ChemDes

Molecular descriptors

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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 .

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Molecular representation	Descriptors	Example(s)
0D	atom counts,bound counts, molecular weight,sun of atomic properties	molecular weight,average molecular weight, number of:hydrogen atoms,carbon atoms, heteroatoms,non-hydrogen atoms, rings,bonds,et,al.
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.
3D-surface properties		mean molecular electrostatic potential, hydrophobicity potential, hydrogen-bonding potential
3D-grid properties		Comparative Molecular Field Analysis(CoMFA)
4D		3D Coordinates + sampling of conformations

• E-Dragon (VCCLab) free (150 molecules), now with GSFRAG, GSFRAG-L, ETState > 3000 descriptors.

• ChemoPy-free package based on Python language for computation of molecular descriptors.
• CDK descriptor GUI (free and open source - using Open Source CDK and Joelib code).
• BlueDesc - Molecular Descriptor Calculator (free and open source - using CDK and Joelib code, requires JAVA 1.6).
• ChemAxon JChem - descriptor package using Marvin JAVA API (free academic license).
• ISIDA/QSPR - free fragment based QSPR descriptor package.
• MOLD2 - (FDA) a free 2D molecule descriptor package.
• Toxicity Estimation Software Tool (T.E.S.T.)- (EPA) contains more than 790 2-dimensional descriptors.(based on Dragon6.0)
• Open3DQSAR- pharmacophore modelling using molecular interaction fields (MIFs).
• Dragon - 4885 molecular descriptors for LINUX and WIN (Todeschini/Talete).
• ADMEWORKS ModelBuilder - 400 descriptors (Jurs) and MOPAC (Stewart) (Fujitsu/Poland).
• ISIDA Fragmentor - The ISIDA Fragmentor2013 software permits the calculation of Substructural Molecular Fragments (SMF) as well as ISIDA Property-Labelled Fragments (IPLF) descriptors.
• jCompoundMapper - An Open Source Java Library and Command-Line Tool for Chemical Fingerprints

• MOLE db - Molecular Descriptors Data Base is a free on-line database constituted of 1124 molecular descriptors calculated on 234773 molecules.
• -Molecular Descriptor CorrelationsThe Molecular Descriptor Correlations is a free tool for the analysis of molecular descriptor correlations calculated on 221,860 molecules from the NCI database.
• OCHEM-The Online Chemical Modeling Environment (OCHEM) is a web-based platform that aims to automate and simplify the typical steps required for QSAR modeling.
• JME-JME Molecular Editor is a Java applet which allows to draw / edit molecules and reactions (including generation of substructure queries) and to depict molecules directly within an HTML page.
• CORINA-Converter form 2D (Smiles) structures to 3D structures
• Enhanced NCI Database browser-The National Cancer Institute (NCI) database of more than 250,000 molecules.Some molecular descriptors are provided.
• PaDEL-Descriptor - based on CDK but includes additional 737 2D and 3D descriptors (NUS/Singapore).
• CDK-The Chemistry Development Kit (CDK) is a Java library for structural chemo- and bioinformatics.

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