From owner-chemistry@ccl.net Sat Aug 22 11:00:01 2009 From: "Andrew Voronkov drugdesign[-]yandex.ru" To: CCL Subject: CCL: protein-ligand binding simulation times with molecular dynamics Message-Id: <-40053-090822015844-17698-5dsmcS9Ycgl/xCm0IsNF1w],[server.ccl.net> X-Original-From: Andrew Voronkov Content-Transfer-Encoding: 7bit Content-Type: text/plain Date: Sat, 22 Aug 2009 09:11:44 +0400 MIME-Version: 1.0 Sent to CCL by: Andrew Voronkov [drugdesign[*]yandex.ru] Dear CCl users, How much time it will take to assess organic compound's binding with Mw=300-400 to the protein's potential binding site with molecular dynamics? Is 1-5 nanoseconds enough? The goal is to assess the stability of protein-ligand complex and then to evaluate its stability by MM-PBSA for selection from ligands databases? Best regards, Andrew From owner-chemistry@ccl.net Sat Aug 22 13:11:00 2009 From: "Anatoli Korkin a_korkin*|*yahoo.com" To: CCL Subject: CCL: And now something completely different! Message-Id: <-40054-090821212606-6666-A4LF5KN6L1W1waExyfCpww(_)server.ccl.net> X-Original-From: Anatoli Korkin Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=iso-8859-1 Date: Fri, 21 Aug 2009 17:25:52 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Anatoli Korkin [a_korkin[#]yahoo.com] I agree with Soren,=0A=0AObviously this youtube video made by Anna Krylov's= team has no direct educational/tutorial value in a sense of explaining stu= dents the fundamentals of light-molecule interactions:=0A=0Ahttp://www.yout= ube.com/watch?v=3DceoO18RTiZI=0A=0AHowever, first, let not lose a sense of = humor and, second, remember, that we live in the era of entertainment, whet= her we like it or not, and professional science educators can only win a ba= ttle with gaming and entertainment industry if they learn the "enemy" (or l= et say competitors) arms and use them properly in the battle for brains and= hearts of new generation. =0A=0AOn that regard I consider the "Britney Spe= ars' Guide to=0ASemiconductor Physics" as a good prject:=0A=0Ahttp://britne= yspears.ac/lasers.htm=0A=0Aand invite everyone who wish to make interesting= tutorial pages on atomic scale science to join my own "Nanotechnology for = Bolnds" educational web site sponsored by Russian STM/AFM maker NT-MDT:=0A= =0Ahttp://www.atomicscaledesign.net/=0A=0ABest regards,=0AAnatoli Korkin=0A= email: korkin/at/nanoandgiga.com=0A=0A--- On Thu, 8/20/09, Soren Eustis sor= eneustis^^^gmail.com wrote:=0A=0A> From: Soren Eu= stis soreneustis^^^gmail.com =0A> Subject: CCL: An= d now something completely different!=0A> To: "Korkin, Anatoli " =0A> Date: Thursday, August 20, 2009, 12:03 PM=0A> =0A> S= ent to CCL by: "Soren Eustis" [soreneustis-x-gmail.com]=0A> =0A> I would ha= ve to say that I am more than a little surprised=0A> at the backlash=0A> > = > from this YouTube posting.=A0 It is elementary=0A> indeed, and no doubt mos= t of us=0A> like to think those we teach are well beyond such=0A> elementar= y things.=0A> However, often there are more than a few people in any=0A> gi= ven class that=0A> benefit enormously by such elementary ways of=0A> teachi= ng.=A0 I am all for=0A> conceptual visualizations, and I think we shouldn't= turn=0A> our nose up at such=0A> a work.=A0 =0A> =0A> No science will come= of it, but perhaps someone will have=0A> an a-ha moment and=0A> then go ba= ck and actually learn something.=0A> =0A> =0A> =0A> Soren N. Eustis, Ph.D.= =0A> Postdoctoral Associate=0A> ETH - Zurich=0A> Institute of Biogeochemist= ry and Pollutant Dynamics=0A> Universitaetstrasse 16=0A> 8092 Zurich=0A> Sw= itzerland=0A> =0A> -----Original Message-----=0A> > From: owner-chemistry+s= oreneustis=3D=3Dgmail.com##ccl.net=0A> [mailto:owner-chemistry+soreneustis= =3D=3Dgmail.com##ccl.net] On=0A> Behalf Of Mihaly=0A> Mezei Mihaly.Mezei * = mssm.edu=0A> Sent: Thursday, August 20, 2009 19:15 =0A> To: Eustis, Soren N= ewman =0A> Subject: CCL: And now something completely different!=0A> =0A> = =0A> Sent to CCL by: Mihaly Mezei [Mihaly.Mezei::mssm.edu]=0A> Greetings,= =0A> =0A> reading Dr. Jensen's comment on the "educational film=0A> explain= ing the=0A> interaction of molecules with light"=A0 =0A> (http://www.youtub= e.com/watch?v=3DceoO18RTiZI)=0A> made me go and watch it. I share Dr. Jense= n's shock. It may=0A> be fun to watch,=0A> but it has hardly anything to do= with pchem research.=0A> =0A> This video reminded me of the blind man's qu= ery about=0A> milk:=0A> =0A> Milk is white, he was told.=0A> =0A> Ok, but w= hat is white?=0A> =0A> Oh, white is like a swan.=0A> =0A> Yes, but what is = a swan?=0A> =0A> You know, the bird with an S-shaped neck.=0A> =0A> Thanks,= Now I know what milk is.=0A> =0A> Mihaly Mezei=0A> =0A> Department of Stru= ctural and Chemical Biology, Mount Sinai=0A> School of=0A> Medicine, NYU=0A= > Voice:=A0 (212) 659-5475=A0=A0=A0Fax: (212)=0A> 849-2456=0A> WWW (MSSM ho= me):=0A> http://www.mountsinai.org/Find%20A%20Faculty/profile.do?id=3D00000= 725000014971=0A> 92632=0A> WWW (Lab home - software, publications): http://= inka.mssm.edu/~mezei=0A> WWW (Department): http://atlas.physbio.mssm.eduhtt= p://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/su= b_unsub.shtmlhttp://www.ccl.net/spammers.txt=0A> =0A> =0A> -=3D This is aut= omatically added to each message by the=0A> mailing script =3D-=0A> To reco= ver the email address of the author of the message,=0A> please change=0A> t= he strange characters on the top line to the :-: sign. 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