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Laboratory
for ChemoMetrics,
Vienna (Austria) Software SubMat |
Software
SubMat
Calculation
of binary substructure descriptors
Version
3.1, June 2004 (free demo version)
A chemical structure can be
represented by a binary vector (a bit string, a series of "0" and
"1", a fingerprint).
A "1" indicates that a
particular substructure is present, a "0" that it is absent.
Software SubMat
calculates such binary substructure descriptors.
The substructures can be defined
by the user, or a set of provided 500 general purpose substructures can be
used.
SubMat is a scientifically
oriented tool for chemoinformatics. See demo
example.
SubMat requires as INPUT:
An input file with n1
molecular structures (in Molfile format, *.SDF),
an input file with n2 substructures (in
Molfile format, *.SDF),
a few parameters (name of output file, format
specification of output file).
SubMat produces as OUTPUT:
A text file with n1 rows (each for one
molecular structure),
and n2 columns (each for a
substructure, containing "0" or "1"),
and optionally some additional data (for
instance identification numbers of structures).
This result file can be easily imported into
other software, for instance for multivariate data analysis.
Typical computing time for 1000 molecular
structures and 200 substructures is 1 second.
Optionally, SubMat
can be called and controlled from another software via a command file.
A file with 500 substructures is included;
they are considered as "general purpose substructures" for organic
compounds.
SubMat is running under MS
Windows 95/98/ME/NT/2000/XP
Authors: H. Scsibrany and K. Varmuza
PRICE: Euro 200.
Orders by email or by fax/letter to
Prof. K. Varmuza
Laboratory for Chemometrics, Institute of Chemical
Engineering
Vienna University of Technology,
Getreidemarkt 9/166-2, A-1060 Vienna, Austria
Fax +43 1 58801 16091
FREE DEMO VERSION (ZIP file, 327 kbyte).
>> DOWNLOAD <<
Includes User Guide for full
version (15 pages, PDF), and demo structure files.
Restrictions of demo version:
maximum 10 structures, maximum 10 atoms and 20 bonds per structure.
MORE INFO
Demo
application with isomers C7 H14 O
PAPERS and
MANUSCRIPTS
Varmuza K., Scsibrany H.:
J. Chem. Inf. Comput. Sci., 40,
308-313 (2000).
Substructure isomorphism matrix.
Scsibrany H., Karlovits M., Demuth W., Müller F.,
Varmuza K.:
Chemom. Intell. Lab. Syst., 67,
95-108 (2003).
Clustering and similarity
of chemical structures represented by binary substructure descriptors.
Varmuza K., Karlovits M., Demuth W.:
Anal. Chim. Acta, 490, 313-324
(2003).
Spectral similarity
versus structural similarity: infrared spectroscopy.
Demuth W., Karlovits M., Varmuza K.:
Anal. Chim. Acta, 516, 75-85 (2004).
Spectral similarity
versus structural similarity: mass spectrometry.
Varmuza K.,
Demuth W., Karlovits M.:
Manuscript for CHEM 2 Conference,
Cairo University, Egypt, March 2002.
Structural and spectral similarity.
Manuscript
(PDF, 185 kB)
POSTER
Varmuza K., Demuth W., Karlovits M., Werther W., Schmid E.R.:
Edinburgh,
Scotland (U.K.): 16th International Mass Spectrometry Conference, 2003-08-31 to 09-05 (2003).
Similarity
between chemical structures of query compounds and found hitlist compounds in
mass spectral similarity searches.
PDF file of
poster (194 kB).
Karlovits
M., Demuth W., Scsibrany H., Müller F., Varmuza K.:
Kyoto
(Japan): 11th German-Japanese Workshop on Chemical Information, 2003-06-12 to
06-13 (2003).
Exploration
of chemical structure sets: Binary molecular descriptors and mapping methods.
PDF file of
poster (207 kB).
Varmuza K., Demuth W., Scsibrany H.:
Dubrovnik
(Croatia): Mathematics, Chemistry & Computer Sciences (19th Intern. Conf.),
2004-06-21 to 06-26 (2004).
Binary
substructure descriptors for organic compounds.
PDF file of
poster (113 kB).
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2005-02-01 |
