335
11 Computational Toxicology in Drug Discovery: Opportunities and Limitations
Name
Source
Definition
AFGen
University of
Minnesota
It generates the set of fragment-based descriptors with
three different types of topologies: paths, acyclic subgraphs, and arbitrary topology subgraphs: http://glaros.
dtc.umn.edu/gkhome/afgen/overview
CDK
Independent
developers
The Chemistry Development Kit (CDK) is a Java library
for structural chemo- and bioinformatics. Calculates 260
types of descriptors: http://cdk.sourceforge.net/
CODESSA University of Florida Program automatically calculates more than 500 types
of descriptors (Constitutional, Topological, Geometrical,
Electrostatic, Thermodynamic, Quantum-chemical):
http://www.codessa-pro.com/index.htm
DRAGON
Talete s.r.l.
Calculates 4885 types of descriptors (represented by all
classes of descriptors): http://www.talete.mi.it/index.htm
E-DRAGON VCCLAB
E-DRAGON remote version of the DRAGON, which is
an application for the calculation of molecular descriptors developed by the Milan group of Prof. Todechini:
http://www.vcclab.org/
ISIDA
Université de
Strasbourg
Software for calculation of Substructural Molecular
Fragments (SMF) as well as ISIDA Property-Labeled
Fragments (IPLF) descriptors: http://infochim.u-strasbg.
fr/spip.php?rubrique49
MODEL
National University of
Singapore
Software for a non-commercial use that calculates about
4000 molecular descriptors based on 3D structure of
a molecule: http://jing.cz3.nus.edu.sg/cgi-bin/model/
model.cgi
MOE
Chemical Computing
Group
Calculates over 600 molecular descriptors including
topological indices, structural keys, E-state indices,
physical properties (such as LogP, molecular weight
and molar refractivity), topological polar surface area
(TPSA) and CCG’s VSA descriptors: http://www.chemcomp.com/software-chem.htm
Mol2D
FDA
Freely available software that calculates more than 700
descriptors types based on a two-dimensional structure
of molecules. http://www.fda.gov/ScienceResearch/BioinformaticsTools/Mold2/default.htm
MOLGEN
MOLGEN
Freely available web-service that calculates 708 arithmetical, topological and geometrical descriptors: http://
molgen.de/
PreADMET PreADMET
Calculates more than 2000 descriptors, including both
2D and 3D descriptors: http://preadmet.bmdrc.org/
PaDEL
National University of
Singapore
The software currently calculates 863 descriptors (729
1D, 2D descriptors and 134 3D descriptors) and 10
types of fingerprints: http://padel.nus.edu.sg/software/
padeldescriptor/
PCLIENT
VCCLAB
PCLIENT (Parameter Client) provides an interface for
different programs, which calculate several groups of
indices. In total, more than 3000 kinds of
descriptors: http://www.vcclab.org/
QSARpro
Vlife
Calculation of over 1000 molecular descriptors of various classes: http://www.vlifesciences.com/products/
QSARPro/Product_QSARpro.php
Table 11.2 Generators of molecular descriptors
11 Computational Toxicology in Drug Discovery: Opportunities and Limitations
Name
Source
Definition
AFGen
University of
Minnesota
It generates the set of fragment-based descriptors with
three different types of topologies: paths, acyclic subgraphs, and arbitrary topology subgraphs: http://glaros.
dtc.umn.edu/gkhome/afgen/overview
CDK
Independent
developers
The Chemistry Development Kit (CDK) is a Java library
for structural chemo- and bioinformatics. Calculates 260
types of descriptors: http://cdk.sourceforge.net/
CODESSA University of Florida Program automatically calculates more than 500 types
of descriptors (Constitutional, Topological, Geometrical,
Electrostatic, Thermodynamic, Quantum-chemical):
http://www.codessa-pro.com/index.htm
DRAGON
Talete s.r.l.
Calculates 4885 types of descriptors (represented by all
classes of descriptors): http://www.talete.mi.it/index.htm
E-DRAGON VCCLAB
E-DRAGON remote version of the DRAGON, which is
an application for the calculation of molecular descriptors developed by the Milan group of Prof. Todechini:
http://www.vcclab.org/
ISIDA
Université de
Strasbourg
Software for calculation of Substructural Molecular
Fragments (SMF) as well as ISIDA Property-Labeled
Fragments (IPLF) descriptors: http://infochim.u-strasbg.
fr/spip.php?rubrique49
MODEL
National University of
Singapore
Software for a non-commercial use that calculates about
4000 molecular descriptors based on 3D structure of
a molecule: http://jing.cz3.nus.edu.sg/cgi-bin/model/
model.cgi
MOE
Chemical Computing
Group
Calculates over 600 molecular descriptors including
topological indices, structural keys, E-state indices,
physical properties (such as LogP, molecular weight
and molar refractivity), topological polar surface area
(TPSA) and CCG’s VSA descriptors: http://www.chemcomp.com/software-chem.htm
Mol2D
FDA
Freely available software that calculates more than 700
descriptors types based on a two-dimensional structure
of molecules. http://www.fda.gov/ScienceResearch/BioinformaticsTools/Mold2/default.htm
MOLGEN
MOLGEN
Freely available web-service that calculates 708 arithmetical, topological and geometrical descriptors: http://
molgen.de/
PreADMET PreADMET
Calculates more than 2000 descriptors, including both
2D and 3D descriptors: http://preadmet.bmdrc.org/
PaDEL
National University of
Singapore
The software currently calculates 863 descriptors (729
1D, 2D descriptors and 134 3D descriptors) and 10
types of fingerprints: http://padel.nus.edu.sg/software/
padeldescriptor/
PCLIENT
VCCLAB
PCLIENT (Parameter Client) provides an interface for
different programs, which calculate several groups of
indices. In total, more than 3000 kinds of
descriptors: http://www.vcclab.org/
QSARpro
Vlife
Calculation of over 1000 molecular descriptors of various classes: http://www.vlifesciences.com/products/
QSARPro/Product_QSARpro.php
Table 11.2 Generators of molecular descriptors