From owner-chemistry@ccl.net Fri Aug 2 10:31:00 2013 From: "Jan H Jensen jhjensen]![chem.ku.dk" To: CCL Subject: CCL: Computational Chemistry Highlights: July issue Message-Id: <-49046-130802093443-16236-DweIQ4W+E7gFa82h9Nsgvw]^[server.ccl.net> X-Original-From: "Jan H Jensen" Date: Fri, 2 Aug 2013 09:34:42 -0400 Sent to CCL by: "Jan H Jensen" [jhjensen[*]chem.ku.dk] The July issue of Computational Chemistry Highlights is out. http://www.compchemhighlights.org/2013_07_01_archive.html CCH is an overlay journal that identifies the most important papers in computational and theoretical chemistry published in the last 1-2 years. CCH is not affiliated with any publisher: it is a free resource run by scientists for scientists. You can read more about it here. Table of content for this issue features contributions from CCH editors Steven Bachrach, Ben Corry, Gerald Monard, Dean Tantillo, and Jan Jensen: Towards First Principles Calculation of Electron Impact Mass Spectra of Molecules http://www.compchemhighlights.org/2013/07/towards-first-principles-calculation-of.html Evaluation of Triplet Aromaticity by the Isomerization Stabilization Energy http://www.compchemhighlights.org/2013/07/evaluation-of-triplet-aromaticity-by.html Tunneling in the Bergman Cyclization http://www.compchemhighlights.org/2013/07/tunneling-in-bergman-cyclization.html Enantioselective Thiourea-Catalyzed Intramolecular Cope-Type Hydroamination http://www.compchemhighlights.org/2013/07/enantioselective-thiourea-catalyzed.html Will molecular dynamics simulations of proteins ever reach equilibrium http://www.compchemhighlights.org/2013/07/will-molecular-dynamics-simulations-of.html Atomic-level simulations of current-voltage relationships in single-file ion channels http://www.compchemhighlights.org/2013/07/atomic-level-simulations-of-current.html Interested in more? There are many ways to subscribe to CCH updates. http://www.compchemhighlights.org/p/get-cch-updates.html From owner-chemistry@ccl.net Fri Aug 2 11:06:00 2013 From: "Diana O Rourke diana.orourke:_:certara.com" To: CCL Subject: CCL: SYBYL-X 2.1 release-new job control system, Python toolkit for QSAR Message-Id: <-49047-130802101911-28626-x+qlvR4iHXLAHxW+hDs8HA%x%server.ccl.net> X-Original-From: "Diana O Rourke" Date: Fri, 2 Aug 2013 10:19:09 -0400 Sent to CCL by: "Diana O Rourke" [diana.orourke*o*certara.com] We're pleased to announce the release and general availability of SYBYL-X 2.1 for all customers with current support contracts. Our goal in the development of SYBYL-X is to provide a comprehensive suite of CADD solutions in an environment that makes your work quick and efficient, and this latest release includes customer-requested enhancements including: - New Job Control System replaces Netbatch, with a consistent interface that is implemented across all of SYBYL-X, allowing remote jobs to be submitted > from Windows, Linux, or Mac to any Linux system where SYBYL-X is installed. This is compatible with popular job queuing systems like Oracle Grid Engine, LSF, and Torque, and provides improved multi-processor support for key applications (Surflex-Sim, Surflex-Dock, Topomer Search, and UNITY), that makes sending computationally intense jobs to a compute cluster a breeze! - Python Toolkit for 3D-QSAR makes QSAR functionality accessible outside of SYBYL-X as standalone Python scripts. Results of Python jobs can be read into SYBYL-X using the new readXML expression generator. SYBYL-X 2.1 also includes updates to the Molecular Data Explorer, Surflex- Dock, CScore, the Protein Viewer, and the QSAR Project Manager. For more information, read the release highlights here: http://bit.ly/163yAdX Customers wishing to download SYBYL-X 2.1 should log on to your profile at www.tripos.com and click on Downloads from the main page, then click on SYBYL and select SYBYL-X 2.1 (for current customers). Warm regards, Diana O'Rourke Marketing Director Certara (formed by integrating Tripos-Pharsight-Simcyp) diana.orourke[at]certara.com 314.951.3310 From owner-chemistry@ccl.net Fri Aug 2 17:53:01 2013 From: "Mezei, Mihaly mihaly.mezei^-^mssm.edu" To: CCL Subject: CCL: Openbabel naming question Message-Id: <-49048-130802173757-25062-8jz0uwivPcI6bYvMDI+YOw,server.ccl.net> X-Original-From: "Mezei, Mihaly" Content-Language: en-US Content-Type: multipart/alternative; boundary="_000_23B1335F43764D4EBFA3AC5C9FB1D10B5EBB10EDEXCH2KXMBXEB1Ex_" Date: Fri, 2 Aug 2013 21:37:49 +0000 MIME-Version: 1.0 Sent to CCL by: "Mezei, Mihaly" [mihaly.mezei]|[mssm.edu] --_000_23B1335F43764D4EBFA3AC5C9FB1D10B5EBB10EDEXCH2KXMBXEB1Ex_ Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Greetings, I created two peptides with Pymol, saved them as a MOL (.mol) file and conv= erted them with OpenBabel. In the 6-residue peptide all atom names were jus= t C1, C2, etc while the 7-residue peptide two of the residues (LYS and GLN)= were recognized and got proper protein residue/atom names. The 6-residue p= eptide did not have LYS nor GLN. Is there a way to coax OpenBabel to recognize the rest? Mihaly Mezei Department of Structural and Chemical Biology, Icahn School of Medicine at = Mount Sinai Voice: (212) 659-5475 Fax: (212) 849-2456 WWW (MSSM home): http://www.mountsinai.org/Find%20A%20Faculty/profile.do?id= =3D0000072500001497192632 WWW (Lab home - software, publications): http://scbx.mssm.edu/mezeilab WWW (Department): http://www.mssm.edu/departments-and-institutes/structural= -and-chemical-biology --_000_23B1335F43764D4EBFA3AC5C9FB1D10B5EBB10EDEXCH2KXMBXEB1Ex_ Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Greetings,

I created two peptides with Pymol, saved them as a MOL (.mol) file and conv= erted them with OpenBabel. In the 6-residue peptide all atom names were jus= t C1, C2, etc while the 7-residue peptide two of the residues (LYS and GLN)= were recognized and got proper protein residue/atom names. The 6-residue peptide did not have LYS nor GLN= .

Is there a way to coax OpenBabel to recognize the rest?
Mihaly Mezei

Department of Structural and Chemical Biology, Ica=
hn School of Medicine at Mount Sinai
Voice:  (212) 659-5475   Fax: (212)=
 849-2456
WWW (MSSM home): http://www.mountsinai.org/Find%20A%20Faculty/profile.do?id=3D000007=
2500001497192632
WWW (Lab home - software, publications): http://sc=
bx.mssm.edu/mezeilab
WWW (Department): http://www.mssm.edu/departmen=
ts-and-institutes/structural-and-chemical-biology

--_000_23B1335F43764D4EBFA3AC5C9FB1D10B5EBB10EDEXCH2KXMBXEB1Ex_-- From owner-chemistry@ccl.net Fri Aug 2 18:48:01 2013 From: "Geoffrey Hutchison geoffh!=!pitt.edu" To: CCL Subject: CCL: Openbabel naming question Message-Id: <-49049-130802184642-18690-9sDBf4KiJxejLsXjyV8+gA]~[server.ccl.net> X-Original-From: Geoffrey Hutchison Content-type: multipart/alternative; boundary="Apple-Mail=_AC7F5A34-1B97-4E8F-BF1E-8CB9F0FE2DF5" Date: Fri, 02 Aug 2013 18:46:37 -0400 MIME-version: 1.0 (Mac OS X Mail 6.5 \(1508\)) Sent to CCL by: Geoffrey Hutchison [geoffh(a)pitt.edu] --Apple-Mail=_AC7F5A34-1B97-4E8F-BF1E-8CB9F0FE2DF5 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=iso-8859-1 > I created two peptides with Pymol, saved them as a MOL (.mol) file and = converted them with OpenBabel. In the 6-residue peptide all atom names = were just C1, C2, etc while the 7-residue peptide two of the residues = (LYS and GLN) were recognized and got proper protein residue/atom names. = The 6-residue peptide did not have LYS nor GLN. > Is there a way to coax OpenBabel to recognize the rest? Well, there's an Open Babel mailing list and bug reporter (via = http://openbabel.org/), which might be helpful for this kind of thing. = It's important to us to have the actual file to see where the problem is = (e.g., if it's an actual bug in the residue perception). But as a general rule, the MOL format kills biomolecule information. I'd = suggest saving as PDB or MOL2 which should retain residue/atom naming. = Obviously Open Babel tries to "perceive" missing data. The best thing, = however, is not to destroy the information in the first place by using a = suitable format. Hope that helps, -Geoff --- Prof. Geoffrey Hutchison Department of Chemistry University of Pittsburgh tel: (412) 648-0492 email: geoffh[#]pitt.edu web: http://hutchison.chem.pitt.edu/= --Apple-Mail=_AC7F5A34-1B97-4E8F-BF1E-8CB9F0FE2DF5 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=iso-8859-1

I = created two peptides with Pymol, saved them as a MOL (.mol) file and = converted them with OpenBabel. In the 6-residue peptide all atom names = were just C1, C2, etc while the 7-residue peptide two of the residues = (LYS and GLN) were recognized and got proper protein residue/atom names. = The 6-residue peptide did not have LYS nor = GLN.


Is = there a way to coax OpenBabel to recognize the = rest?

Well, there's an Open = Babel mailing list and bug reporter (via http://openbabel.org/), which might = be helpful for this kind of thing. It's important to us to have the = actual file to see where the problem is (e.g., if it's an actual bug in = the residue perception).

But as a general rule, = the MOL format kills biomolecule information. I'd suggest saving as PDB = or MOL2 which should retain residue/atom naming. Obviously Open Babel = tries to "perceive" missing data. The best thing, however, is not to = destroy the information in the first place by using a suitable = format.

Hope that = helps,
-Geoff

---
Prof. Geoffrey = Hutchison
Department of Chemistry
University = of Pittsburgh
tel: (412) 648-0492
email: geoffh[#]pitt.edu
web: http://hutchison.chem.pitt.edu/
= --Apple-Mail=_AC7F5A34-1B97-4E8F-BF1E-8CB9F0FE2DF5-- From owner-chemistry@ccl.net Fri Aug 2 23:54:00 2013 From: "Guenter Grethe ggrethe(~)att.net" To: CCL Subject: CCL: Call for Applications - CINF Scholarships for Scientific Excellence Message-Id: <-49050-130802201820-8363-7/BvtmUMduWwQW4IAfxbQg%x%server.ccl.net> X-Original-From: "Guenter Grethe" Date: Fri, 2 Aug 2013 20:18:18 -0400 Sent to CCL by: "Guenter Grethe" [ggrethe~~att.net] CINF Scholarship for Scientific Excellence Co-sponsored by InfoChem and Springer The international scholarship program of the Division of Chemical Information (CINF) of the American Chemical Society (ACS) co-sponsored by InfoChem (www.infochem.de) and Springer (www.springer.com) is designed to reward graduate and postdoctoral students in chemical information and related sciences for scientific excellence and to foster their involvement in CINF. Up to three scholarships valued at $1,000 each will be presented at the 247th ACS National Meeting in Dallas, TX, March 16 20, 2014. Applicants must be enrolled at a certified college or university and must present a poster during the Welcoming Reception of the division on Sunday evening at the National Meeting. Additionally, they will have the option to also show their poster at the Sci-Mix session on Monday night. Abstracts for the poster must be submitted electronically through PACS, the abstract submission system of ACS. To apply, please inform the Chair of the selection committee, Guenter Grethe at ggrethe _ att.net, that you are applying for a scholarship. Submit your abstract at http://abstracts.acs.org using your ACS ID. If you do not have an ACS ID, follow the registration instructions and submit your abstract in the CINF program in the session CINF Scholarship for Scientific Excellence. PACS will be open for abstract submissions on August 12, 2013, and close on October 7, 2013. Additionally, please send a 2,000-word abstract describing the work to be presented in electronic form to the Chair of the selection committee by January 31, 2013. Any questions related to applying for one of the scholarships should be directed to the same e-mail address. Winners will be chosen based on contents, presentation and relevance of the poster and they will be announced during the Sunday reception. The contents shall reflect upon the students work and describe research in the field of cheminformatics and related sciences. Guenter Grethe About InfoChem InfoChem GmbH based in Munich, Germany, is a market leader in structure and reaction handling and retrieval. Founded in 1989, InfoChem focuses on the production and marketing of new chemical information products, including structural and reaction databases, and the development of software tools required for these applications. The main software tools provided are the InfoChem Fast Search Engine (ICFSE), the InfoChem Chemistry Cartridge for Oracle (ICCARTRIDGE) and the widely used InfoChem reaction classification algorithm CLASSIFY. InfoChem distributes one of the largest structural and reaction files worldwide, currently containing 7 million organic compounds and facts and 4 million reactions covering the chemical literature published since 1974 (SPRESI). In addition, InfoChem provides tools for the automatic recognition and extraction of chemical entities and their conversion into chemical structures as well as the semantic enrichment of chemical science documents. Springer GmbH (Berlin) has held a majority interest in InfoChem since 1991. For more infromation go to www.infochem.de.