From owner-chemistry@ccl.net Tue Sep 13 09:18:31 2005 From: "CCL" To: CCL Subject: CCL: Bioisosterism Message-Id: <-29133-050913034320-27390-ETc9kVj+VqHwexQEb/3djg%a%server.ccl.net> X-Original-From: Christian.Pilger%a%basf-ag.de Content-type: text/plain; charset=US-ASCII Date: Tue, 13 Sep 2005 09:05:44 +0200 MIME-Version: 1.0 Sent to CCL by: Christian.Pilger%a%basf-ag.de Dear CCLers, can you provide me with information about bioisosterism ? I am looking for available empirical datasets for isosteric replacements in pharmaceutical or agricultural research. Additionally, I would like to learn about the use of CADD in this field. I read some articles about the use of physico-chemical descriptors and different statistical methods for the proposal/identification of bioisosteric fragments. Hints to academic research groups as well as to commercial solutions are equally wellcome. I will summarize the answers. Best regards, Christian From owner-chemistry@ccl.net Tue Sep 13 09:18:31 2005 From: "CCL" To: CCL Subject: CCL: Dynamol Fingerprints Message-Id: <-29131-050913090447-11575-ETc9kVj+VqHwexQEb/3djg(_)server.ccl.net> X-Original-From: john furr Content-Disposition: inline Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Tue, 13 Sep 2005 08:00:23 -0400 Mime-Version: 1.0 Sent to CCL by: john furr [john.furr(_)gmail.com] Hello CCL'ers I would like to announce a new version of Dynamol available for beta testing. The latest version contains an atom environment fingerprint module. The module is similar to the work of Dr. Andreas Bender. The method uses atom environments derived from the general amber force field atom types, probability based feature selection, and Bayesian classification. The descriptors have been constructed using statistics derived form a unique subset of the ZINC database comprising 1.8 million compounds. A paper is in the works showing the performance of the algorithm across 44 different bioactive sets. The Dynamol software allows you to search a local database file, or a database hosted on the Dynamol servers. Currently we are hosting a ZINC derived database of 1.8 million compounds. Several other databases are in the works and should be available in the coming months. Network searches return the top 100 hits in table format containing all the vendor information necessary to purchase these compounds. I would like to point out that the ZINC database is the work of Dr. Irwin and Dr. Schoicet. While we have done some processing of the database it is by and large still the same database as prepared by the above authors. The software allows you to input a set of active molecules in SD format, and an optional training set. The time required to do a network search of the ZINC database is around 1 minute. The time required to do a local search against 5.5 million compounds in under 4 minutes. This may very with server load. Since this is a beta test you should expect server down times....hey that's why it's still beta! In addition Dynamol now has several molecular descriptors including: 1) Electrotopological State Indices 2) Atom environment bond clusters and angle clusters. 3) Constitutional descriptors Currently there is no means of performing a regression analysis with Dynamol. However the data can be exported and used in a variety of other statistical software packages. Beta testers are no longer required to register. Just follow the links and download. http://www.dynamol.com Enjoy Worried about using software that will become commercial? Consider this: Dynamol has the goal of drastically lowering the cost of drug discovery software. Many of the current features are free and will remain free. The current version comes with a 3 month license. If Dynamol is still doing beta releases at the end of 3 months it will be as simple as downloading the latest version. Once the software leaves the Beta stage the price is estimated to be around $500.00 USD per year. Compare that with the price from other software vendors. Thanks John Furr Dynamol Inc. From owner-chemistry@ccl.net Tue Sep 13 09:18:31 2005 From: "CCL" To: CCL Subject: CCL: Molpro and memory Message-Id: <-29132-050913060856-2690-ETc9kVj+VqHwexQEb/3djg_+_server.ccl.net> X-Original-From: Nick Wilson Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 13 Sep 2005 11:08:01 +0200 MIME-Version: 1.0 Sent to CCL by: Nick Wilson [nickwilson_+_beeb.net] The latest general release is 2002.6 With the 2002.6 molpro rpm on a RedHat9 dual xeon system with 2GB of ram and 2GB of swap I could allocate 250 megawords (~2GB) for a one processor job and 235 megawords per process for a two procesor job Best wishes, Nick Wilson CCL wrote: > > Sent to CCL by: Alexander Martins Silva [alex.msilva]_[uol.com.br] > Hi, > > I'm running the 2002.3 version. Thanks. > > > Alexander. > > CCL wrote: > >> >> Sent to CCL by: Kirk Peterson [kipeters|a|wsu.edu] >> Hi, >> >> I've re-built Molpro without parallel support and I can still >> allocate up to 2GB of memory on 1 processor. After looking through >> the Molpro users mailing list, I noted that there was a problem >> reported with very early versions of molpro2002 (this was back in >> Feb. of 2002). What version of Molpro are you running? The "fix" was >> posted back in July of 2002 where one should make sure the program is >> linked with the system gmalloc rather than the Molpro one. All >> subsequent versions of Molpro have this patched. >> (see also: http://www.molpro.net/molpro-user/archive/all/msg00485.html) >> >> Hope this helps, -Kirk >> >> On Sep 12, 2005, at 7:24 AM, CCL wrote: >> >>> >>> Sent to CCL by: Alexander Martins Silva [alex.msilva(!)uol.com.br] >>> Hi, >>> >>> "Is your kernel compiled with large memory support? " >>> >>> Yes, it is. You are using 1Gb per processor. It is the same >>> problem. I will compile a paralel version of molpro to try to solve >>> partialy my problem. >>> >>> >>> Thank you, >>> >>> >>> Alexander. >>> >>> >>> >>> CCL wrote: >>> >>>> Sent to CCL by: Kirk Peterson [kipeters{=}wsu.edu] >>>> Perhaps this is due to using gcc, but with the Portland Group >>>> compiler we consistently allocate more than 1 GB of memory (up to >>>> 2) with molpro on our >>>> 32-bit athlon cluster (dual node, 3GB RAM, 4GB of swap). Is your >>>> kernel compiled with large memory support? >>>> -Kirk >>>> >>>> >>>> On Fri, Sep 09, 2005 at 11:00:32PM -0400, CCL wrote: >>>> >>>>> Sent to CCL by: "Igor Filippov [Contr]" [igorf|"|helix.nih.gov] >>>>> I seem to remember reading about 1Gb limit per single process too, >>>>> though I can't find the reference now. This is what Linus had said >>>>> about >>>>> the issue - according to him, it's more like 3Gb limit, but >>>>> not all of it can be accessible - due to shared libs taking space >>>>> etc. >>>>> You need to move to 64-bit cpu. >>>>> >>>>> http://www.ussg.iu.edu/hypermail/linux/kernel/9801.2/0194.html >>>>> >>>>> Igor >>>>> >>>>> >>>>> On Fri, 2005-09-09 at 19:04, CCL wrote: >>>>> >>>>>> Sent to CCL by: "Ben Swerts" [ben.swerts/./ua.ac.be] >>>>>> >>>>>> >>>>>> Hi Alexander, >>>>>> >>>>>> I have absolutely no experience with Molpro but I can tell you this: >>>>>> When using GCC as the compiler in 32 bit mode, I noticed a limit >>>>>> of 1 GB for >>>>>> statically allocated memory when compiling fortran codes. I tried >>>>>> a lot of >>>>>> things to circumvent this problem but never succeeded. Now we >>>>>> have 64 bit >>>>>> machines and this 1 GB limit is finally a thing of the past. I >>>>>> guess the problem is related to Linux. Applications just crash when >>>>>> compiled with more than 1 GB. >>>>>> >>>>>> Greetz, >>>>>> >>>>>> >>>>>> Ben >>>>>> >>>>>> >>>>>>> -----Original Message----- >>>>>>> From: owner-chemistry_+_ccl.net [mailto:owner-chemistry_+_ccl.net] >>>>>>> Sent: Friday, September 09, 2005 10:44 PM >>>>>>> To: Swerts, Ben Subject: CCL: Molpro and memory >>>>>>> >>>>>>> >>>>>>> Sent to CCL by: Alexander Martins Silva [alex.msilva---uol.com.br] >>>>>>> >>>>>>> Hi, >>>>>>> >>>>>>> This is my second message about the same issue: >>>>>>> Molpro and memory. I've compiled the Molpro in a Xeon machine >>>>>>> with 2 proc and 4 GB of memory. However, I couldn't use more >>>>>>> than 1Gb of memory when executing jobs. I've already expanded >>>>>>> the kernel.shmall and kernel.shmmax parameters up to 2Gb and >>>>>>> nothing happens. The manual don't tell me nothing about this >>>>>>> subject. Is it a problem related to the Intel Fotran Compiler? >>>>>>> Anybody could help me? >>>>>>> >>>>>>> >>>>>>> Thanks in advance, >>>>>>> >>>>>>> Alexander.> To send >>>>>>> e-mail to subscribers of CCL put the string CCL: on your >>>>>> >>>>>> >>> Subject: line> >>> Send your subscription/unsubscription requests to: >>> CHEMISTRY-REQUEST_+_ccl.net HOME Page: http://www.ccl.net | Jobs >>> Page: http://www.ccl.net/jobs >>> If your is mail bouncing from ccl.net domain due to spam filters, >>> please> >>> -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- >>> +-+> To send e-mail to subscribers of CCL put the string CCL: on your >> >> Subject: line> >> Send your subscription/unsubscription requests to: >> CHEMISTRY-REQUEST_+_ccl.net HOME Page: http://www.ccl.net | Jobs Page: >> http://www.ccl.net/jobs> To send e-mail to subscribers of CCL put the string CCL: on your > Subject: line> > Send your subscription/unsubscription requests to: > CHEMISTRY-REQUEST_+_ccl.net HOME Page: http://www.ccl.net | Jobs Page: > http://www.ccl.net/jobs> > From owner-chemistry@ccl.net Tue Sep 13 09:18:31 2005 From: "CCL" To: CCL Subject: CCL: UK QSAR Autumn Meeting - registration Message-Id: <-29134-050913054327-1564-ETc9kVj+VqHwexQEb/3djg]*[server.ccl.net> X-Original-From: peter.gedeck]*[novartis.com Content-type: text/plain; charset=us-ascii Date: Tue, 13 Sep 2005 09:41:15 +0100 MIME-Version: 1.0 Sent to CCL by: peter.gedeck]*[novartis.com Dear colleague This will be the final reminder for the October 4th meeting of the UK QSAR and ChemoInformatics Group (http://www.ukqsar2005.com). On an administrative note please be advised that for security reasons please register for the meeting ASAP - the web form will be removed on the 22nd September. For your convenience we will be providing free transport timed at Edinburgh airport for 08:45, 09:50 and 17:30. Furthermore, for those arriving the previous day, we will be coordinating taxis to ensure the most rapid and inexpensive transport to your hotel. There is, as is usual, no registration fee. Cheap flights to Edinburgh are available from all major airports in the UK. The agenda has been set to cover both industrial implementation of methodologies and some interesting developments in the field of cheminformatics and modelling. And time has been allocated to ensure there is time to talk informally with the speakers over lunch. I look forward to talking with you in October Brad From owner-chemistry@ccl.net Tue Sep 13 11:40:25 2005 From: "CCL" To: CCL Subject: CCL: Harris functional -2 Message-Id: <-29135-050913105901-13362-o80D67vVBtiLxWnyey+vTg|a|server.ccl.net> X-Original-From: "Telkuni Tsuru" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="windows-1252" Date: Tue, 13 Sep 2005 23:51:44 +0900 MIME-Version: 1.0 Sent to CCL by: "Telkuni Tsuru" [telkuni|a|venus.dti.ne.jp] Thanks a lot, Dr.van Dam. I'm reading the paper which you have introduced. > Hi Telkuni, > > How about: > > J. Harris, Phys.Rev.B 31 (1985) 1770-1779. > > Best wishes, > > Huub Sincerely yours, ---------------------------------------------------- Telkuni Tsuru telkuni|a|venus.dti.ne.jp From owner-chemistry@ccl.net Tue Sep 13 20:11:05 2005 From: "CCL" To: CCL Subject: CCL: W:Any open-source software for generation of common chemical file format Message-Id: <-29136-050913160047-22207-ETc9kVj+VqHwexQEb/3djg!^!server.ccl.net> X-Original-From: "Lei Huang" Sent to CCL by: "Lei Huang" [hxbus!^!yahoo.com] Dear CCLers: I need to convert some short peptide sequences(hundreds of them) into one of the common used chemical file formats (SDF,SMILES etc.) and then use them in JOELib or CDK. I know it can be done in some commerical packages. However, is there any open source software out there that can perform the same task in a batch manner? I'd appreciate if you could give some clues. Lei Huang M/C 563 University of Illinois at Chicago Chicago, IL 60612 Email: hxbus AT yahoo DOT com