From owner-chemistry@ccl.net Fri Jun 18 01:09:01 2010 From: "Dr. Sudhir A. Kulkarni sudhirk:_:vlifesciences.com" To: CCL Subject: CCL: Program for enzyme design Message-Id: <-42135-100617091740-27045-UP1pVvE8MvjmwdYTJ91/VQ:-:server.ccl.net> X-Original-From: "Dr. Sudhir A. Kulkarni" Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=windows-1252; format=flowed Date: Thu, 17 Jun 2010 14:45:44 +0530 MIME-Version: 1.0 Sent to CCL by: "Dr. Sudhir A. Kulkarni" [sudhirk^^^vlifesciences.com] Hello, We have recently done work on in-silico mutation of enzyme and studying interactions with known compound. Please look at Protein Science 2009, 18, 2139—2151. Sudhir Iain Moal Iain.Moal{}cancer.org.uk wrote: > Hello WoA, > The Baker group have managed to design an enzyme de novo, and much of their code is available in their rosetta package (or its python implimentation, pyrosetta). It might take a bit of work to get a small molecule into the package, but otherwise it should work quite well for your purpose. You can optimise the position and orientation of the ligand, as well as the backbone conformation and the side-chain rotamers. When repacking the side-chains, you can select certain residues and ask the program to search for rotamers in all 20 amino acids, hence performing computational mutagenasis on the fly. See workshop #6 on the PyRosetta website. > > Iain > > > -----Original Message----- > >> From: owner-chemistry+iain.moal==cancer.org.uk,ccl.net on behalf of W Agnessi witch.of.agnessi*gmail.com >> > Sent: Tue 15/06/2010 21:38 > To: Iain Moal > Subject: CCL: Program for enzyme design > > > Sent to CCL by: "W Agnessi" [witch.of.agnessi[]gmail.com] > Hello CCLers, > > I'm working on computational design of an enzyme to increase it's affinity for a non-natural substrate. I wish to mutate 2-3 residues at the ligand binding site such that it can bind better a non-natural substrate. Quite a few X-ray structures are available for the apo as well as holo enzyme,with different ligands. However no structure with that non-natural substrate is available. > > I'm looking for freely available softwares, which would be able to computationally re-design the active site. My input to the program would be a (badly) docked structure of the enzyme and my ligand of interest. > > Any suggestions, comments, pointers, relevant literature links are most welcome. > > Thanks in advance > > -WoAhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/spammers.txtThis communication is from Cancer Research UK. Our website is at www.cancerresearchuk.org. We are a charity registered under number 1089464 and a company limited by guarantee registered in England & Wales under number 4325234. Our registered address is 61 Lincoln's Inn Fields, London WC2A 3PX. Our central telephone number is 020 7242 0200. > > This communication and any attachments contain information which is confidential and may also be privileged. It is for the exclusive use of the intended recipient(s). If you are not the intended recipient(s) please note that any form of disclosure, distribution, copying or use of this communication or the information in it or in any attachments is strictly prohibited and may be unlawful. If you have received this communication in error, please notify the sender and delete the email and destroy any copies of it. > > E-mail communications cannot be guaranteed to be secure or error free, as information could be intercepted, corrupted, amended, lost, destroyed, arrive late or incomplete, or contain viruses. We do not accept liability for any such matters or their consequences. Anyone who communicates with us by e-mail is taken to accept the risks in doing so. From owner-chemistry@ccl.net Fri Jun 18 07:51:00 2010 From: "Vitaly Rassolov rassolov]-[mail.chem.sc.edu" To: CCL Subject: CCL: Qchem aborting unexpectedly Message-Id: <-42136-100617215823-14719-2MWc9WhrMRRngvTCuTsHKA^^^server.ccl.net> X-Original-From: Vitaly Rassolov Content-Type: text/plain; charset="US-ASCII"; format=flowed Date: Thu, 17 Jun 2010 21:27:47 -0400 MIME-Version: 1.0 Sent to CCL by: Vitaly Rassolov [rassolov,mail.chem.sc.edu] Q-Chem is unforgiving of the slow I/O. In a serial environment it may crash with with the error message about a particular file being inaccessible. In parallel it sometimes stops (for the same reason of slow I/O) without any warning. We have used SS(V)PE with Q-Chem (various versions of 3.x) in serial without any problems. ---------------------------------------------------------- Vitaly Rassolov Dept. of Chemistry and Biochemistry (803) 777-7811 University of South Carolina fax (803) 777-9521 631 Sumter St Columbia, SC 29208 rassolov,mail.chem.sc.edu On Thu, 17 Jun 2010, Josh Szekely j-szekely.,.onu.edu wrote: > > Sent to CCL by: "Josh Szekely" [j-szekely,onu.edu] > I am trying to run optimization and frequency calculations on qchem using the SS(V)PE solvation > model with DFT theory. The initial SCF cycle for all of my calculations finishes for the gas phase, but > when the solvation method is applied, the calculation aborts without any sort of error message. I've > tried adjusting memory settings and a few other parameters, but the same thing always happens. Does > anyone have any idea as to what may be causing this issue? > > Josh Szekely > j-szekely#,#onu.edu> > From owner-chemistry@ccl.net Fri Jun 18 08:26:00 2010 From: "Harald Lanig harald.lanig]_[chemie.uni-erlangen.de" To: CCL Subject: CCL: =?ISO-8859-1?Q?Symposium_and_80th_birthday_of_Paul_von_Ragu=E9_Schleyer_in_Erlangen,_Germany?= Message-Id: <-42137-100618061310-30734-9j6ceIANzZxtidjrpN+t2Q],[server.ccl.net> X-Original-From: Harald Lanig Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="ISO-8859-1"; format="flowed" Date: Fri, 18 Jun 2010 11:15:31 +0200 MIME-Version: 1.0 Sent to CCL by: Harald Lanig [harald.lanig(!)chemie.uni-erlangen.de] Dear CCL list members, On Friday, August 27th and Saturday, August 28th 2010, the=20 Computer-Chemie-Centrum (CCC) of the Friedrich-Alexander-Universitaet=20 Erlangen-N=FCrnberg, Germany (Department of Chemistry and Pharmacy) will=20 be holding a two-day Symposium entitled Theory and Experiment: Synergy or Competition? in honor of Paul von Ragu=E9 Schleyer's 80th birthday. The symposium will take place in Paul's old stamping ground, the=20 Organische Chemie building in Erlangen. Participation in the symposium=20 is free, but participants must register in advance by sending the=20 completed registration form by mail or Fax (+49-9131-8526565) to=20 Isabelle Schraufstetter or Nadine Scharrer=20 (Sekretariat.CCC-,-chemie.uni-erlangen.de) in the Computer-Chemie-Centrum,=20 who will also book a hotel room if required. The Scientific Program will consist of two full days of lectures by=20 Paul's ex-students and current associates. There will be a Conference=20 dinner (details to be announced, price EUR 100) to round off the=20 Symposium on Saturday evening. The Symposium is taking place directly before the 3rd EuCheMS Chemistry=20 Congress in N=FCrnberg, only 20 km from Erlangen, so that participants ca= n=20 combine the two events. For further information please see the meeting web pages at http://www.chemie.uni-erlangen.de/ccc/schleyer_conference/ Kind regards, -Harald Lanig --=20 ------------------------------------------------------------------------ Dr. Harald Lanig Universitaet Erlangen/Nuernberg Computer-Chemie-Centrum Naegelsbachstr. 25, D-91052 Erlangen Phone +49(0)9131-85 26525 harald DOT lanig AT chemie.uni-erlangen.de Fax +49(0)9131-85 26565 http://www.chemie.uni-erlangen.de/lanig ------------------------------------------------------------------------