From owner-chemistry@ccl.net Thu Dec 5 08:42:00 2013 From: "Oellien, F (Frank) frank.oellien#,#msd.de" To: CCL Subject: CCL: 2. Call For Paper ICCS/GCC 2014 / Submission Open Message-Id: <-49403-131205064243-10734-bQVNL7jnqiiDfdA/hUKhvg(0)server.ccl.net> X-Original-From: "Oellien, F (Frank)" Content-Type: multipart/mixed; boundary="===============0429428509==" Date: Thu, 5 Dec 2013 12:42:30 +0100 MIME-Version: 1.0 MIME-Version: 1.0 Sent to CCL by: "Oellien, F (Frank)" [frank.oellien|msd.de] --===============0429428509== Content-Language: en-US Content-Type: multipart/related; boundary="_004_00FE5FB90A64044BA1B6542C213F3F05011F1575E5F8BEBRMXP5100_"; type="multipart/alternative" --_004_00FE5FB90A64044BA1B6542C213F3F05011F1575E5F8BEBRMXP5100_ Content-Type: multipart/alternative; boundary="_000_00FE5FB90A64044BA1B6542C213F3F05011F1575E5F8BEBRMXP5100_" --_000_00FE5FB90A64044BA1B6542C213F3F05011F1575E5F8BEBRMXP5100_ Content-Type: text/plain; charset="us-ascii" 2. C A L L F O R P A P E R S 10th International Conference on Chemical Structures and 10th German Conference on Chemoinformatics NH Leeuwenhorst Conference Hotel, Noordwijkerhout, The Netherlands 1-5 June 2014 Online Submission is opened now: Please submit your abstracts on the conference website at http://www.int-conf-chem-structures.org/abstract-submission.html The 10th International Conference on Chemical Structures (ICCS) and the 10th German Conference on Chemoinformatics (GCC) are teaming up for their 2014 conferences. Building on past successes of both conference series the 2014 event will offer a strong scientific program covering all aspects of cheminformatics and molecular modeling. For this joint event, the ICCS/GCC is seeking presentations of novel research and emerging technologies for the following plenary sessions: o Cheminformatics > advances in structure representation > molecular similarity and diversity > chemical information visualization > reaction handling and electronic lab notebooks (ELNs) o Structure-Activity and Structure-Property Prediction > industrialized and large-scale model building > multi-objective optimization and multi-property prediction > assessment of uncertainties in predictive modeling > graphical methods for SAR analysis o Structure-Based Drug Design and Virtual Screening > improved understanding of protein-ligand interactions > modeling of protein-protein interactions (PPIs) > modeling of challenging targets > advances in antibody modeling o Analysis of Large Chemistry Spaces > design, profiling and comparison of compound collections and screening sets > machine learning and knowledge extraction from databases > improved visualization of disparate data types > mining of chemical literature and patents o Integration of Chemical Information with other Resources > advances in chemogenomics > integration of medical and biological information with chemical information > semantic technologies as a driving force of integration > chemical information using mobile technologies and social media o Dealing with Biological Complexity > analysis and prediction of poly-pharmacology > analysis of high-content screening data > pathways and biological networks > druggability of targets We also welcome contributions in any aspect of the computer handling of chemical structure information, such as: automatic structure elucidation, computer-aided synthesis planning, combinatorial chemistry and diversity analysis, web technology and its effect on chemical information, electronic publishing, MM or QM/MM simulations, practical free energy calculations, modeling of ADME properties, material sciences, analysis and prediction of crystal structures, grid and cloud computing in cheminformatics. We encourage the submission of papers both on method and algorithm development as well as applications and case studies especially those demonstrating the predictive power of methods by experimental validation. > From the submissions the program committee and the scientific advisory board will select about 30 papers for the plenary sessions. All submissions that cannot be included in the plenary sessions will be automatically considered for the poster sessions. Before and after the official conference program free workshops will be offered by several companies including OpenEye (www.eyesopen.com), Chemical Computing Group (www.chemcomp.com) and Certara (www.certara.com) Joint Organizers: o Division of Chemical Information of the American Chemical Society (ACS) o Chemical Structure Association Trust (CSA Trust) o Division of Chemical Information and Computer Science of the Chemical Society of Japan (CSJ) o Chemistry-Information-Computer Division of the German Chemical Society (GDCh) o Royal Dutch Chemical Society (KNCV) o Chemical Information and Computer Applications Group of the Royal Society of Chemistry (RSC) o Swiss Chemical Society (SCS) Visit the conference website at www.int-conf-chem-structures.org for more information, including details on procedures for online abstract submission and conference registration. The deadline for the submission of abstracts is 31 January 2014. We hope to see you in Noordwijkerhout. Markus Wagener, ICCS Chair Frank Oellien, ICCS Co-Chair Uli Fechner, GCC Chair Dr. Frank Oellien Senior Scientist, Bioinformatics AH - Molecular Discovery Sciences MSD Animal Health Innovation GmbH Zur Propstei 55270 Schwabenheim, Germany E-Mail: frank.oellien{:}msd.de Phone: +49 (6130) 948 365 Fax: +49 (6130) 948 517 Home http://www.msd-animal-health.com [cid:image001.gif{:}01CEF19F.E737A200] --_000_00FE5FB90A64044BA1B6542C213F3F05011F1575E5F8BEBRMXP5100_ Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

2.  C A L L=    F O R   P A P E R S

10th International Conference on Chemical Structures and

<= p class=3DMsoNormal>10th German Conference on Chemoinformatics

 

NH Leeuwen= horst Conference Hotel, Noordwijkerhout, The Netherlands

1-5 June 2014

&nbs= p;

Online Submission is opened now: Please su= bmit your abstracts on the conference website at http://www.int-conf-chem= -structures.org/abstract-submission.html

 

The 10th International Conf= erence on Chemical Structures (ICCS) and the 10th German Conference on Chem= oinformatics (GCC) are teaming up for their 2014 conferences. Building on p= ast successes of both conference series the 2014 event will offer a strong = scientific program covering all aspects of cheminformatics and molecular mo= deling. For this joint event, the ICCS/GCC is seeking presentations of nove= l research and emerging technologies for the following plenary sessions:

 

=    o Cheminformatics

 &nb= sp;      > advances in structure representation=

      &n= bsp; > molecular similarity and diversity

        > chemical informat= ion visualization

   &nbs= p;    > reaction handling and electronic lab notebooks (E= LNs)

 

   o Structure-Activity and Structure-Property Prediction&= nbsp;     

&nb= sp;       > industrialized and large-= scale model building

   &= nbsp;    > multi-objective optimization and multi-propert= y prediction

    &n= bsp;   > assessment of uncertainties in predictive modeli= ng

      &= nbsp; > graphical methods for SAR analysis

 

   o Structure-Ba= sed Drug Design and Virtual Screening      &n= bsp;

     &nbs= p;  > improved understanding of protein-ligand interactions

       = > modeling of protein-protein interactions (PPIs)

        > modeling of c= hallenging targets

   &nb= sp;    > advances in antibody modeling

 

   o A= nalysis of Large Chemistry Spaces       =

      &n= bsp; > design, profiling and comparison of compound collections and= screening sets

    =     > machine learning and knowledge extraction from data= bases

     &nbs= p;  > improved visualization of disparate data types

=

        > mining= of chemical literature and patents

 

   o Integration of Chemica= l Information with other Resources

 = ;       > advances in chemogenomics

        >= ; integration of medical and biological information with chemical informati= on

      &= nbsp; > semantic technologies as a driving force of integration

        > = chemical information using mobile technologies and social media<= /p>

 

 &nb= sp; o Dealing with Biological Complexity

        > analysis and prediction of= poly-pharmacology

   &nb= sp;    > analysis of high-content screening data

        > = pathways and biological networks

 &= nbsp;      > druggability of targets=

 

We also = welcome contributions in any aspect of the computer handling of chemical st= ructure information, such as: automatic structure elucidation, computer-aid= ed synthesis planning, combinatorial chemistry and diversity analysis, web = technology and its effect on chemical information, electronic publishing, M= M or QM/MM simulations, practical free energy calculations, modeling of ADM= E properties, material sciences, analysis and prediction of crystal structu= res, grid and cloud computing in cheminformatics.

 

We encourage the submis= sion of papers both on method and algorithm development as well as applicat= ions and case studies especially those demonstrating the predictive power o= f methods by experimental validation.

 

From the submissions the program co= mmittee and the scientific advisory board will select about 30 papers for t= he plenary sessions. All submissions that cannot be included in the plenary= sessions will be automatically considered for the poster sessions.

 

Befor= e and after the official conference program free workshops will be offered = by several companies including OpenEye (www.eyesopen.com), Chemical Computing Group (www.chemcomp.com) and Certara (w= ww.certara.com)

 

Joint Organizers:

=    o Division of Chemical Information of the American Chemical So= ciety (ACS)

   o Chemical Stru= cture Association Trust (CSA Trust)

&nbs= p;  o Division of Chemical Information and Computer Science of the Che= mical Society of Japan (CSJ)

  = ; o Chemistry-Information-Computer Division of the German Chemical Society = (GDCh)

   o Royal Dutch Chemic= al Society (KNCV)

   o Chemica= l Information and Computer Applications Group of the Royal Society of Chemi= stry (RSC)

   o Swiss Chemical= Society (SCS)

 

Visit the conference website at www.int-conf-chem-structures.org for more inf= ormation, including details on procedures for online abstract submission an= d conference registration.

 

The deadline for the submission of abstracts i= s 31 January 2014.

 

=

We hope to see you in Noordwijkerhout.

<= p class=3DMsoNormal> 

Markus Wagene= r, ICCS Chair

Frank Oellien, ICCS Co-Cha= ir

Uli Fechner, GCC Chair

=

 

 <= /o:p>

 

Dr. Frank Oellien

Senior Scientist, Bioinformatics

AH – Molecular Disc= overy Sciences

MSD Animal Health Innovation GmbH

Zur Propstei

55270 Schwabenheim, Germany

 =

E-Mail: =      frank.oellien{:}msd.de

Phone:     +49 (6130) 948 365   = ;            &n= bsp;            = ;

= Fax: =         +49 (6130) 948 517  &n= bsp;            = ;            &n= bsp; 

H= ome       http://www.msd-animal-health.com =

3D"msd_=

 

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Hierzu geh=C3=B6ren folgende Vertriebsunternehmen: Humanarzneimittel: MSD Sharp & Dohme GmbH, Lindenplatz 1, 85540 Haar; HR M=C3=BCnchen B 6194 Gesch=C3=A4ftsf=C3=BChrer: Hanspeter Quodt (Vors.), Dr. Claus Dollinger, Dr= . Dr. Kristian L=C3=B6bner, Dr. Veit Stoll Aufsichtsratsvorsitzender: Dr. Axel Breitstadt Tierarzneimittel: Intervet Deutschland GmbH, Feldstr. 1a, 85716 Unterschlei=C3=9Fheim; HR M= =C3=BCnchen B 138151 Gesch=C3=A4ftsf=C3=BChrer: Dr. Daniel Sicher (Vors.), Christoph K=C3=B6lsch Weitere Unternehmen der deutschen MSD-Gruppe siehe http://info.msd.de/pflic= htangaben --===============0329900940== Content-Type: text/html; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: quoted-printable

Hinweis: Diese Email wird von einem Unternehmen der deutschen MSD-Gruppe= versandt. Hierzu geh=C3=B6ren folgende Vertriebsunternehmen:

Humanarzneimittel:

MSD Sharp & Dohme GmbH, Lindenplatz 1, 85540 Haar; HR M=C3=BCnchen B= 6194
Gesch=C3=A4ftsf=C3=BChrer: Hanspeter Quodt (Vors.), Dr. Claus Doll= inger, Dr. Dr. Kr= istian L=C3=B6bner, Dr. Veit= Stoll

Aufsichtsratsvorsitzender: Dr. Axel Breitstadt

Tierarzneimittel:

Intervet Deutschland GmbH, Feldstr. 1a, 85716 Unterschlei=C3=9Fheim; HR = M=C3=BCnchen B 138151
Gesch=C3=A4ftsf=C3=BChrer: Dr. Daniel Sicher (Vors= .), Christoph K=C3=B6lsch

Weitere Unternehmen der deutschen MSD-Gruppe siehe http://info.msd.de/pf= lichtangaben

--===============0329900940==-- --===============0429428509==-- From owner-chemistry@ccl.net Thu Dec 5 11:30:00 2013 From: "Victor Rosas Garcia rosas.victor]_[gmail.com" To: CCL Subject: CCL: calculation of hydrophillic factor Message-Id: <-49404-131205112811-29277-1czBJ5ogQFgt1YxB1h67fQ:-:server.ccl.net> X-Original-From: Victor Rosas Garcia Content-Type: multipart/alternative; boundary=90e6ba6e89a2ab171b04eccc03d1 Date: Thu, 5 Dec 2013 10:28:05 -0600 MIME-Version: 1.0 Sent to CCL by: Victor Rosas Garcia [rosas.victor,gmail.com] --90e6ba6e89a2ab171b04eccc03d1 Content-Type: text/plain; charset=ISO-8859-1 Hello everybody, I am looking for the formula or algorithm used to calculate the hydrophillic factor (symbol Hy) used as molecular descriptor in QSAR studies. So far, the only reference I've got is this Todeschini, R. & Consonni, V. Handbook of Molecular Descriptors. Wlley-VCH.Weinheim (Germany), (2000). unfortunately, I don't have access to this handook. Are there any papers that describe how to calculate this? Regards Victor --90e6ba6e89a2ab171b04eccc03d1 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Hello everybody,

I am loo= king for the formula or algorithm used to calculate the hydrophillic factor= (symbol Hy) used as molecular descriptor in QSAR studies. So far, the only= reference I've got is this

Todeschini, R. & Consonni, V. Handbook of Molecular Descriptors. Wl= ley-VCH.Weinheim (Germany), (2000).

unfortunately, I don't have access to this handook.

Are there any papers that describe how to calculate this?

= Regards

Victor
--90e6ba6e89a2ab171b04eccc03d1-- From owner-chemistry@ccl.net Thu Dec 5 15:49:00 2013 From: "partha kundu partha1kundu|*|gmail.com" To: CCL Subject: CCL: scaling factor in frequency calculation Message-Id: <-49405-131205154629-9229-Q273KA54uBemTnHAVaNKSg]^[server.ccl.net> X-Original-From: partha kundu Content-Type: multipart/alternative; boundary=485b3978bfd552d83d04eccf9f88 Date: Fri, 6 Dec 2013 02:15:42 +0530 MIME-Version: 1.0 Sent to CCL by: partha kundu [partha1kundu-#-gmail.com] --485b3978bfd552d83d04eccf9f88 Content-Type: text/plain; charset=ISO-8859-1 Dear Jean, What do I see is if I add scaling factor 0.9 for 1000-1400 , 0.96 for 1400-1500 and 1 for 1500-1700 I getting good matches with theory. However, I saw that generally people use scaling factor close to 1 in the lower wave region and ~0.98 in the upper region. Is it okay to choose the scaling factor like that? Do you know any work where this kind of behavior has been seen? Regards. Partha On Tue, Dec 3, 2013 at 12:56 PM, Jean Jules Fifen julesfifen : gmail.com < owner-chemistry*_*ccl.net> wrote: > > Sent to CCL by: Jean Jules Fifen [julesfifen#,#gmail.com] > Scaling factors are better when they are applied differently in > different frequencies ranges. Thus, it is okay to use dual or more > scaling factors for matching experimental data. For more convenience, > I can suggest you to read the paper of Robert Shields (J. Chem. Theor. > Comput. 2011, 7, 2804-2817) entitled, The Role of Anharmonicity in > Hydrogen-Bonded Systems: The Case of water clusters. > > Best regards. > > On 12/2/13, partha kundu partha1kundu{:}gmail.com > wrote: > > Dear All, > > I am trying to see the effect of Cu2+ binding on a ligand by Raman > > spectroscopy and trying to match those results with DFT. For the ligand, > I > > got a very good match with the experimental spectrum after applying a > > scaling factor. However for the complex if I use the same scaling > factor, I > > see some modes in the 1500-1700 cm-1 regions are underestimated. If I do > > not use any scaling factor in that the match is better. I am using > lanl2dz > > ECP and basis set combination for Cu. Is it okay to use dual scaling > (0.961 > > for 1000-1500 and 1 for the 1500-1700 region) for matching the > experimental > > data. Then I can not directly compare my theoretical results with the > > experiment. Any suggestion would be of great help. > > Partha > > > > > -- > > *-------------------------------------- > * Jean Jules FIFEN, |* > ** Ph. D. in Molecular Physics, |* > ** Department of Physics, |* > ** Faculty of Science, |* > ** University of Ngaoundere, Cameroon |* > ** P.O. BOX 454 Ngaoundere | > * > ** Phone number: 00237 75 21 61 39 | > * > **---------------------------------------------------------> > > --485b3978bfd552d83d04eccf9f88 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Dear Jean,
What do I see is if I add sc= aling factor 0.9 for 1000-1400 , 0.96 for 1400-1500 and 1 for 1500-1700 I g= etting good matches with theory. However, I saw that generally people use s= caling factor close to 1=A0 in the lower wave region and=A0 ~0.98 in the up= per region. Is it okay to choose the scaling factor like that? Do you know = any work where this kind of behavior has been seen?
Regards.

Partha


On Tue, Dec 3, 2013 at 12:56 PM, Jean Ju= les Fifen julesfifen : gmail.com <owner-chemistry*_*ccl.net> wrote:

Sent to CCL by: Jean Jules Fifen [julesfifen#,#gmail.com]
Scaling factors are better when they are applied differently = in
different frequencies ranges. Thus, it is okay = to use dual or more
scaling factors for matching experimental data. For more conv= enience,
I can suggest you to read the paper of Robert Shields (J. Chem. Theo= r.
Comput. 2011, 7, 2804-2817) entitled, The Role of Anharmonicity in
Hydrogen-Bonded Systems: The Case of water clusters.

Best regards.

On 12/2/13, partha kundu partha1kundu{:}gmail.com
<owner-chemistry**ccl.net> wrote:
> Dear All,
> I am trying to see the effect of Cu2+ binding on a ligand by Raman
> spectroscopy and trying to match those results with DFT.= For the ligand, I
> got a very good match with the experimental spectrum aft= er applying a
> scaling factor. However for the complex if I use the sam= e scaling factor, I
> see some modes in the 1500-1700 cm-1 regions are underes= timated. If I do
> not use any scaling factor in that the match is better. = I am using lanl2dz
> ECP and basis set combination for Cu. Is it okay to use dual scaling (= 0.961
> for 1000-1500 and 1 for the 1500-1700 region) for matchi= ng the experimental
> data. Then I can not directly compare my theoretical res= ults with the
> experiment. Any suggestion would be of great help.
> Partha
>


--

*--------------------------------------
* Jean Jules FIFEN, =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0|*
** Ph. D. in Molecular Physics, =A0 =A0 =A0 |*<= br> ** Department of Physics, =A0 =A0 =A0 =A0 =A0 =A0 |*
** Faculty of Science, =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0|*
** University of Ngaoundere, Cameroon |*
** P.O. BOX 454 Ngaoundere =A0 =A0 =A0 =A0 =A0 =A0|
*
** Phone number: 00237 75 21 61 39 =A0 =A0|
*
**---------------------------------------------------------



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