From owner-chemistry@ccl.net Wed May 7 01:49:00 2008 From: "Thilagavathi Ramasamy thilagavathir===yahoo.com" To: CCL Subject: CCL: ligand based pharmacophore generation-free softwares Message-Id: <-36900-080507012403-12425-1bWQpb8zKvQ2ihZTvsy3JQ .. server.ccl.net> X-Original-From: "Thilagavathi Ramasamy" Date: Wed, 7 May 2008 01:23:59 -0400 Sent to CCL by: "Thilagavathi Ramasamy" [thilagavathir:yahoo.com] Hi all, Could you please let me know the available free softwares (for academic research) that can be used to generate pharmacophores and 3-D database search? Thanks, Thilagavathi From owner-chemistry@ccl.net Wed May 7 03:33:00 2008 From: "Arthur computationalboy-.-gmail.com" To: CCL Subject: CCL: ligand based pharmacophore generation-free softwares Message-Id: <-36901-080507032919-30502-BxcFXkHlxfRv3ltCuBHs6g|a|server.ccl.net> X-Original-From: "Arthur" Content-Type: multipart/alternative; boundary="----=_NextPart_08050714235328127228220_002" Date: Wed, 7 May 2008 14:23:56 +0800 MIME-Version: 1.0 Sent to CCL by: "Arthur"[computationalboy a gmail.com] ------=_NextPart_08050714235328127228220_002 Content-Type: text/plain; charset="GB2312" Content-Transfer-Encoding: base64 SSByZWNvbW1lbmQgcG9ja2V0IGRldmVsb3BwZWQgYnkgTGFpbHVodWEgaW4gQmVpamluZyBVbml2 ZXJzaXR5LCB3aGljaCBjYW4gYmUgdXNlZCBmb3IgcmVjZXB0b3ItYmFzZWQgcGhhcm1hY29waG9y ZSBnZW5lcmF0aW9uLg0KSXQgaXMgZnJlZSwgYW5kIGlmIHlvdSBhcmUgaW50ZXJlc3RlZCBpbiBp dCwgcGxlYXNlZCBsZXQgbWUga25vdy4NCg0KDQpBcnRodXIsIGNvbXB1dGF0aW9uYWxib3lAZ21h 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pharmacophore generation-free softwares Message-Id: <-36902-080507050852-26690-zx73J/9iNTKeB127QqyPhA:server.ccl.net> X-Original-From: "Egon Willighagen" Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Wed, 7 May 2008 10:13:57 +0200 MIME-Version: 1.0 Sent to CCL by: "Egon Willighagen" [egon.willighagen^gmail.com] On Wed, May 7, 2008 at 7:23 AM, Thilagavathi Ramasamy thilagavathir===yahoo.com wrote: > Sent to CCL by: "Thilagavathi Ramasamy" [thilagavathir:yahoo.com] > Could you please let me know the available free softwares (for academic research) that can be used to generate > pharmacophores and 3-D database search? You might find the following paper interesting: R. Guha, J.H. van Drie, 'Pharmacophore Representation and Searching', CDK News, 2008, asap Open Acces (*) available from: http://www.steinbeck-molecular.de/cdknews/index.php/CDKNews/article/view/29 Egon True Open Access: GNU FDL license. -- ---- http://chem-bla-ics.blogspot.com/ From owner-chemistry@ccl.net Wed May 7 05:49:01 2008 From: "Gerard Pujadas gerard.pujadas]![gmail.com" To: CCL Subject: CCL: ligand based pharmacophore generation-free softwares Message-Id: <-36903-080507035750-3086-joc6O4FfksehdL8CWzcl7w=-=server.ccl.net> X-Original-From: "Gerard Pujadas" Content-Type: multipart/alternative; boundary="----=_Part_9990_13674402.1210143385942" Date: Wed, 7 May 2008 08:56:25 +0200 MIME-Version: 1.0 Sent to CCL by: "Gerard Pujadas" [gerard.pujadas(a)gmail.com] ------=_Part_9990_13674402.1210143385942 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Dear Thilagavathi 2008/5/7, Thilagavathi Ramasamy thilagavathir===yahoo.com < owner-chemistry[-]ccl.net>: > > > Sent to CCL by: "Thilagavathi Ramasamy" [thilagavathir:yahoo.com] > Hi all, > Could you please let me know the available free softwares (for academic > research) that can be used to generate pharmacophores and 3-D database > search? > Thanks, > Thilagavathi try LASSO (http://www.simbiosys.ca/ehits_lasso/index.html). It is free for academic research Best regards Gerard ------=_Part_9990_13674402.1210143385942 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Dear Thilagavathi

2008/5/7, Thilagavathi Ramasamy thilagavathir===yahoo.com <owner-chemistry[-]ccl.net>:

Sent to CCL by: "Thilagavathi  Ramasamy" [thilagavathir:yahoo.com]
Hi all,
Could you please let me know the available free softwares (for academic research) that can be used to generate pharmacophores and 3-D database search?
Thanks,
Thilagavathi


try LASSO (http://www.simbiosys.ca/ehits_lasso/index.html). It is free for academic research

Best regards

Gerard
------=_Part_9990_13674402.1210143385942-- From owner-chemistry@ccl.net Wed May 7 08:57:00 2008 From: "Rajarshi Guha rguha ~ indiana.edu" To: CCL Subject: CCL: ligand based pharmacophore generation-free softwares Message-Id: <-36904-080507083041-8366-K2SIUHMYfUainovWkMegDg!^!server.ccl.net> X-Original-From: Rajarshi Guha Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Date: Wed, 7 May 2008 08:30:24 -0400 Mime-Version: 1.0 (Apple Message framework v753) Sent to CCL by: Rajarshi Guha [rguha!^!indiana.edu] -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 On May 7, 2008, at 1:23 AM, Thilagavathi Ramasamy thilagavathir===yahoo.com wrote: > > Sent to CCL by: "Thilagavathi Ramasamy" [thilagavathir:yahoo.com] > Hi all, > Could you please let me know the available free softwares (for > academic research) that can be used to generate pharmacophores and > 3-D database search? If you have a pharmacophore definition that uses only distance constraints (though angle constraints will be available soon) you can take a look at http://cheminfo.informatics.indiana.edu/~rguha/code/java/#pcore - ------------------------------------------------------------------- Rajarshi Guha GPG Fingerprint: D070 5427 CC5B 7938 929C DD13 66A1 922C 51E7 9E84 - ------------------------------------------------------------------- A motion to adjourn is always in order. -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.8 (Darwin) iEYEARECAAYFAkghoOAACgkQZqGSLFHnnoQ98QCg8e5ltUUjgz1acnuVC5mRclfU fpMAnjEDUfOsyY3mHHzsRejcdpC8mNGE =v92a -----END PGP SIGNATURE----- From owner-chemistry@ccl.net Wed May 7 18:04:00 2008 From: "John McKelvey jmmckel.-,-.gmail.com" To: CCL Subject: CCL: Using FORK and WAIT on typical linux boxes Message-Id: <-36905-080507174714-18567-YKGAkw9/wenP5ujG8ZJIEA-,-server.ccl.net> X-Original-From: "John McKelvey" Content-Type: multipart/alternative; boundary="----=_Part_20282_12487719.1210196818128" Date: Wed, 7 May 2008 17:46:58 -0400 MIME-Version: 1.0 Sent to CCL by: "John McKelvey" [jmmckel]|[gmail.com] ------=_Part_20282_12487719.1210196818128 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline CCLERs Most linux compiler such as gnu and Intel do not have fork and wait in their libraries. Is is possib;le to compile the fortran program calling these with the Intel fortran compiler, and include the Intel C libraries at link time? Any other suggestions? Looks like the Lahey/Fujitsu linux fortarn compilers avoid the problem, but $$$. Thanks! John McKelvey ------=_Part_20282_12487719.1210196818128 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline CCLERs

Most linux compiler such as gnu and Intel do not have fork and wait in their libraries.  Is is possib;le to compile the fortran program calling these with the Intel fortran compiler, and include the Intel C libraries at link time?   Any other suggestions?

Looks like the Lahey/Fujitsu linux fortarn compilers avoid the problem, but $$$.


Thanks!

John McKelvey
------=_Part_20282_12487719.1210196818128-- From owner-chemistry@ccl.net Wed May 7 23:02:01 2008 From: "Venable, Richard (NIH/NHLBI) E venabler%x%nhlbi.nih.gov" To: CCL Subject: CCL: Using FORK and WAIT on typical linux boxes Message-Id: <-36906-080507220935-10197-71pBc8waJF0SEQ7Ti0qHOg .. server.ccl.net> X-Original-From: "Venable, Richard (NIH/NHLBI) [E]" Content-class: urn:content-classes:message Content-Type: multipart/mixed; boundary="----_=_NextPart_001_01C8B0AC.07B5A180" Date: Wed, 7 May 2008 21:37:09 -0400 MIME-Version: 1.0 Sent to CCL by: "Venable, Richard (NIH/NHLBI) [E]" [venabler-$-nhlbi.nih.gov] This is a multi-part message in MIME format. ------_=_NextPart_001_01C8B0AC.07B5A180 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable I've seen short C 'wrapper' routines used for this sort of thing; the C = routine makes the actual call to one of the myriad OS utility routines, = and provides a Fortran callable interface. The wrapper usually has to = handle string conversion, if strings are being passed as arguments. -- Rick Venable 5635FL/T906 Membrane Biophysics Section NIH/NHLBI Lab. of Computational Biology Bethesda, MD 20892-9314 U.S.A. (301) 496-1905 venabler AT nhlbi*nih*gov -----Original Message----- > From: John McKelvey jmmckel. : .gmail.com [mailto:owner-chemistry : ccl.net] Sent: Wed 07-May-08 5:46 PM To: Venable, Richard (NIH/NHLBI) [E] Subject: CCL: Using FORK and WAIT on typical linux boxes =20 CCLERs Most linux compiler such as gnu and Intel do not have fork and wait in = their libraries. Is is possib;le to compile the fortran program calling these with the Intel fortran compiler, and include the Intel C libraries at = link time? Any other suggestions? Looks like the Lahey/Fujitsu linux fortarn compilers avoid the problem, = but $$$. Thanks! John McKelvey ------_=_NextPart_001_01C8B0AC.07B5A180--