What's a good current free viewer for CML structures embedded in HTML,
if we're looking at 2D-Structures only?
Right now I'm lookinig at JChemPaint; I wonder whether there are any recent
projects I'm overlooking.
Thanks!
-- Eugen* Leitl <a href="http://leitl.org">leitl</a>
______________________________________________________________
ICBM: 48.07078, 11.61144 http://www.leitl.org
8B29F6BE: 099D 78BA 2FD3 B014 B08A 7779 75B0 2443 8B29 F6BE
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
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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-.
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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
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
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.
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)