University of Tuebingen Lehrstuhl Kognitive Systeme, Prof Dr. Zell
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Chapter 5. Descriptors

Native values

The native values like simple atom/group counts and complexity measures are suitable to build primitive QSAR prediction models for structure property relations, which has a good correlation to the molecular complexity. for more biological relevant models we recommend to use transformation based descriptors (the Section called Transformations) based on atom properties (the Section called Atom properties).

Number of acidic groups

Number of acidic groups.

Number of aliphatic hydroxy groups

Number of aliphatic hydroxy groups.

Number of aromatic bonds

Number of aromatic bonds.

Number of basic groups

Number of basic groups.

Fraction of rotatable bonds

Fraction of rotatable bonds.

Geometrical diameter

Geometrical diameter.

Geometrical radius

Geometrical radius.

Geometrical shape coefficient

Geometrical shape coefficient.

Graph shape coefficient

Graph shape coefficient.

Number of Hydrogen Bond Acceptors (HBA) 1

Number of Hydrogen Bond Acceptors (HBA) 1. The default SMARTS pattern is: [$([!#6;+0]);!$([F,Cl,Br,I]);!$([o,s,nX3]);!$([Nv5,Pv5,Sv4,Sv6])].

Number of Hydrogen Bond Acceptors (HBA) 2

Number of Hydrogen Bond Acceptors (HBA) 2. The default SMARTS pattern is: [$([$([#8,#16]);!$(*=N~O);!$(*~N=O);X1,X2]),$([#7;v3;!$([nH]);!$(*(-a)-a)])].

Number of Hydrogen Bond Donors (HBD) 1

Number of Hydrogen Bond Donors (HBD) 1. The default SMARTS pattern is: [!#6;!H0].

Number of Hydrogen Bond Donors (HBD) 2

Number of Hydrogen Bond Donors (HBD) 2. The default SMARTS pattern is: [$([O;H1,-&!$(*-N=O)]),$([S;H1&X2,-&X1]),$([#7;H;!$(*(S(=O)=O)C(F)(F)F);!$(n1nnnc1);!$(n1nncn1)]),$([#7;-])].

Number of heavy bonds

Number of heavy bonds.

Number of heterocycles

Number of heterocycles.

Number of hydrophobic groups

Number of hydrophobic groups.

Kier Shape 1

The Kier shape 1κ descriptor [tc00] can be defined as :

Equation 5-1. Kier shape 1

Pmax is the maximum number of paths of length 1. Pmin is the minimum number of paths of length 1 in a molecule graph of same atom number. P1 is the number of paths in the given molecule of length 1. or:

Equation 5-2. Kier shape 1 (alternative formulation)

A means the number of nodes in the molecules graph. P1 is the number of paths of length 1 in the given molecule.

Kier shape 2

The Kier shape 2κ descriptor [tc00] can be defined as :

Equation 5-3. Kier shape 2

A means the number of nodes in the molecules graph. P2 is the number of paths of length 2 in the given molecule.

Kier shape 3

The Kier shape 3κ descriptor [tc00] can be defined as :

Equation 5-4. Kier shape 3

A means the number of nodes in the molecules graph. P3 is the number of paths of length 3 in the given molecule.

Octanol/Water partition coefficient (logP)

Octanol/Water partition coefficient (logP) or hydrophobicity [wc99].

Molar refractivity (MR)

Molar refractivity (MR) [wc99].

Molecular weight (MW)

Molecular weight (MW).

Number of atoms

Number of atoms.

Number of boron atoms

Number of boron atoms.

Number of bromine atoms

Number of bromine atoms.

Number of bonds

Number of bonds.

Number of chlorine atoms

Number of chlorine atoms.

Number of halogen atoms

Number of halogen atoms.

Number of iodine atoms

Number of iodine atoms.

Number of fluorine atoms

Number of fluorine atoms.

Number of nitrogen atoms

Number of nitrogen atoms.

Number of oxygen atoms

Number of oxygen atoms.

Number of phosphorus atoms

Number of phosphorus atoms.

Number of sulfur atoms

Number of sulfur atoms.

Number of -NO2 groups

Number of -NO2 groups.

Number of -OSO atoms

Number of -OSO atoms.

Polar surface area (PSA)

Polar surface area (PSA) [ers00].

Number of rotatable bonds

Number of rotatable bonds, where the atoms are heavy atoms with bond order one and a hybridization which is not one (no sp). Additionally the bond is a non-ring-bond.

Number of -SO groups

Number of -SO groups.

Number of -SO2 atoms

Number of -SO2 atoms.

Topological diameter

Topological diameter.

Topological radius

Topological radius.

Zagreb index 1

Zagreb index 1 [tc00].

Equation 5-5. Zagreb index 1

where a are all atoms of the hydrogen depleted graph and is the vertex degree.

Zagreb index 2

Zagreb index 2 [tc00].

Equation 5-6. Zagreb index 2

where b are all bonds of the hydrogen depleted graph and is the vertex degree. i and j are the atom indices of the atoms connected to the bond b.


Last changes: 08.12.2010, 16:50 CET (UTC/GMT +1 hour) wegner.
http://www.ra.cs.uni-tuebingen.de/software/joelib/tutorial/descriptors/descriptors.html
2003 University of Tübingen, Germany