From owner-chemistry@ccl.net Fri Jul 20 04:24:00 2007 From: "Michel Petitjean ptitjean]~[itodys.jussieu.fr" To: CCL Subject: CCL: OSRA: Optical Structure Recognition Message-Id: <-34766-070720041522-27266-/jnGhlt/9Yox/Zi1nxF3Mw(_)server.ccl.net> X-Original-From: Michel Petitjean Date: Fri, 20 Jul 2007 09:44:00 +0200 (MEST) Sent to CCL by: Michel Petitjean [ptitjean++itodys.jussieu.fr] To: "CCL Subscribers" Subject: CCL: Re: OSRA: Optical Structure Recognition Great work. Congratulations. But generating a connection table is much more useful. In fact I never encountered situations requiring linear codes such as SMILES, WLN, ... Michel Petitjean, Email: petitjean . itodys.jussieu.fr ITODYS (CNRS, UMR 7086) ptitjean . ccr.jussieu.fr 1 rue Guy de la Brosse Phone: +33 (0)1 44 27 48 57 75005 Paris, France. FAX : +33 (0)1 44 27 68 14 http://petitjeanmichel.free.fr/itoweb.petitjean.graphs.html ....................................................................... Sent to CCL by: "Igor Filippov [Contr]" [igorf%a%helix.nih.gov] Dear Colleagues, We would like to announce a new addition to the set of chemoinformatics tools available from the Computer-Aided Drug Design Group at the NCI-Frederick. OSRA is a utility designed to convert graphical representations of chemical structures, such as they appear in journal articles, patent documents, textbooks, trade magazines etc., into SMILES. OSRA can read a document in any of the over 90 graphical formats parseable by ImageMagick (GIF, JPEG, PNG, TIFF, PDF, PS etc.) and generate the SMILES representation of the molecular structure images encountered within that document. You are welcome to download the free standalone version of the software at http://cactus.nci.nih.gov/osra/ or try our web-based interface to OSRA available at http://cactus.nci.nih.gov/cgi-bin/osra/index.cgi Comments, criticisms, contribution of ideas and participation in further development of OSRA are most welcome. Igor Filippov, Marc Nicklaus ------------------------------------------------------------------------ CADD Group NIH/NCI at Frederick E-mail addresses: Bldg 376 igorf]![helix.nih.gov 376 Boyles Street mn1]![helix.nih.gov FREDERICK, MD 21702 USA Laboratory of Medicinal Chemistry, Center for Cancer Research, National Cancer Institute at Frederick, National Institutes of Health http://ccr.cancer.gov/Staff/Staff.asp?profileid=6282 ------------------------------------------------------------------------ From owner-chemistry@ccl.net Fri Jul 20 07:38:00 2007 From: "Igor Filippov Contr igorf . helix.nih.gov" To: CCL Subject: CCL: OSRA: Optical Structure Recognition Message-Id: <-34767-070720072646-12159-zbZFQwxtfyy5pcouzVB/aA(0)server.ccl.net> X-Original-From: "Igor Filippov [Contr]" Content-Transfer-Encoding: 7bit Content-Type: text/plain Date: Fri, 20 Jul 2007 06:39:40 -0400 Mime-Version: 1.0 Sent to CCL by: "Igor Filippov [Contr]" [igorf{:}helix.nih.gov] Dear Michel, Thank you for the kind words! We do not generate a connection table directly for two reasons: 1) OpenBabel which we use for translating internal format into a recognizable output does not yet generate coordinates, a connection table without the coordinates often leads to crashes/misinterpretation in various chemoinformatics software tools. 2) In any case the generated 2D or 3D coordinates would not be something that was present in the original data (image file), we hesitate implicitly generating knowledge that was not present in the input. However, recognizing the importance of having a choice in the output format there is an option to convert the resulting SMILES from OSRA web interface using our SMILES Translator. Once you click on the "Get SMILES" button two links will appear at the lower right corner of the interface - one direct link to CSLS (allows you to look up the structure in over 39 million records that we have in our database), another - to SMILES Translator, which will allow you to convert SMILES into SDF or PDB formats. The underlying coordinate generation will be done by CACTVS toolkit for 2D and CORINA for 3D. You can always use our SMILES Translator and CSLS as separate services, independent of OSRA as well, of course. Best regards, Igor On Fri, 2007-07-20 at 09:44 +0200, Michel Petitjean ptitjean]~[itodys.jussieu.fr wrote: > Sent to CCL by: Michel Petitjean [ptitjean++itodys.jussieu.fr] > To: "CCL Subscribers" > Subject: CCL: Re: OSRA: Optical Structure Recognition > > Great work. Congratulations. > But generating a connection table is much more useful. > In fact I never encountered situations requiring linear codes > such as SMILES, WLN, ... > > Michel Petitjean, Email: petitjean * itodys.jussieu.fr > ITODYS (CNRS, UMR 7086) ptitjean * ccr.jussieu.fr > 1 rue Guy de la Brosse Phone: +33 (0)1 44 27 48 57 > 75005 Paris, France. FAX : +33 (0)1 44 27 68 14 > http://petitjeanmichel.free.fr/itoweb.petitjean.graphs.html > ....................................................................... > Sent to CCL by: "Igor Filippov [Contr]" [igorf%a%helix.nih.gov] > Dear Colleagues, > > We would like to announce a new addition to the set of chemoinformatics > tools available from the Computer-Aided Drug Design Group at the > NCI-Frederick. OSRA is a utility designed to convert graphical > representations of chemical structures, such as they appear in journal > articles, patent documents, textbooks, trade magazines etc., into > SMILES. > > OSRA can read a document in any of the over 90 graphical formats > parseable by ImageMagick (GIF, JPEG, PNG, TIFF, PDF, PS etc.) and > generate the SMILES representation of the molecular structure images > encountered within that document. > > You are welcome to download the free standalone version of the software > at > http://cactus.nci.nih.gov/osra/ > or try our web-based interface to OSRA available at > http://cactus.nci.nih.gov/cgi-bin/osra/index.cgi > > Comments, criticisms, contribution of ideas and participation in further > development of OSRA are most welcome. > > Igor Filippov, Marc Nicklaus > > ------------------------------------------------------------------------ > CADD Group NIH/NCI at Frederick > E-mail addresses: Bldg 376 > igorf]![helix.nih.gov 376 Boyles Street > mn1]![helix.nih.gov FREDERICK, MD 21702 USA > Laboratory of Medicinal Chemistry, Center for Cancer Research, > National Cancer Institute at Frederick, National Institutes of Health > http://ccr.cancer.gov/Staff/Staff.asp?profileid=6282 > -------------------------------------------------------------------------- Igor Filippov [Contr] From owner-chemistry@ccl.net Fri Jul 20 08:47:00 2007 From: "Egon Willighagen egon.willighagen ~ gmail.com" To: CCL Subject: CCL: OSRA: Optical Structure Recognition Message-Id: <-34768-070720062223-3665-MT6U0O+Iomwm1tCkS/6kqg|,|server.ccl.net> X-Original-From: "Egon Willighagen" Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 20 Jul 2007 12:14:54 +0200 MIME-Version: 1.0 Sent to CCL by: "Egon Willighagen" [egon.willighagen:-:gmail.com] On 7/20/07, Michel Petitjean ptitjean]~[itodys.jussieu.fr wrote: > Great work. Congratulations. > But generating a connection table is much more useful. > In fact I never encountered situations requiring linear codes > such as SMILES, WLN, ... Agreed, I would have like to see InChI as default output. However, it does not really matter, as the website says it uses OpenBabel, so it should be trivial to patch the source code to output InChI/MDL molfile/whatever instead of SMILES. Egon From owner-chemistry@ccl.net Fri Jul 20 11:47:00 2007 From: "Troy Wymore wymore]=[psc.edu" To: CCL Subject: CCL: QM/MM Workshop at PSC/NRBSC Message-Id: <-34769-070720114212-27075-HQIjm3o2MBQCySLsBh1tdA . server.ccl.net> X-Original-From: "Troy Wymore" Date: Fri, 20 Jul 2007 11:42:09 -0400 Sent to CCL by: "Troy Wymore" [wymore::psc.edu] Methods and Applications of Hybrid QM/MM Simulations to Biomolecular Systems September 10-13, 2007 Pittsburgh, PA Funded by NIH-National Center for Research Resources Application Deadline: August 3, 2007 Application forms can be found at: www.nrbsc.org/sb/workshops/qmmm.php DESCRIPTION: The workshop will explore computational approaches for the simulation of enzymatic reactions. The course will present the relevant theoretical background including ab initio and semiempirical molecular orbital methods, density functional theory, molecular mechanics force fields, hybrid Quantum Mechanical/Molecular Mechanical potential energy functions, and simulation techniques on high performance computers. Case studies based on determining the free energy profile for a reaction in the gas phase, in water (using both implicit and explicit solvent) and in an enzyme active site will be presented using primarily the DYNAMO library. Experience with DYNAMO is helpful but not a prerequisite for attendance. The workshop is designed for graduate students, post-doctoral researchers and faculty in computational biophysics and physical organic chemistry who have some experience with computational chemistry methods and seek to enhance their capabilities to include the modeling of enzymatic reactions. Participants are encouraged to discuss and work on biomolecular systems from their own research during the workshop. TOPICS Model Chemistries Transition state searches Implicit solvent models Parameterization of Semiempirical Methods Hybrid QM/MM potentials Umbrella sampling Nudged Elastic Band FINANCIAL INFORMATION This workshop is funded by grants from the NIH National Center for Research Resources. These grants provide tuition and hotel costs, supercomputing time, and workshop materials for US academic participants. ALL participants are responsible for paying their own travel expenses. Complimentary continental breakfasts and lunches will be provided the days of the workshop. A few positions may be available for US government employees and corporate and industrial researchers. These participants are responsible for their own hotel accommodations, and tuition costs are as follows: a. Tuition for US government employees is 350 in advance to cover the workshop materials and supercomputing time. Contract government employees will be considered an academic participant and therefore their tuition costs will be waived if they submit a letter from their department head. Letters can be sent to the NRBSC contacts. b.Tuition for corporate and industrial participants is 975 in advance to cover the workshop materials and supercomputing time. More information is available at the workshop website: www.nrbsc.org/sb/workshops/qmmm.php or contact Dr. Troy Wymore (wymore%%psc.edu) From owner-chemistry@ccl.net Fri Jul 20 12:54:00 2007 From: "Egon Willighagen egon.willighagen[-]gmail.com" To: CCL Subject: CCL: OSRA: Optical Structure Recognition Message-Id: <-34770-070720065519-7545-/OPCiZJpfbZAuHI1LWn7lQ,,server.ccl.net> X-Original-From: "Egon Willighagen" Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 20 Jul 2007 11:52:22 +0200 MIME-Version: 1.0 Sent to CCL by: "Egon Willighagen" [egon.willighagen_+_gmail.com] Dear Igor, On 7/19/07, Igor Filippov Contr igorf%a%helix.nih.gov wrote: > Sent to CCL by: "Igor Filippov [Contr]" [igorf%a%helix.nih.gov] > OSRA can read a document in any of the over 90 graphical formats > parseable by ImageMagick (GIF, JPEG, PNG, TIFF, PDF, PS etc.) and > generate the SMILES representation of the molecular structure images > encountered within that document. On the webpage you mention it can process images from PubChem... so I assume you actually did this; what is the fail rate on PubChem? Are there a particular class of drawings it cannot handle well? How well does it work on stereochemistry? Does it also recognize the labels below drawing, things like compound '1'? (Yes, I tried the 'patent' demo, but that's just the demo...) Great to see this addition to the growing list of open source chemoinformatics tools! Egon From owner-chemistry@ccl.net Fri Jul 20 13:27:00 2007 From: "Karen.Green,sanofi-aventis.com" To: CCL Subject: CCL: OSRA: Optical Structure Recognition Message-Id: <-34771-070720125328-27301-6FSp5qT5fshJ0OD9khptIQ+/-server.ccl.net> X-Original-From: content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Fri, 20 Jul 2007 09:52:49 -0700 MIME-Version: 1.0 Sent to CCL by: [Karen.Green_+_sanofi-aventis.com] Thank you, Igor, for your efforts. Have you seen: http://www.chemspider.com/blog/?p=83 ? (More excitement for implications of use of your software in enabling the semantic web for chemistry...) Karen -----Original Message----- > From: owner-chemistry---ccl.net [mailto:owner-chemistry---ccl.net] Sent: Friday, July 20, 2007 3:40 AM To: Green, Karen M. PH/US Subject: CCL: OSRA: Optical Structure Recognition Sent to CCL by: "Igor Filippov [Contr]" [igorf{:}helix.nih.gov] Dear Michel, Thank you for the kind words! We do not generate a connection table directly for two reasons: 1) OpenBabel which we use for translating internal format into a recognizable output does not yet generate coordinates, a connection table without the coordinates often leads to crashes/misinterpretation in various chemoinformatics software tools. 2) In any case the generated 2D or 3D coordinates would not be something that was present in the original data (image file), we hesitate implicitly generating knowledge that was not present in the input. However, recognizing the importance of having a choice in the output format there is an option to convert the resulting SMILES from OSRA web interface using our SMILES Translator. Once you click on the "Get SMILES" button two links will appear at the lower right corner of the interface - one direct link to CSLS (allows you to look up the structure in over 39 million records that we have in our database), another - to SMILES Translator, which will allow you to convert SMILES into SDF or PDB formats. The underlying coordinate generation will be done by CACTVS toolkit for 2D and CORINA for 3D. You can always use our SMILES Translator and CSLS as separate services, independent of OSRA as well, of course. Best regards, Igor On Fri, 2007-07-20 at 09:44 +0200, Michel Petitjean ptitjean]~[itodys.jussieu.fr wrote: > Sent to CCL by: Michel Petitjean [ptitjean++itodys.jussieu.fr] > To: "CCL Subscribers" > Subject: CCL: Re: OSRA: Optical Structure Recognition > > Great work. Congratulations. > But generating a connection table is much more useful. > In fact I never encountered situations requiring linear codes such as > SMILES, WLN, ... > > Michel Petitjean, Email: petitjean * itodys.jussieu.fr > ITODYS (CNRS, UMR 7086) ptitjean * ccr.jussieu.fr > 1 rue Guy de la Brosse Phone: +33 (0)1 44 27 48 57 > 75005 Paris, France. FAX : +33 (0)1 44 27 68 14 > http://petitjeanmichel.free.fr/itoweb.petitjean.graphs.html > ....................................................................... > Sent to CCL by: "Igor Filippov [Contr]" [igorf%a%helix.nih.gov] Dear > Colleagues, > > We would like to announce a new addition to the set of > chemoinformatics tools available from the Computer-Aided Drug Design > Group at the NCI-Frederick. OSRA is a utility designed to convert > graphical representations of chemical structures, such as they appear > in journal articles, patent documents, textbooks, trade magazines > etc., into SMILES. > > OSRA can read a document in any of the over 90 graphical formats > parseable by ImageMagick (GIF, JPEG, PNG, TIFF, PDF, PS etc.) and > generate the SMILES representation of the molecular structure images > encountered within that document. > > You are welcome to download the free standalone version of the > software at http://cactus.nci.nih.gov/osra/ or try our web-based > interface to OSRA available at > http://cactus.nci.nih.gov/cgi-bin/osra/index.cgi > > Comments, criticisms, contribution of ideas and participation in > further development of OSRA are most welcome. > > Igor Filippov, Marc Nicklaus > > ------------------------------------------------------------------------ > CADD Group NIH/NCI at Frederick > E-mail addresses: Bldg 376 > igorf]![helix.nih.gov 376 Boyles Street > mn1]![helix.nih.gov FREDERICK, MD 21702 USA > Laboratory of Medicinal Chemistry, Center for Cancer Research, > National Cancer Institute at Frederick, National Institutes of Health > http://ccr.cancer.gov/Staff/Staff.asp?profileid=6282 > ---------------------------------------------------------------------- > ---- Igor Filippov [Contr] To: CCL Subject: CCL: scoring energetic function Message-Id: <-34772-070720115128-30141-4xzKZMdWJhGoBVu6HWM1Fg_+_server.ccl.net> X-Original-From: andrea spitaleri Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Fri, 20 Jul 2007 16:59:07 +0200 MIME-Version: 1.0 Sent to CCL by: andrea spitaleri [spitaleri.andrea,hsr.it] Hi guys, I have been using different server in order to calculate the binding affinity between protein-peptide in a complex obtained by docking procedure (fastcontact, dcomplex, foldx the most reliables). However, I have noticed that they do not take in account the presence of ions in the interactions. They just neglect them. For my purpose I need to "quantify" the binding affinity in which the ion play a fundamental role in the interactions. Do you have any suggestion about programs or server which perform this kind of calculation? Free energy using MD is one of my target, however I'd like to carry out first something quicker. Thanks in advance, andrea -- ------------------------------- Andrea Spitaleri PhD Dulbecco Telethon Institute c/o DIBIT Scientific Institute Biomolecular NMR, 1B4 Via Olgettina 58 20132 Milano (Italy) http://biomolecularnmr.ihsr.dom/ Tel: 0039-0226433497/4922 Fax: 0039-0226434153 ------------------------------- ******************************************************************** Sostieni la ricerca del San Raffaele con il 5permille! E' SEMPLICE E NON COSTA NULLA. Basta indicare nell'apposito riquadro della dichiarazione dei redditi ("Ricerca sanitaria") il codice fiscale della Fondazione Centro S. Raffaele del Monte Tabor: 03 06 42 80 153 e ricordarsi di firmare. Se vuoi saperne di piu' scrivi a 5permille**hsr.it o vai sul sito w w w . 5 x m i l l e . o r g From owner-chemistry@ccl.net Fri Jul 20 15:40:00 2007 From: "Igor Filippov Contr igorf~!~helix.nih.gov" To: CCL Subject: CCL: OSRA: Optical Structure Recognition Message-Id: <-34773-070720152000-16158-XBv5HLGA0HiSTcUJNgXKWg^-^server.ccl.net> X-Original-From: "Igor Filippov [Contr]" Content-Transfer-Encoding: 7bit Content-Type: text/plain Date: Fri, 20 Jul 2007 15:19:25 -0400 Mime-Version: 1.0 Sent to CCL by: "Igor Filippov [Contr]" [igorf++helix.nih.gov] Dear Egon, > > On the webpage you mention it can process images from PubChem... so I > assume you actually did this; what is the fail rate on PubChem? Are > there a particular class of drawings it cannot handle well? We did tested it with computer-generated ones (i.e. 72 dpi) and actually these type of images was the first batch in my test set. If it is a sufficiently large size image (for example 300x300px) it seemed to have worked very well in our test cases - though our set is by necessity limited. Could you send me the image(s) that are causing problems? > How well > does it work on stereochemistry? It makes an attempt to recognize stereochemistry - that is, hash and wedge bonds and cis/trans stereo around the double bonds. But the wedge bonds are more or less reliably recognized only in high resolution images (300dpi.) OpenBabel unfortunately complicates the situation as SMILES generation there seem to mess up stereo, CAN (canonical smiles) format works better, but since it appeared only in the recent versions we are probably the first to actually check how well it works :) > Does it also recognize the labels > below drawing, things like compound '1'? (Yes, I tried the 'patent' > demo, but that's just the demo...) > No, there is no attempt to do that currently. > Great to see this addition to the growing list of open source > chemoinformatics tools! > Thank you! Igor > Egon From owner-chemistry@ccl.net Fri Jul 20 16:15:00 2007 From: "Jun Cui juc9++pitt.edu" To: CCL Subject: CCL: AMBER periodic box alignment Message-Id: <-34774-070720151408-14003-LDunhSfTTEZ+CigbSnRioQ^-^server.ccl.net> X-Original-From: "Jun Cui" Date: Fri, 20 Jul 2007 15:14:05 -0400 Sent to CCL by: "Jun Cui" [juc9]=[pitt.edu] Hi, everyone, Does amber 9 need the periodic box to be parallel to the xy, yz, and xz planes? If yes, is there any good tool to rotate an existing system to be parallel to the axis planes? I tried to code and do not have a good way to find the new axises for the system. Thanks. From owner-chemistry@ccl.net Fri Jul 20 21:25:00 2007 From: "Reaz Uddin riaasuddin,yahoo.com" To: CCL Subject: CCL: Arranging electric charges to manage Dipole moment ..???? Message-Id: <-34775-070720212308-4306-chKzFRpKWzla0G5wkLXr3g===server.ccl.net> X-Original-From: "Reaz Uddin" Date: Fri, 20 Jul 2007 21:23:03 -0400 Sent to CCL by: "Reaz Uddin" [riaasuddin : yahoo.com] Hi, Can anybody explain me the arrangement of charges with respect to the dipole moment. I mean, How can I arrange a small number(lets say 8 or 12) of charges where I could find at certain arrangement no dipole moment (like they cancel out each other) or at certain arrangement they show the dipole moment. Take an example of 12 charges in which 4 are + and 4 are -. I would say I arranged them in the following manner: +-+- ++-- +--+ Does the above arrangement show dipole moment,? if yes then please arrange it in a way so that they dont show any dipole moment. Hope I'd get an explanatory answer in this regard. Thanks in advance. I appreciate you guys. REAZ