An integrated web-based platform for molecular descriptor and fingerprint computation

Molecular descriptors

There are three keys to the success of any QSAR model building exercise: descriptors,descriptors, and descriptors.

A. Tropsha,Comprehensive Medicinal Chemistry II Volume 4 : Computer-Assisted Drug Design.

   Molecular descriptors are used to calculate and to develop methods for chemical property calculations (QSPR - quantitative structure-property relationship) or chemical activity (QSAR - quantitative structure-activity relationship) calculations. Today,it is widely used in QSAR/SAR, virtual screening, database search, ranking, drug ADME/T prediction and other drug discovery processes.A common classification method for descriptors can be taken from 'ChemoInformatics textbooks' and a collection of common molecular descriptors in the Handbook of molecular descriptors .

  Different molecular representations

Molecular representation Descriptors Example(s)

atom counts,bound counts,

molecular weight,sun of atomic


molecular weight,average molecular weight,

number of:hydrogen atoms,carbon atoms,

heteroatoms,non-hydrogen atoms,


1D fragments counts

number of: primary C(sp3),secondary C(sp3),tertiary C(sp3),

isocyanates,N in hydrazines,nitro groups,imides,

carboxylic acids.ethers;number of H-bond donor atoms,

number of H-bond acceptor atoms,

fragment-based polar surface area,et,al.

2D topological descriptors

Zagreb index,Wiener index,Balaban J index,

connectivity indices chi(χ),kappa(κ) shape indices,molecular walk counts,

BCUT descriptors,2D autocorrelation vector,et,al.

3D geometrical descriptorts

molecular exxentricity,radius of gyration,E-state topolocal parameter,

3D Wiener index,3D Balaban index,

3D MoRSE descriptors,radial distribution function(RDF code),

WHIM descriptors,GETAWAY descriptors,3D autocorrelation vector,et,al.




mean molecular electrostatic potential,

hydrophobicity potential, hydrogen-bonding potential



  Comparative Molecular Field Analysis(CoMFA)
4D   3D Coordinates + sampling of conformations
  Online tools
  Software and packages
  Other resources

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