he molecular rendering in ChemSpider and "Save Picture As", then = use the=A0PNG directly in your paper.
=A0
=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D
Jesse Gordon
Application Scientist
Dotmatics Inc.
=
400 West Cummings Park #5450, Woburn MA 01801
T: +1 781-305-= 3114
M: +1-617-320-6989
Skype: jessegordon
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=A0
See the latest in Dotmatics Suite of Solutions at:=
Booth # 11 CHI Drug Discovery Chemistry, April 17-19, 2012, Hilt= on San Diego Resort & Spa, San Diego, CA, www.drugdiscoverychemistry.com
Booth # 323 Bio-IT World Conference, April 24-26, 2012, World Trade ce= nter,=A0 Boston,=A0 MA, www.bio-= itworldexpo.com=A0
=A0
On 16 April 2012 14:09, S SC= lcqsigi]~[hotmail.com <owner-chemistry##ccl.net= > wrote:

Sent to CCL by: "S =A0SC" [lcqsigi/a\hotmail.com]
Dear all,

Is there a freeware that is able to convert CAS numbers into Chemdraw-like = molecular structures.

That is I am looking for a software that can translate CAS numbers into the= chemical structures that are used in published papers (i.e., the 2D struct= ures depicted by the pubchem database).

Thanks,



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Jesse Gordon
Application Scientist
Dotmatics Inc.
400 West Cummings Park #5450, Woburn MA 01801
T: +1 781-305-3114
M: +1-617-320-6989
Skype: jessegordon
=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D
=A0
See the latest in Dotmatics Suite of Solutions at:
=
Booth # 11 CHI Drug Discovery Chemistry, April 17-19, 2012, Hilton San= Diego Resort & Spa, San Diego, CA, www.drugdiscoverychemistry.com
Booth # 323 Bio-IT World Conference, April 24-26, 2012, World Trade ce= nter,=A0 Boston,=A0 MA, www.bio-itworldexpo.com

-- =

Disclaimer: This electronic mail and its attachments are intended solely =
for
the person(s) to whom they are addressed and contain information which is=
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confidential or otherwise protected from disclosure, except for the purpo=
se
for which they are intended. Dissemination, distribution, or reproduction=
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anyone other than the intended recipients is prohibited and may be illega=
l.
If you are not an intended recipient, please immediately inform the sende=
r
and return the electronic mail and its attachments and destroy any copies=

which may be in your possession. Dotmatics Limited screens electronic mai=
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for viruses but does not warrant that this electronic mail is free of any=

viruses. Dotmatics Limited accepts no liability for any damage caused by
any virus transmitted by this electronic mail. Dotmatics Limited is =

registered in England & Wales No. 5614524 with offices at The Old Monaste=
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Windhill, Bishops Stortford, Herts, CM23 2ND, UK.
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From owner-chemistry@ccl.net Tue Apr 17 18:13:01 2012
From: "Joy Ku joyku_+_stanford.edu" 
To: CCL
Subject: CCL: OpenMM 2012 Visiting Scholar Program at Stanford University
Message-Id: <-46716-120417144158-14677-GsHsO4tbpoyhlrEOqGZcxw,+,server.ccl.net>
X-Original-From: "Joy  Ku" 
Date: Tue, 17 Apr 2012 14:41:55 -0400


Sent to CCL by: "Joy  Ku" [joyku::stanford.edu]
The OpenMM 2012 Visiting Scholar Program will select up to three individuals this year to visit Simbios at Stanford University for a 4-week period between July and October to advance their OpenMM projects.  

OpenMM (http://simtk.org/home/openmm) is an open-source software project led by Dr. Vijay Pande that enables molecular dynamic calculations to be accelerated on high-performance computer architectures. The latest version of OpenMM (release 4.0) includes an application layer that allows non-programmers to easily and quickly run molecular dynamics simulations and develop custom algorithms on GPUs, while programmers can incorporate the OpenMM library into their own applications.

Each visiting scholar will receive a $7000 stipend to cover their expenses.  During their visits, awardees will receive training and mentoring to help them achieve their goals. They will have the opportunity to participate in formal meetings and in discussions with OpenMM experts.  We are particularly interested in proposals that take advantage of the new application layer in our 4.0 release and in new features to be added to OpenMM.

DEADLINE:  May 13, 2012

To apply and learn more, visit http://simbios.stanford.edu/OpenMMVisitingScholar.htm.