Subject: Summary: Freeware for Drug Design

From: "Parthiban Srinivasan" <[email-masked]>
Date: Tue, 11 Jun 2002 09:06:45 +0530

Dear Friends:
Here is the first list of summary on freeware for drug design. If you have
any
additional info other than that I summarised below, please let me know.
I will make second part of the summary. Thanks and Regards
- Parthiban S
--------------------my query--------------
Dear Friends:
I am looking for downloadable programs (trivial to sophisticated) applicable
in
various stages of drug discovery pipeline. Kindly send me the URL and/or
any other helpful info. As an useful prcatice, I will summarise the replies.
Thanks and Regards
S Parthiban
Jubilant Biosys

------------------Summary of replies-----------------

From: "Dr. N. SUKUMAR" <[email-masked]>

http://www.chem.rpi.edu/chemweb/recondoc/WinRecon.html
http://www.drugmining.com/

RECON is an algorithm for the rapid reconstruction of molecular charge
densities and charge density-based electronic properties of molecules,
using atomic charge density fragments precomputed from ab initio
wavefunctions. The method is based on Bader's quantum theory of Atoms in
Molecules.
A library of atomic charge density fragments has been built in a form that
allows for the rapid retrieval of the fragments and molecular assembly. The
RECON algorithm reads in a molecular database, determines atom types and
environments, assigns the closest match from the library of atom types and
combines the densities of the atomic fragments to compute a large set of
new and traditional QSAR descriptors. QSPR and QSER indices for large
pharmaceutical databases or proteins can be computed within seconds.
Dr. N. Sukumar, Professor Curt M. Breneman
Rensselaer Department of Chemistry
---------

From: Stephen Bowlus [email-masked]

A wealth of information is in the CCL archives, so you might want to search
these.  Cheap (but not free!) SW is also available through QCPE or its
Japanese equivalent.

There are several tools from Illinois, like VMD and NAMD.  A complete list
is at
http://www.ks.uiuc.edu/#serv/

Vega is a nice, small-molecule program:
http://users.unimi.it/~ddl/

MOPAC for Windows is useful.  The page quoted is a bit wierd, but if you
have a problem, e-mail the page contact; he is very helpful:
http://members.fortunecity.com/winmopac/

And if you can work on the net (using servers, not downloading the
programs), be sure to look at what is available at the following.  This is
more focused on receptor modeling, but I have found them useful in the past:
RCSB:  http://www.rcsb.org/pdb/
NCBI:  http://www.ncbi.nlm.nih.gov/Database/index.html
ExPASy:  http://www.expasy.org/
PredictProtein:
http://cubic.bioc.columbia.edu/predictprotein/predictprotein.html

------

From: michael hanlon (BITS) [email-masked]

MODELLER is popular for protein modelling, including within the drug
discovery sector. It's free to academics:
 http://tatiana.rockefeller.edu/modeller/
 Autodock is pretty widely used for molecular docking, and comes up on this
list a fair bit:
 http://www.scripps.edu/pub/olson-web/doc/autodock/
 Mike

------
From: "Sergio Manzetti" <[email-masked]>

Hey you can download a demo of the molecular modelling builder ChemSite
it lasts for 60 days I think..
http://www.chemsw.com/d_10202.htm
For protein modelling get Swiss PDB Viewer, which is much better than
Modeller:
www.expasy.org/spdbv
Sergio

----------
From: Giulio Vistoli [email-masked]

Dear S Parthiban,

Our program VEGA (http://users.unimi.it/~ddl) can be useful in several
stages of drug desing and molecular modelling: indeed it can convert several
file formats, analyze molecular trajectories and ligand-receptor complexes,
assign atom types and atomic charges. Moreover VEGA has a graphical
interface for Win32 PCs and it is expansible with a plugin architecture
system.
 Giulio Vistoli
http://users.unimi.it/~ddl

----------
From: "Fabien Fontaine" <[email-masked]>

Try this
http://www.qspr.pe.kr/CS-content1.html
and also
www.miasrl.com/software.htm
Fabien
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