From owner-chemistry@ccl.net Fri Feb 20 02:20:00 2009 From: "Markus Kaukonen markus.kaukonen%iki.fi" To: CCL Subject: CCL: Gromacs installation on Dell Ubuntu Message-Id: <-38680-090220021058-447-j7A4aiQSQf5m3j+JOGBfoA-#-server.ccl.net> X-Original-From: Markus Kaukonen Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Fri, 20 Feb 2009 09:10:40 +0200 MIME-Version: 1.0 Sent to CCL by: Markus Kaukonen [markus.kaukonen()iki.fi] Gromacs is part of the Ubuntu distribution. So just install package 'gromacs' in Ubuntu 8.04 (or gromacs-openmpi for parallel runs). Nice and easy! Cheers, Markus On Fri, Feb 20, 2009 at 1:34 AM, Lukasz Cwiklik cwiklik_+_gmail.com wrote: > > Sent to CCL by: Lukasz Cwiklik [cwiklik#,#gmail.com] > Dear Maura, > Have you seen this "Quick and dirty installation" guide? > http://wiki.gromacs.org/index.php/quick_and_dirty_installation > It gives a concise yet full description of the installation process. > > Best, > Lukasz > > -- > Lukasz Cwiklik > http://cwiklik.wordpress.com > > > On Tue, Feb 17, 2009 at 6:35 PM, Maura Mooney mmooney05()qub.ac.uk > wrote: > [...] >> I am having problem configuring gromacs on my dell machine. I have unzipped the gromacs archive and also the fftw3...tar.gz file (required as a prerequisite). The next step requires >> >> cd to the gromacs directory and ./configure. >> >> But I can't seem to locate the gromacs directory, or the configure program, thus I cannot go any further with the configuration/installation.> > > -- --www=http://www.iki.fi/markus.kaukonen --Markus.Kaukonen]-[iki.fi --office: N102 Nano building FIN-02015 TKK --home: Viinirinne 3 F 12, 02630 Espoo, FIN --tel: h 045-1242068, w 4518694, 050-5112785 --Rikos ei kannata, eika maatalous --Suomessa. (Paimio 1998) --- From owner-chemistry@ccl.net Fri Feb 20 05:58:01 2009 From: "Jens Spanget-Larsen spanget-x-ruc.dk" To: CCL Subject: CCL:G: oxygen charge varies using b3lyp/631g* and aug-cc-pvdz in gaussian 03 Message-Id: <-38681-090219122328-32276-zd5Ei9k+Niz3MufhMLxLzg|,|server.ccl.net> X-Original-From: Jens Spanget-Larsen Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 19 Feb 2009 16:22:16 +0100 MIME-Version: 1.0 Sent to CCL by: Jens Spanget-Larsen [spanget[-]ruc.dk] Dear Sohail, the results of a Mulliken population analysis with a basis set like aug-cc-pvdz that includes diffuse functions are essentially meaningless. In a Mulliken analysis, population due to the diffuse functions is counted as a contribution to the center where the functions are defined, but these functions tend to have large amplitude on the neighbouring centers! - You should perform, e.g., a "natural population analysis", or one of the analyses based on the fitting of electrostatic potentials and so forth. There are several possibilities, that are much less basis set dependent. Yours, Jens >--< ------------------------------------------------------ JENS SPANGET-LARSEN Office: +45 4674 2710 Dept. of Science (18.1) Fax: +45 4674 3011 Roskilde University Mobile: +45 2320 6246 P.O.Box 260 E-Mail: spanget/a\ruc.dk DK-4000 Roskilde, Denmark http://www.ruc.dk/~spanget ------------------------------------------------------ sohail sohail meandme_meandme2003[-]yahoo.com wrote: > Sent to CCL by: "sohail sohail" [meandme_meandme2003[]yahoo.com] > hi, i have done optimization of dodecahedron water clusters using gaussian 03 program. My question is that mulliken charges on oxygen atoms are around -1.2 using b3lyp/631g* while xygen charge is -0.3 using b3lyp/aug-cc-pvdz. can u pls tell me why this so much charge difference by using 2 different basis sets on the same level of theory. how should i put the results in paper if there is this much variation in results. > thanks. > sohail.> > > From owner-chemistry@ccl.net Fri Feb 20 06:03:02 2009 From: "Stan van Gisbergen vangisbergen]![scm.com" To: CCL Subject: CCL:G: van der Waals coefficient C6 Message-Id: <-38682-090220042526-6006-ncoiXkERCR5O6/h1qg88VQ*|*server.ccl.net> X-Original-From: Stan van Gisbergen Content-Type: multipart/alternative; boundary=Apple-Mail-1--886603541 Date: Fri, 20 Feb 2009 09:30:34 +0100 Mime-Version: 1.0 (Apple Message framework v753.1) Sent to CCL by: Stan van Gisbergen [vangisbergen:+:scm.com] --Apple-Mail-1--886603541 Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Dear Tian, ADF contains a tool called DISPER which calculates isotropic and anisotropic C6 up to C10 van der Waals dispersion coefficients: http://www.scm.com/Doc/Doc2008.01/ADF/Properties/page50.html http://www.scm.com/Doc/Doc2008.01/ADF/Examples/page77.html As input it uses polarizabilities at a number of imaginary frequencies. These are produced by ADF, but in principle they could be provided by any other code as well. Best regards, Stan On Feb 19, 2009, at 8:28 PM, Green Power powergreen-,-gmail.com wrote: > Dear All, > I wonder if there is any code to calculate van der Waals > coefficient C6 based the polarizability calculations with Gaussian. > Thanks > Tian Dr. S.J.A. van Gisbergen Chief Executive Officer Scientific Computing & Modelling NV Theoretical Chemistry, Vrije Universiteit De Boelelaan 1083 1081 HV Amsterdam The Netherlands vangisbergen(_)scm.com http://www.scm.com (web site recently restyled) T: +31-20-5987626 F: +31-20-5987629 --Apple-Mail-1--886603541 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=ISO-8859-1
Dear Tian,=A0

ADF contains a tool called = DISPER which calculates isotropic and anisotropic C6 up to C10 van der = Waals dispersion coefficients:
http= ://www.scm.com/Doc/Doc2008.01/ADF/Properties/page50.html
http://ww= w.scm.com/Doc/Doc2008.01/ADF/Examples/page77.html

A= s input it uses polarizabilities at a number of imaginary frequencies. = These are produced by ADF, but in principle they could be provided by = any other code as well.=A0

Best = regards,
Stan

On Feb 19, 2009, at 8:28 = PM, Green Power powergreen-,-gmail.com wrote:

Dear = All,
I wonder if there is any code to calculate van der Waals = coefficient C6 based the polarizability calculations with Gaussian. = Thanks
Tian

Dr. S.J.A. van Gisbergen
Chief Executive Officer
De = Boelelaan 1083
1081 HV Amsterdam
The Netherlands=A0=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 = =A0 =A0 =A0 =A0 =A0 =A0 =A0
(web site recently restyled)
T: +31-20-5987626 =A0 =A0
F: +31-20-5987629



= --Apple-Mail-1--886603541-- From owner-chemistry@ccl.net Fri Feb 20 06:04:01 2009 From: "Gerard Pujadas gerard.pujadas*gmail.com" To: CCL Subject: CCL: Is there any database that collects which ligands coordinates (derived from the PDB files) are reliable? Message-Id: <-38683-090220050854-11202-J+nfq/vOWC9qpbSXXB8DZA{:}server.ccl.net> X-Original-From: Gerard Pujadas Content-Type: multipart/alternative; boundary=0015174a0fbaf3b9f1046356d5fe Date: Fri, 20 Feb 2009 11:08:34 +0100 MIME-Version: 1.0 Sent to CCL by: Gerard Pujadas [gerard.pujadas^_^gmail.com] --0015174a0fbaf3b9f1046356d5fe Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Dear CCL list subscribers, first of all, sorry for cross-posting I wonder if is there any database that collects which ligands coordinates (derived from protein-ligand complexes available from the PDB files) are reliable. I would like to use the PDB files with reliable coordinates for their ligands to analyze the performance of different protein-ligand docking algorithms in redocking experiments (*i.e.* split the protein and the ligand > from the PDB file; redock them again; and finally compare the coordinates of the top one predicted pose with the experimental coordinates). Obviously, for making sense in such comparison, I need to be sure that the experimental coordinates of the ligand are correct. I know that I could use the "Advanced Search Page" in http://www.pdb.org to search which X-ray-derived PDB structures correspond to protein-ligand complexes have, simultaneously: *(1)* a good resolution (equal or higher than 2.0 angstroms); and *(2)* R-Value equal or lower than 0.200. Moreover, I could compare the temperature factors of the ligands in the resulting set with that of the protein in the corresponding PDB file ... Nevertheless, what I am looking for is for a database that quantifies how well the ligand coordinates fit in the corresponding electron density map (or something like that). Is there any place with such information? With many thanks in advances for your help Yours sincerely Gerard --0015174a0fbaf3b9f1046356d5fe Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Dear CCL list subscribers,

first of all, sorry for cross-posting

I wonder if is there any database that collects which ligands coordinates (derived from protein-ligand complexes available from the PDB files) are reliable. I would like to use the PDB files with reliable coordinates for their ligands to analyze the performance of different protein-ligand docking algorithms in redocking experiments (i.e. split the protein and the ligand from the PDB file; redock them again; and finally compare the coordinates of the top one predicted pose with the experimental coordinates). Obviously, for making sense in such comparison, I need to be sure that the experimental coordinates of the ligand are correct.

I know that I could use the "Advanced Search Page" in http://www.pdb.org to search which X-ray-derived PDB structures correspond to protein-ligand complexes have, simultaneously: (1) a good resolution (equal or higher than 2.0 angstroms); and (2) R-Value equal or lower than 0.200. Moreover, I could compare the temperature factors of the ligands in the resulting set with that of the protein in the corresponding PDB file ...

Nevertheless, what I am looking for is for a database that quantifies how well the ligand coordinates fit in the corresponding electron density map (or something like that).

Is there any place with such information?

With many thanks in advances for your help

Yours sincerely

Gerard
--0015174a0fbaf3b9f1046356d5fe-- From owner-chemistry@ccl.net Fri Feb 20 08:48:01 2009 From: "John Begemann begemann,,tripos.com" To: CCL Subject: CCL: Announcing the Tripos Science Summit 2009 Message-Id: <-38684-090219185643-19030-f8yH8uBjqutyLPJAUkMwsA[A]server.ccl.net> X-Original-From: "John Begemann" Date: Thu, 19 Feb 2009 18:56:39 -0500 Sent to CCL by: "John Begemann" [begemann|,|tripos.com] Plan now to attend 2nd annual Tripos Science Summit September 30-October 1, 2009 in Philadelphia, PA, USA The meeting will cover a broad series of topics with the goal of bringing together scientists and users of Tripos software tools from all areas of computational and medicinal chemistry. Youll interact with your peers, hear about or share innovative research strategies, and discuss the complexities of today's drug discovery environment. Call for Abstracts Deadline March 30, 2009 We invite you to share your experiences and accomplishments using Tripos solutions with the Tripos User Community. If you are interested in presenting a talk please email us with your topic and a brief abstract (50-75 words) describing your proposed talk. The deadline for abstracts is March 30, 2009. The meeting will be held again at the Union League of Philadelphia on S. Broad Street. For more details; please contact us at marketing*o*tripos.com John Begemann VP Discovery Software Tripos A Certara Company Phone: 314-951-3357 email: begemann*o*tripos.com From owner-chemistry@ccl.net Fri Feb 20 09:26:00 2009 From: "Didier Rognan didier.rognan+*+pharma.u-strasbg.fr" To: CCL Subject: CCL: Is there any database that collects which ligands coordinates (derived from the PDB files) are reliable? Message-Id: <-38685-090220085239-26451-jsMWQUARX4KjRfKWsLgCNQ%server.ccl.net> X-Original-From: Didier Rognan Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 20 Feb 2009 14:14:42 +0100 MIME-Version: 1.0 Sent to CCL by: Didier Rognan [didier.rognan%%pharma.u-strasbg.fr] Gerard Pujadas gerard.pujadas*gmail.com a écrit : > Dear CCL list subscribers, > > first of all, sorry for cross-posting > > I wonder if is there any database that collects which ligands > coordinates (derived from protein-ligand complexes available from the > PDB files) are reliable. I would like to use the PDB files with > reliable coordinates for their ligands to analyze the performance of > different protein-ligand docking algorithms in redocking experiments > (/i.e./ split the protein and the ligand from the PDB file; redock > them again; and finally compare the coordinates of the top one > predicted pose with the experimental coordinates). Obviously, for > making sense in such comparison, I need to be sure that the > experimental coordinates of the ligand are correct. > > I know that I could use the "Advanced Search Page" in > http://www.pdb.org to search which X-ray-derived PDB structures > correspond to protein-ligand complexes have, simultaneously: *(1)* a > good resolution (equal or higher than 2.0 angstroms); and *(2)* > R-Value equal or lower than 0.200. Moreover, I could compare the > temperature factors of the ligands in the resulting set with that of > the protein in the corresponding PDB file ... > > Nevertheless, what I am looking for is for a database that quantifies > how well the ligand coordinates fit in the corresponding electron > density map (or something like that). > > Is there any place with such information? > > With many thanks in advances for your help > > Yours sincerely > > Gerard Dear Gerard You can use the sc-PDB database which is a collection of 5952 protein-ligand complexes from the PDB where active sites and ligands have been carefully selected according to their druggability. You can download atomic coodinates for proteins, actives sites and their corresponding ligands in various file formats. Have a look at: http://bioinfo-pharma.u-strasbg.fr/scPDB Didier -- Dr. Didier ROGNAN Structural Chemogenomics Group Laboratory of Therapeutic Innovation UMR 7200 CNRS-UdS 74 route du Rhin F-67400 Illkirch direct line: +33 (0)3 90 24 42 35 secretary: +33(0)3 90 24 42 20 fax: +33 (0)3 90 24 43 10 email: didier.rognan*o*pharma.u-strasbg.fr www:http://bioinfo-pharma.u-strasbg.fr From owner-chemistry@ccl.net Fri Feb 20 09:57:01 2009 From: "=?gbk?B?QXJ0aHVy?= computationalboy_+_gmail.com" To: CCL Subject: CCL: Is there any database that collects which ligands coordinates (derived from the PDB files) are reliable? 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T1VORC1QT1NJVElPTjogcmlnaHQgdG9wOyBXSURUSDogYXV0bzsgQkFDS0dST1VORC1SRVBF QVQ6IHJlcGVhdC14IiBjZWxsU3BhY2luZz0wIGNlbGxQYWRkaW5nPTAgd2lkdGg9IjEwMCUi IGFsaWduPWNlbnRlciBiYWNrZ3JvdW5kPWh0dHA6Ly9yZXMubWFpbC5xcS5jb20vemhfQ04v aW1hZ2VzL3N0YXRpb25lcnkvbG92ZS82Mi9ib3R0b20tYmcuZ2lmIGJvcmRlcj0wPg0KPFRC T0RZPg0KPFRSPg0KPFREPjwvVEQ+DQo8VEQ+PC9URD4NCjxURCB3aWR0aD0xMjMgYmFja2dy b3VuZD1odHRwOi8vcmVzLm1haWwucXEuY29tL3poX0NOL2ltYWdlcy9zdGF0aW9uZXJ5L2xv dmUvNjIvYm90dG9tLXIuZ2lmIGhlaWdodD0zND48L1REPjwvVFI+PC9UQk9EWT48L1RBQkxF Pg0KPFRBQkxFIHN0eWxlPSJGT05ULVNJWkU6IDBweDsgSEVJR0hUOiAwcHgiIGNlbGxTcGFj aW5nPTAgY2VsbFBhZGRpbmc9MCBib3JkZXI9MD4NCjxUQk9EWT4NCjxUUj4NCjxURD48L1RE PjwvVFI+PC9UQk9EWT48L1RBQkxFPg== ------=_NextPart_499EA391_0863DAF0_16059096-- From owner-chemistry@ccl.net Fri Feb 20 10:33:01 2009 From: "Gustavo Seabra gustavo.seabra(a)gmail.com" To: CCL Subject: CCL: NPT better than NVT for implicit solvation model? Message-Id: <-38687-090219164615-21759-KP3byABLGjB1m/u+mrKnhw!A!server.ccl.net> X-Original-From: Gustavo Seabra Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Thu, 19 Feb 2009 16:46:03 -0500 MIME-Version: 1.0 Sent to CCL by: Gustavo Seabra [gustavo.seabra_+_gmail.com] On Wed, Feb 18, 2009 at 12:03 PM, wrote: > > I am an undergraduate student studying the structure of amyloid fibrils > by MD simulations. I used periodic boundary condition with implicit > solvent model to mimic an infinite long fibrils. Concerning the > following two approaches: > 1. energy minimization --> NPT (200 ps) --> NVT (2 ns) > 2. energy minimization --> NPT (2.2 ns) > it's not clear to me which one is better for my project. Being a newbie > in MD simulations, I would like to know under what circumstances NPT > would be better than NVT, and vice versa. Any comments/advices are > greatly appreciated. > > Thanks a lot, > William One thing you may want to consider is which one is more relevant to your system. why are you even considering NVT? Are you looking at a problem that really happens at constant volume? Most biological processes occur at constant pressure instead. Gustavo. From owner-chemistry@ccl.net Fri Feb 20 11:17:01 2009 From: "carlos simmerling carlos.simmerling]*[gmail.com" To: CCL Subject: CCL: HP Outstanding Junior Faculty Awards in Computational Chemistry Message-Id: <-38688-090220111146-2927-/ZIpBpjBzjFIGCuJ/UCM1w-,-server.ccl.net> X-Original-From: "carlos simmerling" Date: Fri, 20 Feb 2009 11:11:43 -0500 Sent to CCL by: "carlos simmerling" [carlos.simmerling^^gmail.com] The HP Outstanding Junior Faculty Award program provides $1,000 to each of four outstanding tenure-track junior faculty members to present their work in COMP symposia at ACS National Meetings. The Awards are designed to assist new faculty members in gaining visibility within the COMP community. Award certificates and $1,000 prizes will be presented at the COMP Poster session. While special consideration will be given to Assistant Professors presenting work in the area of algorithm and methods development, applications for HP Outstanding Junior Faculty Awards are invited from all current tenure-track junior faculty who are members of ACS and the ACS Division of Computers in Chemistry. Postdoctoral researchers in transition to faculty appointments may also be considered. Selection criteria will include the novelty and importance of the work to be presented, as well as the level of Departmental support as indicated by a letter of support by the Chair or Chair designee. To apply for an award for the ACS National Meeting in Washington, DC, August 16-20, 2009, an extended abstract of the work (no more than 2 pages), a CV and the letter of departmental support should be sent as pdf or text files to carlos.simmerling..gmail.com IMPORTANT: APPLICATION MATERIALS MUST BE RECEIVED BY 9AM EASTERN TIME ON MARCH 9, 2009. Applicants will receive email confirmation of receipt of materials. If you do not receive confirmation by March 10, 2009, please contact the organizer immediately by telephone (see below). In addition, you must submit your normal abstract to the "HP Outstanding Junior Faculty Award" symposium on the OASYS system (the COMP OASYS deadline is March 16th for the Washing DC ACS Meeting). Note that this is an abstract for the poster presentation. We also suggest that HP award applicants submit a separate abstract to OASYS for an oral presentation, in addition to their poster abstract in the HP award section (note that acceptance into the oral sessions is not guaranteed). More information on awards offered by the ACS COMP division can be found on the web site at http://www.acscomp.org/Awards/index.html Carlos Simmerling Chair, ACS COMP Division Awards Committee Professor, Department of Chemistry Stony Brook University Stony Brook, NY 11794-3400 631-384-9248 carlos.simmerling..gmail.com From owner-chemistry@ccl.net Fri Feb 20 11:52:00 2009 From: "carlos simmerling carlos.simmerling[*]gmail.com" To: CCL Subject: CCL: Fall 2009 ACS/CCG Graduate Student Travel Award March 9 Deadline Message-Id: <-38689-090220111604-4890-NjblqZL+k7zjQU36+ZF/sA#server.ccl.net> X-Original-From: "carlos simmerling" Date: Fri, 20 Feb 2009 11:16:00 -0500 Sent to CCL by: "carlos simmerling" [carlos.simmerling^^gmail.com] Five $1,150 ACS/CCG Excellence Student Travel Award Stipends Available for the Fall 2009 Washington DC ACS National Meeting The CCG Excellence Awards have been created to stimulate graduate student participation in ACS COMP Division activities (symposia and poster sessions) at ACS National Meetings. Those eligible for a CCG Excellence Award are graduate students in good standing who present work within the COMP program, either in oral or poster format. Winners receive $1,150, as well as a copy of CCG's MOE (Molecular Operating Environment) software with a one-year license. They are also honored during a ceremony at the COMP Division Poster Session. The awardees are chosen on the basis of the quality and significance of the research to be presented, as well as the strength of the supporting letter and other materials. All graduate students of the Americas (North, South or Central) are encouraged to submit applications. Awards will be given only to those individuals making presentations, not co-authors. To apply for an award for the ACS National Meeting in Washington, DC, August 16-20, 2009, an extended abstract of the work (no more than 2 pages), a two page CV along with a letter of support from the research advisor, and a personal statement (no more than 1 page) should be sent as pdf or text files to carlos.simmerling:_:gmail.com IMPORTANT: APPLICATION MATERIALS MUST BE RECEIVED BY 9AM EASTERN TIME ON MARCH 9, 2009. Applicants will receive email confirmation of receipt of materials. If you do not receive confirmation by March 10, 2009, please contact the organizer immediately by telephone (see below). In addition, you must submit your normal poster abstract to the "Chemical Computing Group Excellence Award" symposium on the OASYS system (the COMP OASYS deadline is March 16th for the Washing DC ACS Meeting). More information on awards offered by the ACS COMP division can be found on the web site at http://www.acscomp.org/Awards/index.html Carlos Simmerling Chair, ACS COMP Division Awards Committee Professor, Department of Chemistry Stony Brook University Stony Brook, NY 11794-3400 631-384-9248 carlos.simmerling:_:gmail.com From owner-chemistry@ccl.net Fri Feb 20 12:26:01 2009 From: "John Edward jeedward(~)yahoo.com" To: CCL Subject: CCL: Draft paper submission deadline extended: BCBGC-09 Message-Id: <-38690-090220112148-9384-Qy34UurLqywvJgettWgPGg[-]server.ccl.net> X-Original-From: John Edward Content-Type: multipart/alternative; boundary="0-1320563202-1235143620=:26407" Date: Fri, 20 Feb 2009 07:27:00 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: John Edward [jeedward[#]yahoo.com] --0-1320563202-1235143620=:26407 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Draft paper submission deadline extended: BCBGC-09 =A0 The deadline for draft paper submission at the 2009 International Conferenc= e on Bioinformatics, Computational Biology, Genomics and Chemoinformatics (= BCBGC-09) (website: http://www.PromoteResearch.org ) is extended due to num= erous requests from the authors. The conference will be held during July 13= -16 2009 in Orlando, FL, USA. We invite draft paper submissions. The confer= ence will take place at the same time and venue where several other interna= tional conferences are taking place. The other conferences include: =B7=A0=A0=A0=A0=A0=A0=A0=A0 International Conference on Artificial Intellig= ence and Pattern Recognition (AIPR-09)=20 =B7=A0=A0=A0=A0=A0=A0=A0=A0 International Conference on Automation, Robotic= s and Control Systems (ARCS-09) =B7=A0=A0=A0=A0=A0=A0=A0=A0 International Conference on Enterprise Informat= ion Systems and Web Technologies (EISWT-09) =B7=A0=A0=A0=A0=A0=A0=A0=A0 International Conference on High Performance Co= mputing, Networking and Communication Systems (HPCNCS-09)=20 =B7=A0=A0=A0=A0=A0=A0=A0=A0 International Conference on Information Securit= y and Privacy (ISP-09) =B7=A0=A0=A0=A0=A0=A0=A0=A0 International Conference on Recent Advances in = Information Technology and Applications (RAITA-09) =B7=A0=A0=A0=A0=A0=A0=A0=A0 International Conference on Software Engineerin= g Theory and Practice (SETP-09)=20 =B7=A0=A0=A0=A0=A0=A0=A0=A0 International Conference on Theory and Applicat= ions of Computational Science (TACS-09) =B7=A0=A0=A0=A0=A0=A0=A0=A0 International Conference on Theoretical and Mat= hematical Foundations of Computer Science (TMFCS-09) =A0 The website http://www.PromoteResearch.org contains more details. =A0 Sincerely John Edward Publicity committee=0A=0A=0A --0-1320563202-1235143620=:26407 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable

Draft paper submission deadline extend= ed: BCBGC-09

 

The deadline for draft paper submission at the 2009 International Conference on Bioinformatics, Computational Biolog= y, Genomics and Chemoinformatics (BCBGC-09) (website: = http://www.PromoteResearch= ..org ) is extended due to numerous requ= ests from the authors. The conference will be held during July 13-16 2009 i= n Orlando, FL, USA. We invite draft paper submissions. The conference will take place at the same time a= nd venue where several other international conferences are taking place. Th= e other conferences include:=

=B7         <= /FONT>

=B7         =B7         =B7         =B7         =B7         =B7         =B7         =B7          

The website http://www.PromoteResearch.org<= SPAN style=3D"mso-bookmark: OLE_LINK4"> contains more details.

 

Sincerely

John Edward

Publicity committee


=0A= =0A --0-1320563202-1235143620=:26407-- From owner-chemistry@ccl.net Fri Feb 20 13:01:00 2009 From: "M. Nicklaus mn1*helix.nih.gov" To: CCL Subject: CCL: Is there any database that collects which ligands coordinates (derived from the PDB files) are reliable? Message-Id: <-38691-090220114314-25458-UxPxIym2qY4q1JJ2ImJ25Q**server.ccl.net> X-Original-From: "M. Nicklaus" Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed Date: Fri, 20 Feb 2009 11:12:48 -0500 (Eastern Standard Time) MIME-Version: 1.0 Sent to CCL by: "M. Nicklaus" [mn1 ~ helix.nih.gov] Dear Gerard, We are working on something very much like this. We do have what one could call an early beta version of such a database. For a very preliminary account on this project, see http://echeminfo.colayer.net/comty_conf08filippoviv. (Some of the other talks in this session may also be of interest to you, see http://echeminfo.colayer.net/comty_confprog08pdbligands.) To do this really right, however, is a highly non-trivial task. It will require contributions from experts from different fields, i.e. crystallographers, quantum chemistry folks, people involved with the various ligand-related databases, chemoinformaticians etc. We are currently working on helping such a group come together. Marc ------------------------------------------------------------------------ Marc C. Nicklaus, Ph.D. NIH/NCI at Frederick E-mail: mn1-$-helix.nih.gov Bldg 376, Rm 207 Phone: (301) 846-5903 376 Boyles Street Fax: (301) 846-6033 FREDERICK, MD 21702 USA Head, Computer-Aided Drug Design (CADD) Group 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 ------------------------------------------------------------------------ On Fri, 20 Feb 2009, Gerard Pujadas gerard.pujadas*gmail.com wrote: > Dear CCL list subscribers, > > first of all, sorry for cross-posting > > I wonder if is there any database that collects which ligands coordinates > (derived from protein-ligand complexes available from the PDB files) are > reliable. I would like to use the PDB files with reliable coordinates for > their ligands to analyze the performance of different protein-ligand docking > algorithms in redocking experiments (*i.e.* split the protein and the ligand >> from the PDB file; redock them again; and finally compare the coordinates of > the top one predicted pose with the experimental coordinates). Obviously, > for making sense in such comparison, I need to be sure that the experimental > coordinates of the ligand are correct. > > I know that I could use the "Advanced Search Page" in http://www.pdb.org to > search which X-ray-derived PDB structures correspond to protein-ligand > complexes have, simultaneously: *(1)* a good resolution (equal or higher > than 2.0 angstroms); and *(2)* R-Value equal or lower than 0.200. Moreover, > I could compare the temperature factors of the ligands in the resulting set > with that of the protein in the corresponding PDB file ... > > Nevertheless, what I am looking for is for a database that quantifies how > well the ligand coordinates fit in the corresponding electron density map > (or something like that). > > Is there any place with such information? > > With many thanks in advances for your help > > Yours sincerely > > Gerard > From owner-chemistry@ccl.net Fri Feb 20 13:40:01 2009 From: "Greg Warren greg*eyesopen.com" To: CCL Subject: CCL: Is there any database that collects which ligands coordinates (derived from the PDB files) are reliable? Message-Id: <-38692-090220122638-28929-HBLL7+//jZ2YwdhvhA0L0A[]server.ccl.net> X-Original-From: Greg Warren Content-Language: en-US Content-Type: multipart/alternative; boundary="_000_BB3CCF2D3D6B094D96588383620C5F3E2580A11CB1EXVMBX01811ex_" Date: Fri, 20 Feb 2009 08:55:32 -0800 MIME-Version: 1.0 Sent to CCL by: Greg Warren [greg{:}eyesopen.com] --_000_BB3CCF2D3D6B094D96588383620C5F3E2580A11CB1EXVMBX01811ex_ Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable Gerard, Unfortunately to my knowledge no such database exists. The only method tha= t allows you to get a mostly reliable measure of ligand fit to density is a= real-space R-factor or real space correlation coefficient. You can obtain= this data by mining the EDS server (or by typing each code individually) h= ttp://eds.bmc.uu.se/eds/. So you could go through previously published doc= king data bases and use the data derived from the EDS to select structures = that meet whatever criteria you decide are appropriate. OpenEye Scientific Software is working on a database which they will freely= provide to the public hopefully before the end of the year. The databas= e will be annotated to include measures of the quality of the overall stru= cture and quality of the ligand fit to density as well. In addition, all th= e structures in this database will have had the ligand coordinates re-refin= ed to relieve unrealistic geometric strain. However, this does not solve y= ou immediate problem. Regards, Greg > From: owner-chemistry+greg=3D=3Deyesopen.com~!~ccl.net [mailto:owner-chemistr= y+greg=3D=3Deyesopen.com~!~ccl.net] On Behalf Of Gerard Pujadas gerard.pujada= s*gmail.com Sent: Friday, February 20, 2009 3:09 AM To: Greg Warren Subject: CCL: Is there any database that collects which ligands coordinates= (derived from the PDB files) are reliable? Dear CCL list subscribers, first of all, sorry for cross-posting I wonder if is there any database that collects which ligands coordinates (= derived from protein-ligand complexes available from the PDB files) are rel= iable. I would like to use the PDB files with reliable coordinates for thei= r ligands to analyze the performance of different protein-ligand docking al= gorithms in redocking experiments (i.e. split the protein and the ligand fr= om the PDB file; redock them again; and finally compare the coordinates of = the top one predicted pose with the experimental coordinates). Obviously, f= or making sense in such comparison, I need to be sure that the experimental= coordinates of the ligand are correct. I know that I could use the "Advanced Search Page" in http://www.pdb.org to= search which X-ray-derived PDB structures correspond to protein-ligand com= plexes have, simultaneously: (1) a good resolution (equal or higher than 2.= 0 angstroms); and (2) R-Value equal or lower than 0.200. Moreover, I could = compare the temperature factors of the ligands in the resulting set with th= at of the protein in the corresponding PDB file ... Nevertheless, what I am looking for is for a database that quantifies how w= ell the ligand coordinates fit in the corresponding electron density map (o= r something like that). Is there any place with such information? With many thanks in advances for your help Yours sincerely Gerard --_000_BB3CCF2D3D6B094D96588383620C5F3E2580A11CB1EXVMBX01811ex_ Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

Gerard,

 

Unfortunately to my knowledge no such database exists. = The only method that allows you to get a mostly reliable measure of ligand fit = to density is a real-space R-factor or real space correlation coefficient.&nbs= p; You can obtain this data by mining the EDS server (or by typing each code indiv= idually) http://eds.bmc.uu.se/eds/.  = So you could go through previously published docking data bases and use the data derived from the EDS to select structures that meet whatever criteria you decide are appropriate.

 

OpenEye Scientific Software is working on a database which t= hey will freely provide to the public hopefully before the end of the year.  &n= bsp; The database will be annotated to include measures of the quality of the overal= l  structure and quality of the ligand fit to density as well. In addition, all the structures in this database will have had the ligand coordinates re-refined= to relieve unrealistic geometric strain.  However, this does not solve you immedi= ate problem.

 

Regards,

 

Greg

 

From: owner-chemistry+greg=3D=3Deyesopen.com~!~ccl.net [mailto:owner-chemistry+greg=3D=3Deyesopen.com~!~ccl.net] On Behalf Of Gerard Pujadas gerard.pujadas*gmail.com
Sent: Friday, February 20, 2009 3:09 AM
To: Greg Warren
Subject: CCL: Is there any database that collects which ligands coordinates (derived from the PDB files) are reliable?

 

Dear CCL list subscribers,

first of all, sorry for cross-posting

I wonder if is there any database that collects which ligands coordinates (derived from protein-ligand complexes available from the PDB files) are reliable. I would like to use the PDB files with reliable coordinates for t= heir ligands to analyze the performance of different protein-ligand docking algorithms in redocking experiments (i.e. split the protein and the ligand from the PDB file; redock them again; and finally compare the coordinates of the top one predicted pose with the experimental coordinates= ). Obviously, for making sense in such comparison, I need to be sure that the experimental coordinates of the ligand are correct.

I know that I could use the "Advanced Search Page" in http://www.pdb.org to search which X-ray-de= rived PDB structures correspond to protein-ligand complexes have, simultaneously:= (1) a good resolution (equal or higher than 2.0 angstroms); and (2) R-Va= lue equal or lower than 0.200. Moreover, I could compare the temperature factor= s of the ligands in the resulting set with that of the protein in the correspond= ing PDB file ...

Nevertheless, what I am looking for is for a database that quantifies how w= ell the ligand coordinates fit in the corresponding electron density map (or someth= ing like that).

Is there any place with such information?

With many thanks in advances for your help

Yours sincerely

Gerard

--_000_BB3CCF2D3D6B094D96588383620C5F3E2580A11CB1EXVMBX01811ex_-- From owner-chemistry@ccl.net Fri Feb 20 14:12:01 2009 From: "anjan roy aroy25!=!gmail.com" To: CCL Subject: CCL: calculate plane b/w 2 tryptophans Message-Id: <-38693-090220130638-30979-JZAKDZ8elNIlZKjjCP0zdQ##server.ccl.net> X-Original-From: "anjan roy" Date: Fri, 20 Feb 2009 13:06:34 -0500 Sent to CCL by: "anjan roy" [aroy25|a|gmail.com] Hello all, I would like to calculate the angle b/w the plane running through 2 tryptophans, can pymol do it? Any ideas will help. Anjan From owner-chemistry@ccl.net Fri Feb 20 18:07:01 2009 From: "Wayne Steinmetz WES04747:_:pomona.edu" To: CCL Subject: CCL: calculate plane b/w 2 tryptophans Message-Id: <-38694-090220180313-7546-amBZuDHNuvcRrpdRNoUf0Q]*[server.ccl.net> X-Original-From: "Wayne Steinmetz" Content-class: urn:content-classes:message Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="us-ascii" Date: Fri, 20 Feb 2009 15:02:40 -0800 MIME-Version: 1.0 Sent to CCL by: "Wayne Steinmetz" [WES04747(0)pomona.edu] SYBYL can perform the task. It can generate each plane, provide the equation defining the plane, and calculate the angle between any two planes. In the absence of SYBYL, all you need are the coordinates of the atoms in each tryptophan ring. The remainder of the task is a problem in vector algebra. Wayne E. Steinmetz Professor Emeritus of Chemistry USFS Volunteer Chemistry Department Pomona College 645 North College Avenue Claremont, California 91711-6338 USA phone: 1-909-621-8447 FAX: 1-909-607-7726 Email: wsteinmetz++pomona.edu WWW: pages.pomona.edu/~wsteinmetz =20 -----Original Message----- > From: owner-chemistry+wsteinmetz=3D=3Dpomona.claremont.edu++ccl.net [mailto:owner-chemistry+wsteinmetz=3D=3Dpomona.claremont.edu++ccl.net] On Behalf Of anjan roy aroy25!=3D!gmail.com Sent: Friday, February 20, 2009 10:07 AM To: Wayne Steinmetz Subject: CCL: calculate plane b/w 2 tryptophans Sent to CCL by: "anjan roy" [aroy25|a|gmail.com] Hello all, I would like to calculate the angle b/w the plane running through 2 tryptophans, can pymol do it? Any ideas will help. Anjan -=3D This is automatically added to each message by the mailing script = =3D-http://www.ccl.net/cgi-bin/ccl/send_ccl_messageSubscribe/Unsubscribe:=20Job: http://www.ccl.net/jobs=20http://www.ccl.net/spammers.txt------------------------------------------------------------- This message has been scanned by Postini anti-virus software. =0D