From owner-chemistry@ccl.net Thu Apr 15 05:32:00 2010 From: "Andrew Voronkov drugdesign-*-yandex.ru" To: CCL Subject: CCL: has anyone made implementation fo scroing and consensus scoring functions to GoldSuite? Message-Id: <-41664-100413051849-15259-SELILZ9BsOGWAje/AScyqQ|server.ccl.net> X-Original-From: Andrew Voronkov Content-Transfer-Encoding: 7bit Content-Type: text/plain Date: Tue, 13 Apr 2010 12:48:58 +0400 MIME-Version: 1.0 Sent to CCL by: Andrew Voronkov [drugdesign(0)yandex.ru] Dear CCL users, the GoldSuite software allows user-defined scoring functions implementation. However I haven't found references on CCDC web site on groups\publications where additional scoring functions will be implemented. Has anyone here tried to do it or maybe to design own consensus scoring function? Best regards, Andrew From owner-chemistry@ccl.net Thu Apr 15 07:49:00 2010 From: "Michelle Kuttel mkuttel__cs.uct.ac.za" To: CCL Subject: CCL: CUDA enabled docking codes Message-Id: <-41665-100415042415-16730-Zay2eQ5fXC72GWGpVUTeMA|a|server.ccl.net> X-Original-From: Michelle Kuttel Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=WINDOWS-1252; format=flowed; delsp=yes Date: Thu, 15 Apr 2010 09:44:54 +0200 Mime-Version: 1.0 (Apple Message framework v936) Sent to CCL by: Michelle Kuttel [mkuttel*cs.uct.ac.za] Hi Carlos It's intended for *large* structures, but we have developed an =20 implementation of the Kim-Hummer course-grained model[1] for Replica =20= Exchange Monte Carlo simulations on protein-protein docking on =20 combined multiCore CPU/GPU architectures. The code is complete and =20 shows very good speed-up for large systems (>800 times) but not for =20 small systems. We are not quite at the point of generally releasing the code, but if =20= your would like to give it a try, do contact me. regards Michelle [1] Y. Kim and G. Hummer, J. Mol. Biol. (2008) 375, 1416=961433 --------------------------------------------- Dr Michelle Kuttel Department of Computer Science University of Cape Town Cape Town South Africa mkuttel{:}cs.uct.ac.za PH: +27 21 6505107 --------------------------------------------- On 13 Apr 2010, at 12:32 PM, Andrew Voronkov drugdesign:+:yandex.ru =20 wrote: > > Sent to CCL by: Andrew Voronkov [drugdesign,yandex.ru] > > Hi Carlos! > There are some attempts to develop Autodock for Nvidia using CUDA. > http://sourceforge.net/projects/gpuautodock/ > We are trying to work on it too. Please let me know if you can =20 > participate in development of such software. > > Best regards, > Andrew > > 11.04.10, 23:26, "Carlos F Lagos cflagos=3D=3D=3Duc.cl" chemistry[*]ccl.net>: > >> >> Sent to CCL by: "Carlos F Lagos" [cflagos[]uc.cl] >> Hello everyone, please I would like to have information about small =20= >> molecule-protein docking codes available for CUDA >> Regards >> >> QF Carlos F. Lagos >> Medicinal Chemistry Laboratory MCL, Faculty of Chemistry >> P. Universidad Catolica de Chile >> Portugal 49, Zocalo I 8330025 Santiago-Chile >> Phone: +56 2 3541911 I http://www.quimica.uc.cl> >> >> >> > > > > -=3D This is automatically added to each message by the mailing script = =20 > =3D- > To recover the email address of the author of the message, please =20 > change> Conferences: http://server.ccl.net/chemistry/announcements/=20 > conferences/> > From owner-chemistry@ccl.net Thu Apr 15 13:30:00 2010 From: "Sumit Gupta sugupta*_*nvidia.com" To: CCL Subject: CCL: CUDA enabled docking codes Message-Id: <-41666-100415132651-12449-PMHidxmoh1ORZpaU4oLamg .. server.ccl.net> X-Original-From: Sumit Gupta Content-Language: en-US Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="us-ascii" Date: Thu, 15 Apr 2010 10:26:37 -0700 MIME-Version: 1.0 Sent to CCL by: Sumit Gupta [sugupta[A]nvidia.com] The HEX Protein-Protein docking software is already available on CUDA: http://www.loria.fr/~ritchied/hex/ Sumit -----Original Message----- > From: owner-chemistry+sugupta=3D=3Dnvidia.com()ccl.net [mailto:owner-chemi= stry+sugupta=3D=3Dnvidia.com()ccl.net] On Behalf Of Michelle Kuttel mkutte= l__cs.uct.ac.za Sent: Thursday, April 15, 2010 00:45 To: Sumit Gupta Subject: CCL: CUDA enabled docking codes Sent to CCL by: Michelle Kuttel [mkuttel*cs.uct.ac.za] Hi Carlos It's intended for *large* structures, but we have developed an =20 implementation of the Kim-Hummer course-grained model[1] for Replica =20 Exchange Monte Carlo simulations on protein-protein docking on =20 combined multiCore CPU/GPU architectures. The code is complete and =20 shows very good speed-up for large systems (>800 times) but not for =20 small systems. We are not quite at the point of generally releasing the code, but if =20 your would like to give it a try, do contact me. regards Michelle [1] Y. Kim and G. Hummer, J. Mol. Biol. (2008) 375, 1416-1433 --------------------------------------------- Dr Michelle Kuttel Department of Computer Science University of Cape Town Cape Town South Africa mkuttel_._cs.uct.ac.za PH: +27 21 6505107 --------------------------------------------- On 13 Apr 2010, at 12:32 PM, Andrew Voronkov drugdesign:+:yandex.ru =20 wrote: > > Sent to CCL by: Andrew Voronkov [drugdesign,yandex.ru] > > Hi Carlos! > There are some attempts to develop Autodock for Nvidia using CUDA. > http://sourceforge.net/projects/gpuautodock/ > We are trying to work on it too. Please let me know if you can =20 > participate in development of such software. > > Best regards, > Andrew > > 11.04.10, 23:26, "Carlos F Lagos cflagos=3D=3D=3Duc.cl" chemistry[*]ccl.net>: > >> >> Sent to CCL by: "Carlos F Lagos" [cflagos[]uc.cl] >> Hello everyone, please I would like to have information about small =20 >> molecule-protein docking codes available for CUDA >> Regards >> >> QF Carlos F. Lagos >> Medicinal Chemistry Laboratory MCL, Faculty of Chemistry >> P. Universidad Catolica de Chile >> Portugal 49, Zocalo I 8330025 Santiago-Chile >> Phone: +56 2 3541911 I http://www.quimica.uc.cl> >> >> >> > > > > -=3D This is automatically added to each message by the mailing script = =20 > =3D- > To recover the email address of the author of the message, please =20 > change> Conferences: http://server.ccl.net/chemistry/announcements/=20 > conferences/> > -=3Dis is automatically added to each message by the mailing script =3D=20=20Subscribe/Unsubscribe:=20 =20Job: http://www.ccl.net/jobs=20=20-------------------------------------------------------------------------= ---------- This email message is for the sole use of the intended recipient(s) and m= ay contain confidential information. Any unauthorized review, use, disclosure or di= stribution is prohibited. If you are not the intended recipient, please contact the= =20sender by reply email and destroy all copies of the original message. -------------------------------------------------------------------------= ---------- From owner-chemistry@ccl.net Thu Apr 15 14:22:00 2010 From: "Michel Petitjean petitjean.chiral%%gmail.com" To: CCL Subject: CCL: Smiles convention for stereoisomers ? Message-Id: <-41667-100415133518-10151-l9dfurI4W3mgSAt2ug0olQ*o*server.ccl.net> X-Original-From: Michel Petitjean Content-Type: text/plain; charset=ISO-8859-1 Date: Thu, 15 Apr 2010 18:38:18 +0200 MIME-Version: 1.0 Sent to CCL by: Michel Petitjean [petitjean.chiral_+_gmail.com] Hi there, Does anybody know about the exact convention to specify atoms positions from a SMILES having stereocenters in rings ? It seems there is a difference in treatment for ring closure and other atoms ? For instance for C[C|,||,|H]1C[C|,||,|H](O)CC(=O)O1 For the second center, not a ring closure, we look from the CC bond, and we have H,O,C clockwise. For the first one how does one proceed ? If one looks from first C to second C, then H, C, O should be positioned clockwise, whereas actually it seems it is countercloskwise. Idem from the example on their site : http://www.daylight.com/dayhtml/doc/theory/theory.smiles.html C[C|,|H]1CCCCO1 I could not understand the few sentences on SMILES theory related to ring closure digit appearance. Thanks by advance Michel Petitjean. From owner-chemistry@ccl.net Thu Apr 15 18:17:00 2010 From: "Eiman Abd Elrahman Osman abdelrah:staff.uni-marburg.de" To: CCL Subject: CCL: How to use TOWHEE program Message-Id: <-41668-100415105749-21967-iuhTQn2FpfQCL0g+OMqxjw]|[server.ccl.net> X-Original-From: "Eiman Abd Elrahman Osman" Date: Thu, 15 Apr 2010 10:57:48 -0400 Sent to CCL by: "Eiman Abd Elrahman Osman" [abdelrah .. staff.uni-marburg.de] I would like use TOWHEE to calculate the vapor liquid equilibria for some fluids.But I don't know how to compose an initial and input files for TOWHEE and how to run the Simulation with it. Eiman Abdelrahman Osman physical chemistry(computer simulation) Philipps university-Marburg