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some CADD tools released
by gentamicin5 19 Nov '03

19 Nov '03

Dear all, I have written some CADD tools, and the details are described below. All of these programs are released under GNU/GPL. You can download them from: http://home.pchome.com.tw/team/gentamicin/mol/mol.htm ------------------------------------------------------------------- CADD tools (linux & irix) pscan_2.2.0 PSCAN is a small but a practical tool for finding any potential binding site of a protein. It can picture the size and appearance of a binding site, and point out the possible pharmacophore.Thus it is helpful for drug design. While running DOCK, QCPE_MS is necessary for autoMS and even the next step sphgen. QCPE_MS, however, is a commercial package. Now, PSCAN and SPHBOX can do the same job. After removing all dots outside of the target binding site by SPDBV (or others), and choosing several positions you are interesting, run SPHBOX to generate sph and box files. pmol2q_2.1.1_rc2 PMOL2Q is a specific file format converter for protein pdb file to mol2 file with adding hydrogens and partial charges. From v2.1.1, PMOL2Q can also output pdbq and pdbqs format. (The pdbqs format is added solvation data according with ADDSOL in AutoDock) It can recognize each amino acid and reconstruct the coordination precisely. The bond length of 109 pm for C-H, 101 pm for N-H, 96 pm for O-H and 134 pm for S-H are used for adding hydrogens.You can choose to add global hydrogens or only polar hydrogens. KOLL and AMBER95 partial charges are available in PMOL2Q. PMOL2Q can also check probabel error of protein coordination, including incomplete atom_missing residues and atom bumps. Hydrogens will not be added on incomplete residues if they exist. You need to fix it by other program before converting file format. (ex. SPDBV can fix the incomplete residues by mutate function) dbfilter_2.2.1 DBFILTER can check the mol2 format database, and pick out any problematic structure which results in "segmentation fault" of DOCK during flexible docking. (for example, salt or structure which contains multi-molecular built in....) And DBFILTER will output a new database which you want. There are also 12 kinds of filters for spotlighting drug-like properties. Including: Common_atoms_only, Molecular_weight, LogP, H_bond_donors, H_bond_acceptors, Sum_of_N+O, Halogens, Rings, Big_ring_members, Rotatable_bonds, CH3(CH2)n- , CF3(CF2)n-. ----------------------------------------------------------------- 每天都 Yahoo!奇摩海的顏色、風的氣息、愛你的溫度，盡在信紙底圖 http://tw.promo.yahoo.com/mail_premium/stationery.html

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Symposium on grid computing
by Dr. Wendy A. Warr 17 Nov '03

17 Nov '03

I am posting this on behalf of my co-organizer, Guenter Grethe. Note that the closing date for abstracts is fast approaching. This notice has been published on several listservers. We apologize for any inconvenience. You are invited to present a paper at the symposium "Research collaboratories, virtual laboratories, and Grid computing" organized jointly by the Division of Chemical Information (CINF) and the CSA Trust during the 227th National Meeting of the American Chemical Society (ACS) in Anaheim, March 28 - April 1, 2004. We specifically solicit papers discussing research, design, and development of Grid technologies that help in solving large-scale compute and data intensive applications in the broader area ofbiomolecular informatics, including software tools and resource brokers that facilitate large-scale molecular studies on geographically distributed computational and data resources. Abstracts should be submitted online using OASYS (http://oasys.acs.org) The deadline for submission is November 25, 2003. Any changes to an abstract can be made until December 1st. If you have any questions regarding the symposium or problems with submitting your abstract please call or e-mail me (see below). Co-organizer of the symposium is Dr. Wendy Warr of Wendy Warr & Associates. The targeted length of a presentation is 30 minutes including 5 minutes for Q&A. When planning your presentation, consider a back-up person from your organization who could deliver your talk if for any reason you are prevented from attending the meeting. Speakers are responsible for their own travel and registration costs. One-day registration fees will be paid by the Division after approval by the organizers for speakers who are non-US scientists or non-ACS members Dr. Guenter Grethe 352 Channing Way Alameda, CA 94502-7409 Tel/Fax: 510-865-5152 Mobile: 510-333-7526 e-mail: ggrethe(a)comcast.net -- Dr Wendy A Warr Wendy Warr & Associates, 6 Berwick Court Holmes Chapel, Cheshire CW4 7HZ, England Tel/fax +44 (0)1477 533837 wendy(a)warr.com http://www.warr.com

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What is a WiKi
by Rzepa, Henry 03 Nov '03

03 Nov '03

Earlier this year, I posted about the "Blog" phenomenon, and how it had grown up into RSS. Well, here is another "ground up" phenomenon; the WiKi (or WiKiWiKi). If you follow http://dirac.cnrs-orleans.fr/fsatom_wiki/ you will find out what Wiki means. The above is actually one set up by the FSAtom community, but there may well be a few others in the chemical community (and if anyone has seen a good one, let this list know!). The concept is somewhere in between a Blog (or personal web page), and an email or chat list. Several interesting concepts pervade; thus a WiKi is in one way what the creator of the Web TimBL intended all along, which is one which is much less asymmetric (the Web is a write by one, read by many medium) in that a WiKi is a write by many/read by many system. Lest you worry that what one person writes, another could delete, a full revision history is kept (so in that sense it is similar to the CVS system used by programmers to record the development of code). I found out recently that postgraduate students here are starting to use WiKis to keep laboratory notebooks of their research; the FSAtom WiKi is a group of chemists interested in atomic-scale simulations, and so forth. As a collaborative phenomenon, its both sophisticated enough to provide a rich environment, and simple enough that the learning curve is not steep. And to revert to the opening sentence of this post, RSS has been fully assimilated into some WiKis, hence providing another link into data rich environments. If you want to set one up, one place is http://phpwiki.sourceforge.net/, but you will need a PHP module (and probably a MySQL database) as part of your web service. In this sense, like the Web, its a server/client model with the former a single point of failure (or suppression). If anyone knows of a peer2peer version, do let us know! -- Henry Rzepa. +44 (020) 7594 5774 (Voice); +44 (0870) 132 3747 (eFax) http://www.ch.ic.ac.uk/rzepa/ Dept. Chemistry, Imperial College London, SW7 2AZ, UK.

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Chime => Jmol
by Rzepa, Henry 02 Nov '03

02 Nov '03

Take a sneak preview at http://jmol.sourceforge.net/preview/ to see how JMol has come on. The first 8 demos work well for me on the "awkward" Macintosh (using OS X 10.3 and Safari). The chime2jmol Perl script is also available for conversion from the <embed> syntax used by Chime to the <applet> used by JMol (but see my previous posting about Microsoft changing how both these will function in Internet Explorer). No doubt the chime2jmol script could be extended to take this into account. -- Henry Rzepa. Imperial College, Chemistry Dept. +44 0778 626 8220 +44 020 7594 5804 (Fax)

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Molecule of the Month - November
by Paul May 30 Oct '03

30 Oct '03

Hi, Noveber's MOTM is S-Adenosyl Methionine, which is an important biological methylating agent. It was written by Rich Blatchly of Keene State College, Keene, New Hampshire, USA, and comes as an HTMl-only web page. http://www.bristol.ac.uk/Depts/Chemistry/MOTM/motm.htm#nov2003 Regards, ----------------------------------------------------------------------------- Dr Paul May, School of Chemistry, University of Bristol, UK tel: +44 (0)117 928-9927 fax: +44 (0)117 925-1295 <mailto:paul.may@bris.ac.uk> Mobile: 07811371539 Home URL: <http://www.bris.ac.uk/Depts/Chemistry/staff/pwm.htm> Molecule of the Month: <http://www.bristol.ac.uk/Depts/Chemistry/MOTM/motm.htm> ------------------------------------------------------------------------------

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Changes to the way chemical content is viewed in Web pages
by Rzepa, Henry 22 Oct '03

22 Oct '03

The site http://www.rnsoft.com/products/iewebfix/ describes a "fix" to Web pages necessitated by a court case Microsoft has recently lost. Apparently it dates back to a patent on "in-lined" content of the type produced in Web browsers by the <object>, <embed> and <applet> pages. This patent was apparently infringed by Web browsers and Microsoft, is having to preface each invocation of such content by some sort of disclaimer. This will mean that pages having this sort of content will not display unless the reader dismisses these dialogs. This means that many of the pages written for chemical application, whereby 3D molecular coordinates, spectra etc are inlined into a page, will be disrupted by the above procedures. The solution is to replace the direct <object>, <embed> and <applet> HYML codes by Javascript equivalents that write it out dynamically. The above site provides a converter that does this, although one must assume that many "legacy" pages will not be converted, and hence will become "unviewable". This in the first instance on IE, but it seems inevitable that other browsers will have to follow suite. This sorry saga reminds me of the attempts by I think BT to claim that the hyperlink itself was covered by a patent, and the earlier GIF saga whereby royalties on the compression algorithm were payable. Whether this court case over the in-lined patent will do the chemistry and science communities any good remains to be seen; whatever else, it certainly will be disruptive. -- Henry Rzepa. Imperial College, Chemistry Dept. +44 0778 626 8220 +44 020 7594 5804 (Fax)

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Combichem/HTS links
by Wendy Warr 09 Oct '03

09 Oct '03

(Apologies for duplicate postings) Colleagues, We have updated our list of resources in combichem and high throughput screening: http://www.warr.com/ombichem.html Details of the latest issue (August 2003) in our cheminformatics series of reports are at http://www.warr.com Wendy Dr Wendy A Warr Wendy Warr & Associates, 6 Berwick Court Holmes Chapel, Cheshire CW4 7HZ, England Tel/fax +44 (0)1477 533837 wendy(a)warr.com http://www.warr.com

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Chemical RSS feeds
by Ivan Tubert-Brohman 02 Oct '03

02 Oct '03

Dear Chemweb, Thanks to Henry, I'm getting interested in the applications of RSS in chemistry. It is sad that the chemistry societies don't make use of this technology. Therefore I decided to try and "scrape" the content alert emails that I get from ACS and convert them to RSS. It's still a proof of concept, but you can find them at http://ivan.tubert.org/rss/ . I know scraping is never a permanent solution, but sometimes it is surprising how fast a vendor decides to provide a service when they see how people are willing to go around them and do it on their own. At least it will be useful for me, because I'll be able to aggregate it with other sources of interest. If you think it's useful feel free to use it. I may add more journals later. Best regards, Ivan

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Molecule of the Month - october
by Paul May 30 Sep '03

30 Sep '03

Hi, October's MOTM is Dimethyl Mercury, the toxic compound that caused the Mimamata disaster in Japan in the 1950s. The page has been written by Simon Cotton from Uppingham School, Rutland, and is available in 5 formats. This is the first MOTM to use the Jmol format for displaying 3D chemical structures without the need for a plug-in. http://www.bristol.ac.uk/Depts/Chemistry/MOTM/motm.htm#oct2003 Regards, ----------------------------------------------------------------------------- Dr Paul May, School of Chemistry, University of Bristol, UK tel: +44 (0)117 928-9927 fax: +44 (0)117 925-1295 <mailto:paul.may@bris.ac.uk> Mobile: 07811371539 Home URL: <http://www.bris.ac.uk/Depts/Chemistry/staff/pwm.htm> Molecule of the Month: <http://www.bristol.ac.uk/Depts/Chemistry/MOTM/motm.htm> Bumper sticker: "Where are we going? And why are we in this hand-basket?" ------------------------------------------------------------------------------

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ACS Award
by Wendy Warr 16 Sep '03

16 Sep '03

Excuse multiple postings. In 2004, the ACS Award for Computers in Chemical and Pharmaceutical Research (sponsored by Accelrys) will be awarded to Prof. W. Graham Richards, of the University of Oxford. The Awards Ceremony will be held on March 30, 2004, at the ACS meeting in Anaheim, California. Wendy Dr Wendy A Warr Wendy Warr & Associates, 6 Berwick Court Holmes Chapel, Cheshire CW4 7HZ, England Tel/fax +44 (0)1477 533837 wendy(a)warr.com http://www.warr.com

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