From owner-chemistry@ccl.net Fri Nov 6 01:52:01 2009 From: "Chris Swain swain],[mac.com" To: CCL Subject: CCL: Warren L. DeLano Message-Id: <-40620-091106015036-32473-iuDx584H1PjfQPE3ZDf2wA!=!server.ccl.net> X-Original-From: Chris Swain Content-transfer-encoding: 7BIT Content-type: text/plain; charset=US-ASCII; format=flowed; delsp=yes Date: Fri, 06 Nov 2009 06:50:23 +0000 MIME-version: 1.0 Sent to CCL by: Chris Swain [swain()mac.com] Dear All, I know Warren was well known in the scientific community so it is with sadness I bring the news of his sudden death. More details here. http://www.macresearch.org/memoriam-warren-l-delano In Sadness, Chris From owner-chemistry@ccl.net Fri Nov 6 07:09:00 2009 From: "john furr john.furr]![gmail.com" To: CCL Subject: CCL: Warren L. DeLano Message-Id: <-40621-091106070727-12720-ftUXhnqMREizk8CYHFH56Q|server.ccl.net> X-Original-From: john furr Content-Type: multipart/alternative; boundary=0016e65b623aefe5490477b246b8 Date: Fri, 6 Nov 2009 06:38:04 -0500 MIME-Version: 1.0 Sent to CCL by: john furr [john.furr.*o*.gmail.com] --0016e65b623aefe5490477b246b8 Content-Type: text/plain; charset=ISO-8859-1 I'm greatly saddened by this. I remember flying out to California and meeting Warren for the first time. We were discussing how to combine software projects at the time. I have not met another person that would talk about computational graphics in the way he could. My heart goes out to his family and other collegues that were closer to him than I. The community just suffered a large loss because of this. John Fur On Fri, Nov 6, 2009 at 1:50 AM, Chris Swain swain],[mac.com < owner-chemistry*o*ccl.net> wrote: > > Sent to CCL by: Chris Swain [swain()mac.com] > Dear All, > > I know Warren was well known in the scientific community so it is with > sadness I bring the news of his sudden death. > > More details here. > > http://www.macresearch.org/memoriam-warren-l-delano > > In Sadness, > > Chrishttp://www.ccl.net/chemistry/sub_unsub.shtml> > Job: http://www.ccl.net/jobsConferences: > http://server.ccl.net/chemistry/announcements/conferences/> > > --0016e65b623aefe5490477b246b8 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable I'm greatly saddened by this.=A0 I remember flying out to California an= d meeting Warren for the first time.=A0 We were discussing how to combine s= oftware projects at the time.=A0 I have not met another person that would t= alk about computational graphics in the way he could.=A0 My heart goes out = to his family and other collegues that were closer to him than I.

The community just suffered a large loss because of this.

John F= ur

On Fri, Nov 6, 2009 at 1:50 AM, Chris = Swain swain],[mac.com <= owner-chemistry*o*ccl.net><= /span> wrote:

Sent to CCL by: Chris Swain [swain()mac.com]
Dear All,

I know Warren was well known in the scientific community so it is with sadn= ess I bring the news of his sudden death.

More details here.

http://www.macresearch.org/memoriam-warren-l-delano

In Sadness,

Chris



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--0016e65b623aefe5490477b246b8-- From owner-chemistry@ccl.net Fri Nov 6 08:05:00 2009 From: "John W Daily john.daily+*+colorado.edu" To: CCL Subject: CCL: using TINKER Message-Id: <-40622-091105221754-808-9Ep1ymlGYRPMV5enu3A23Q|,|server.ccl.net> X-Original-From: John W Daily Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii; format=flowed; delsp=yes Date: Thu, 5 Nov 2009 19:45:25 -0700 Mime-Version: 1.0 (Apple Message framework v1076) Sent to CCL by: John W Daily [john.daily_-_colorado.edu] Jonas, I have never had luck running tinker from FFE. Instead I run it directly from the command line. Of course you have to compile it for the machine of your choice. The distribution I have has all the programs and subroutines in one directory. There are make files for a variety of machines and compilers other directories. It is relatively straightforward to modify one for your own use. In most cases all the subroutines are compiled and then places in a library. The main programs can then be linked with the library. You can figure out which are the main programs because they are listed in the manual. John On Nov 5, 2009, at 6:36 PM, Jonas Baltrusaitis jasius_1||yahoo.com wrote: > > Sent to CCL by: "Jonas Baltrusaitis" [jasius_1_-_yahoo.com] > Dear all, > > is anybody using TINKER by any chance? I have been trying to run > jobs using FFE but found it impossible. Manual is to concise and I > can;t run any jobs as I find pdbxyz, nucleic and protein commands > only, whereas in the manual it clearly shows Optimize, no idea how > to get there. > > is there any mailing list or board for Tinker? > > thanks > > Jonas > > > > -= This is automatically added to each message by the mailing script > =- > To recover the email address of the author of the message, please > change> Conferences: http://server.ccl.net/chemistry/announcements/ > conferences/> > From owner-chemistry@ccl.net Fri Nov 6 09:35:00 2009 From: "Justin Finnerty justin.finnerty{}uni-oldenburg.de" To: CCL Subject: CCL: Level of Theory for zwitterionic species Message-Id: <-40623-091106081937-2678-ZybRhjhzkf1PcfbBeBGiIw|a|server.ccl.net> X-Original-From: Justin Finnerty Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=utf-8 Date: Fri, 06 Nov 2009 13:17:52 +0100 Mime-Version: 1.0 Sent to CCL by: Justin Finnerty [justin.finnerty(~)uni-oldenburg.de] On Thu, 2009-11-05 at 10:11 -0500, Sarah Ann Kebbell sarah.kebbell2_-_mail.dcu.ie wrote: > Sent to CCL by: "Sarah Ann Kebbell" [sarah.kebbell2^-^mail.dcu.ie] > Dear CCLers, > > just wondering if anybody has an previous experience in locating intermediates that are zwitterionic in nature and if so, is B3LYP/6-31G(d) a sufficient level of theory to locate zwitterions at or do I need to change the theory/basis set to do so? > > Many thanks, > Sarah Dear Sarah, myself, Rainer Koch and a number of others have worked with the well-known experimentalist Prof Curt Wentrup in the field of reactive intermediates. We have successfully used B3LYP/6-31G(d) to predict the base geometry of a range of formally zwitterionic intermediates. This was always combined with improved energy predictions using single-point calculations with large basis-sets and/or better theories. As Tanja said, solvation can be a major factor and we have had to use both the implicit solvation model (eg SCRF) and more rarely explicit solvation. However, the improvement in computing resources now means we use the 6-311++G** basis set for both geometry optimistation and thermochemistry. We are finding this to give much improved results for determining reaction pathways that had formerly eluded us. We are also investigating alternative functionals, such as MPW1K, as possible alternatives to the venerable B3LYP. One point that I see is that the zwitterionic character is not readily apparent in the molecular orbital picture, particularly for gas-phase calculations. It usually requires full NBO style analysis to get a more "chemist'S intuitive" picture with formal charges on atoms. However, I, myself, prefer the MO picture where you consider "zwitterions" as having volumes with increased or decreased electron density rather than the notion of formal charges. Cheers Justin -- Dr Justin Finnerty Rm W3-1-165 Ph 49 (441) 798 3726 Carl von Ossietzky Universität Oldenburg From owner-chemistry@ccl.net Fri Nov 6 10:35:01 2009 From: "Jan Labanowski janl~~speakeasy.net" To: CCL Subject: CCL: Warren Lyford DeLano is no longer with us Message-Id: <-40624-091106090304-27464-hrfNMfZCsEKmIOksq6l77w{:}server.ccl.net> X-Original-From: Jan Labanowski Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="iso-8859-1" Date: Fri, 06 Nov 2009 08:53:33 EST MIME-Version: 1.0 Sent to CCL by: Jan Labanowski [janl.:.speakeasy.net] While this sad news already appeared on CCL I will post a copy of the messa= ge that appeared on the CCP4 Bulletin Board. This is such a loss for computati= onal chemistry community. Jan =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 > From: Axel Brunger Date: Thu, Nov 5, 2009 at 1:54 PM Subject: [ccp4bb] Warren DeLano To: CCP4BB_+_jiscmail.ac.uk Dear CCP4 Community: I write today with very sad news about Dr. Warren Lyford DeLano. I was informed by his family today that Warren suddenly passed away at home= on Tuesday morning, November 3rd.=20=20 While at Yale, Warren made countless contributions to the computational too= ls and methods developed in my laboratory (the X-PLOR and CNS programs), including= the direct rotation function, the first prediction of helical coiled coil struc= tures, the scripting and parsing tools that made CNS a universal computational crystallography program.=20 He then joined Dr. Jim Wells laboratory at USCF and Genentech where he purs= ued a Ph.D. in biophysics, discovering some of the principles that govern protein-protein interactions. Warren then made a fundamental contribution to biological sciences by creat= ing the Open Source molecular graphics program PyMOL that is widely used throug= hout the world. Nearly all publications that display macromolecular structures u= se PyMOL. Warren was a strong advocate of freely available software and the Open Sour= ce movement.=20 Warren's family is planning to announce a memorial service, but arrangement= s have not yet been made. I will send more information as I receive it.=20 Please join me in extending our condolences to Warren's family.=20 Sincerely yours, Axel Brunger Axel T. Brunger Investigator, Howard Hughes Medical Institute Professor of Molecular and Cellular Physiology Stanford University From owner-chemistry@ccl.net Fri Nov 6 11:09:00 2009 From: "Jakob Petersen petersen.jakob.!A!.gmail.com" To: CCL Subject: CCL: using TINKER Message-Id: <-40625-091106032650-19297-bP80qyjeyaNQQXdqqsnzsg!A!server.ccl.net> X-Original-From: Jakob Petersen Content-Type: multipart/alternative; boundary=00032555acde6701670477ae9fd0 Date: Fri, 6 Nov 2009 08:16:29 +0100 MIME-Version: 1.0 Sent to CCL by: Jakob Petersen [petersen.jakob__gmail.com] --00032555acde6701670477ae9fd0 Content-Type: text/plain; charset=ISO-8859-1 Dear Jonas, I'm using the TINKER package for windows (running with FFE) and linux (running with shell script), and during the last 5 months I have been looking for a mailing list too. Now my calculations are running fine, but writing the .xyz and .key files (and making it all work) was a tedious job. Mostly, I'm using TINKER for molecular dynamics simulations, but I guess, that some of the "problems" I have encountered is universal for TINKER. If you have a specific question, let me know - maybe I can help you out. Greetings, Jakob On Fri, Nov 6, 2009 at 5:06 AM, A VM fray.gory###gmail.com < owner-chemistry]_[ccl.net> wrote: > > Dear Jonas, > > For linux... > > To me the greatest trick resides in defining correctly the PATH variable > in the shell that you are using. > (I mean, in my case, PATH=/opt/MolecularStructure/tinker/bin:$PATH) > > Also, as I work is generating the coordinates files with MOLDEN, and > assigning carefully the parameters with the 'FF' in the control window, > see MOLDEN web page, and saving them as TINKER xyz. > > Hope that it helps (at least a little bit). > > Alvaro > > > > Alvaro Vazquez-Mayagoitia > > > > On Thu, Nov 5, 2009 at 8:36 PM, Jonas Baltrusaitis jasius_1||yahoo.com < > owner-chemistry*ccl.net> wrote: > >> >> Sent to CCL by: "Jonas Baltrusaitis" [jasius_1_-_yahoo.com] >> Dear all, >> >> is anybody using TINKER by any chance? I have been trying to run jobs >> using FFE but found it impossible. Manual is to concise and I can;t run any >> jobs as I find pdbxyz, nucleic and protein commands only, whereas in the >> manual it clearly shows Optimize, no idea how to get there. >> >> is there any mailing list or board for Tinker? >> >> thanks >> >> Jonas>> E-mail to subscribers: CHEMISTRY*ccl.net or use:>> >> E-mail to administrators: CHEMISTRY-REQUEST*ccl.net or use>> >> >> > > --00032555acde6701670477ae9fd0 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear Jonas,

I'm using the TINKER package for windows (running wi= th FFE) and linux (running with shell script), and during the last 5 months= I have been looking for a mailing list too. Now my calculations are runnin= g fine, but writing the .xyz and .key files (and making it all work) was a = tedious job. Mostly, I'm using TINKER for molecular dynamics simulation= s, but I guess, that some of the "problems" I have encountered is= universal for TINKER. If you have a specific question, let me know - maybe= I can help you out.

Greetings,
Jakob

On Fri, Nov 6, 20= 09 at 5:06 AM, A VM fray.gory###gmail.com = <owner-chem= istry]_[ccl.net> wrote:

Dear Jonas,
For linux...

To me the greatest trick resides in defining corr= ectly the PATH variable
in the shell that you are using.
(I mean, in my case, PATH=3D/opt/Molecu= larStructure/tinker/bin:$PATH)

Also, as I work is generating the coordinates files with MOLDEN, and=A0=
assigning carefully the parameters with the 'FF' in the control= window,
see MOLDEN web page, and saving them as TINKER xyz.

Hope= that it helps (at least a little bit).

Alvaro



Alvaro Vazquez-Mayagoitia



On Thu, Nov 5, 2009 at 8:36 PM, = Jonas Baltrusaitis jasius_1||yahoo.com <owner-chemistry*ccl.net> wrote:

Sent to CCL by: "Jonas =A0Baltrusaitis" [jasius_1_-_yahoo.com]
Dear all,

is anybody using TINKER by any chance? I have been trying to run jobs using= FFE but found it impossible. Manual is to concise and I can;t run any jobs= as I find pdbxyz, nucleic and protein commands only, whereas in the manual= it clearly shows Optimize, no idea how to get there.

is there any mailing list or board for Tinker?

thanks

Jonas



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--00032555acde6701670477ae9fd0-- From owner-chemistry@ccl.net Fri Nov 6 11:44:00 2009 From: "Herbert Fruchtl herbert.fruchtl^^^st-andrews.ac.uk" To: CCL Subject: CCL:G: non-integer NBO spin occupations with MP2 Message-Id: <-40626-091106090031-26668-Fqk45eP5S3z5OIOyLjKgOw() server.ccl.net> X-Original-From: Herbert Fruchtl Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 06 Nov 2009 13:59:15 +0000 MIME-Version: 1.0 Sent to CCL by: Herbert Fruchtl [herbert.fruchtl]_[st-andrews.ac.uk] We are doing calculations with different methods on a set of organic radical anions using Gaussian 03. When I add up the alpha and beta electrons in all NBO orbitals on all atoms with SCF or DFT, I get a difference of 1.0 as expected. When using MP2 and Density=Current, the difference is non-integer. Is this to be expected, and what does it mean? Spin contamination does not look outrageous; I don't think this is the cause. Any ideas? Herbert -- Herbert Fruchtl Senior Scientific Computing Officer School of Chemistry, School of Mathematics and Statistics University of St Andrews -- The University of St Andrews is a charity registered in Scotland: No SC013532 From owner-chemistry@ccl.net Fri Nov 6 12:20:00 2009 From: "TJ O Donnell tjo++acm.org" To: CCL Subject: CCL: Warren L. DeLano Message-Id: <-40627-091106121738-7897-cJ33iu7WORPfWEq0nbDjDQ]*[server.ccl.net> X-Original-From: "TJ O'Donnell" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 06 Nov 2009 07:28:00 -0800 MIME-Version: 1.0 Sent to CCL by: "TJ O'Donnell" [tjo|-|acm.org] After many years of chatting with Warren, I finally had the chance to work closely with him over the past two years. His independent spirit, dedication and creativity were an inspiration. TJ O'Donnell Chris Swain swain],[mac.com wrote: > > Sent to CCL by: Chris Swain [swain()mac.com] > Dear All, > > I know Warren was well known in the scientific community so it is with > sadness I bring the news of his sudden death. > > More details here. > > http://www.macresearch.org/memoriam-warren-l-delano > > In Sadness, > > Chrishttp://www.ccl.net/chemistry/sub_unsub.shtml> > Job: http://www.ccl.net/jobsConferences: > http://server.ccl.net/chemistry/announcements/conferences/> > From owner-chemistry@ccl.net Fri Nov 6 15:36:00 2009 From: "Nuno A. G. Bandeira nuno.bandeira*o*ist.utl.pt" To: CCL Subject: CCL:G: non-integer NBO spin occupations with MP2 Message-Id: <-40628-091106135144-21530-JrI6RUigVRAaLU7s7WzPxg * server.ccl.net> X-Original-From: "Nuno A. G. Bandeira" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="ISO-8859-1"; format=flowed Date: Fri, 6 Nov 2009 19:14:21 +0100 MIME-Version: 1.0 Sent to CCL by: "Nuno A. G. Bandeira" [nuno.bandeira[A]ist.utl.pt] Em 06-11-2009 14:59, Herbert Fruchtl herbert.fruchtl^^^st-andrews.ac.uk escreveu: > > Sent to CCL by: Herbert Fruchtl [herbert.fruchtl]_[st-andrews.ac.uk] > We are doing calculations with different methods on a set of organic > radical anions using Gaussian 03. When I add up the alpha and beta > electrons in all NBO orbitals on all atoms with SCF or DFT, I get a > difference of 1.0 as expected. When using MP2 and Density=Current, the > difference is non-integer. Is this to be expected, and what does it > mean? Spin contamination does not look outrageous; I don't think this is > the cause. Have a look at the NBO FAQ (http://www.chem.wisc.edu/~nbo5/faq.htm) My guess is that your observation has something to do with question#8. -- Nuno A. G. Bandeira, AMRSC Laboratoire de Chimie LR6 Ecole Normale Superieure de Lyon 46, Allee d'Italie 69364 Lyon Cedex 07 - France http://cqb.fc.ul.pt/intheochem/nuno.html -- From owner-chemistry@ccl.net Fri Nov 6 17:27:01 2009 From: "Shikha Varma SVarma^^accelrys.com" To: CCL Subject: CCL: Homology modeling and loop refinement Message-Id: <-40629-091106162633-7095-7IhothXvfnZCTBFvu1gQSw]^[server.ccl.net> X-Original-From: Shikha Varma Content-Language: en-US Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="iso-8859-1" Date: Fri, 6 Nov 2009 16:26:16 -0500 MIME-Version: 1.0 Sent to CCL by: Shikha Varma [SVarma%x%accelrys.com] Dear Werner, You can try MODELER for homology modeling and CHARMm based algorithm Looper= for loop refinement. Both methods are implemented in Accelrys Discovery S= tudio modeling package. MODELER program is developed by Andrej Sali (http://salilab.org/index.html)= and is the best homology modeling package available. It is used as the of= ficial model building program by CASP (http://predictioncenter.org/index.cg= i), a community organized Critical Assessment of techniques for protein Str= ucture Prediction. It is highly automated and has many unique features, su= ch as allowing you to create model including ligands, build multiple chain = protein with symmetry constraints, etc, to make the model building easy and= accurate. Looper (Spassov, V.Z., et al, Protein Engineering Design and Selection 2008= , 21(2), 91-100) is an algorithm developed at Accelrys and is a very fast a= nd accurate loop prediction method. It is based on the well known CHARMm (= CHARMM) simulation engine developed at Harvard university. The implementati= on of LOOPER algorithm in Loop Refinement protocol is based on CHARMm ene= rgy calculations and it is flexible to a choice of most of CHARMm forcefi= elds what allows the predicted structures to be used directly by other mode= ling protocols, such as MD simulations, pK predictions etc. Publications of interest: 1. Spassov, V. Z.; Yan, L. A fast and accurate computational approach to pr= otein ionization. Protein Sci. 2008, 17, 1955-1970.=20 2.Koska, J.; Spassov, V. Z.; Maynard, A. J.; Yan, L.; Austin, N.; Flook, P.= K.; Venkatachalam, C. M. Fully automated molecular mechanics based induced= fit protein-ligand docking method. J. Chem. Inf. Model. 2008, 48, 1965-197= 3.=20 3. Eswar, N.; Eramian, D.; Webb, B.; Shen, M. Y.; Sali, A. Protein structur= e modeling with MODELLER. Methods Mol. Biol. 2008, 426, 145-159.=20 4. Spassov, V.; Yan, L.; Flook, P. The dominant role of side-chain backbone= interactions in structural realization of amino acid code. ChiRotor: a sid= e-chain prediction algorithm based on side-chain backbone interactions. Pro= tein Sci. 2007, 16, 494-506.=20 5. Marti-Renom, M. A.; Madhusudhan, M. S.; Sali, A. Alignment of protein se= quences by their profiles. Protein Sci. 2004, 13, 1071-1087.=20 6. Li, L.; Chen, R.; Weng, Z. RDOCK: refinement of rigid-body protein docki= ng predictions. Proteins 2003, 53, 693-707.=20 Chen, R.; Li, L.; Weng, Z. ZDOCK: an initial-stage protein-docking algorith= m. Proteins 2003, 52, 80-87.=20 Morea, V.; Lesk, A.; Tramontano, A. Antibody modeling: implications for eng= ineering and design. Methods 2000, 20, 267-279.=20 7. Sali, A.; Pottertone, L.; Yuan, F.; van Vlijmen, H.; Karplus, M.; Evalua= tion of comparative protein modeling by MODELLER. Proteins 1995, 23, 318-32= 6. 8. N. Eswar, M. A. Marti-Renom, B. Webb, M. S. Madhusudhan, D. Eramian, M. = Shen, U. Pieper, A. Sali. Comparative Protein Structure Modeling With MODEL= LER. Current Protocols in Bioinformatics, John Wiley & Sons, Inc., Suppleme= nt 15, 5.6.1-5.6.30, 2006.=20 9. M.A. Marti-Renom, A. Stuart, A. Fiser, R. S=E1nchez, F. Melo, A. Sali. C= omparative protein structure modeling of genes and genomes. Annu. Rev. Biop= hys. Biomol. Struct. 29, 291-325, 2000.=20 A. Sali & T.L. Blundell. Comparative protein modelling by satisfaction of s= patial restraints. J. Mol. Biol. 234, 779-815, 1993.=20 10. A. Fiser, R.K. Do, & A. Sali. Modeling of loops in protein structures, = Protein Science 9. 1753-1773, 2000. Shikha Varma-O'Brien, Ph.D. Director, LS Modeling & Simulations Accelrys, Inc. 10188 Telesis Court, Suite 100 San Diego, CA 92121, USA Ph: +1 858 799 5607 Fax: +1 858 799 5100 =20 Stay Connected with Accelrys and the Scientific & Engineering Community Blog | Forum | Website | Support -----Original Message----- > From: owner-chemistry+shikha=3D=3Daccelrys.com_._ccl.net [mailto:owner-chemis= try+shikha=3D=3Daccelrys.com_._ccl.net] On Behalf Of Werner K werner.schroedi= nger-x-googlemail.com Sent: Wednesday, November 04, 2009 8:53 AM To: Shikha Varma Subject: CCL: Homology modeling and loop refinement Sent to CCL by: "Werner K" [werner.schroedinger^-^googlemail.com] Hi, what are in your opinion the best softwares, free and commercial, for prote= in homology modeling and loop refinement? Thanks WS -=3D This is automatically added to each message by the mailing script =3D-http://www.ccl.net/cgi-bin/ccl/send_ccl_messageSubscribe/Unsubscribe:=20Job: http://www.ccl.net/jobs=20http://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Fri Nov 6 19:24:00 2009 From: "Andrew Orry andy/a\molsoft.com" To: CCL Subject: CCL: Homology modeling and loop refinement Message-Id: <-40630-091106191848-15776-sSf71vWAguoQUUQXXAHEzw:server.ccl.net> X-Original-From: Andrew Orry Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 06 Nov 2009 15:37:30 -0800 MIME-Version: 1.0 Sent to CCL by: Andrew Orry [andy:-:molsoft.com] Werner, Please also consider MolSoft's ( http://www.molsoft.com/ ) software called ICM-Pro + Homology. ICM has a long history of success in homology and loop modeling. ICM also performed very well in the recent GPCR modeling competition see: dx.doi.org/10.1038/nrd2877 References to other success stories can be found here: http://www.molsoft.com/homology.html . Please see dx.doi.org/10.1007/978-1-60761-274-2_11 for a good overview of MolSoft's ICM ligand based modeling. Thanks, Andy -- Andrew Orry Ph.D. Senior Scientist MolSoft LLC 3366 North Torrey Pines Court Suite 300 La Jolla, CA 92037 U S A Phone: (858) 625-2000 (x108) Fax: (858) 625-2888 www.molsoft.com Latest ICM News: www.molsoft.com/news.html > > -----Original Message----- > >> From: owner-chemistry+shikha==accelrys.com-*-ccl.net [mailto:owner-chemistry+shikha==accelrys.com-*-ccl.net] On Behalf Of Werner K werner.schroedinger-x-googlemail.com >> > Sent: Wednesday, November 04, 2009 8:53 AM > To: Shikha Varma > Subject: CCL: Homology modeling and loop refinement > > > Sent to CCL by: "Werner K" [werner.schroedinger^-^googlemail.com] > Hi, > > what are in your opinion the best softwares, free and commercial, for protein homology modeling and loop refinement? > > Thanks > > WShttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/spammers.txt > > > -> > >