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Table 6 Main features of commonly used tools for molecular descriptors (MDs) calculations

From: QuBiLS-MAS, open source multi-platform software for atom- and bond-based topological (2D) and chiral (2.5D) algebraic molecular descriptors computations

Software Number of types of MDs Configuration of MDs parameters Advantages Disadvantages Additional remarks and online reference
QuBiLS-MAS v1.0 2080 (linear, quadratic and bilinear) 1. Atom- or Bond-Based 1. Computes MDs based on algebraic maps 1. Only accepts MDL files (MOL or SDF) as input formats 1. Uses CDK to read molecular files and calculate atomic properties
   2. Atomic properties 2. 10 atom weighting schemes   2. Requires Java JRE 1.7 or above http://www.tomocomd.com
   3. Local-fragments 3. Graphic user-friendly interface and command-line interface   
   4. Matrix approaches 4. Platform-independency   
   5. Aggregation operators 5. Supports any organic molecules   
   6. Add (or remove) hydrogen atoms 6. Free download and support   
   7. Consider lone-pair electrons 7. Batch mode processing   
    8. Data cleaning module   
    9. Parallel processing   
PaDEL-Descriptor v2.0 43 None 1. Graphic user interface 1. One functionality for data cleaning tasks (remove salts) 1. Uses CDK to read molecular files and calculate most of the descriptors and fingerprints
    2. Fully cross-platform 2. No MDs batch processing 2. Employs Java Web Start technology
    3. Command line interface   
    4. Free and Open Source   
    5. Accepts multiple file formats (>90 formats)   
    6. Parallel processing   
DRAGON v6.0 29 1. Predefined atom weighting schemes 1. Graphic user-friendly interface 1. Only Windows and Linux platforms Academic permanent license: 900 euros (to be installed on 3 PCs)
   2. Selection of single molecular descriptors included in the different blocks 2. Command line interface 2. No parallel processing http://www.talete.mi.it/products/dragon_description.htm
    3. Batch mode processing 3. No data cleaning functionalities  
    4. Supports any organic molecules 4. Does not allow selection of local-fragments  
    5. Accepts the formats: MDL, Sybyl, HyperChem, Macromodel, Smiles, CML and HyperChem 5. Commercial cost  
CDK Descriptor Calculator v1.3.9 48 1. Add (or remove) hydrogen atom 1. Graphic user interface 1. Only accepts MDL files (MOL or SDF) as input formats Use CDK library and requires JRE 1.6
    2. Command line execution 2. No data cleaning functionalities http://www.rguha.net/code/java/cdkdesc.html
    3. Fully cross-platform 3. Does not allow selection of local-fragments  
    4. Free software 4. Does not allow selection of atom weighting schemes  
    5. Batch mode processing   
BlueDesc 36 None 1. Free and Open Source 1. No graphic user interface Use CDK and JOELib2 library and requires Java JRE 1.6
    2. Fully cross-platform 2. Only accepts MDL files (MOL or SDF) as input formats http://www.ra.cs.uni-tuebingen.de/software/bluedesc/welcome_e.html
     3. No parallel processing  
     4. No data cleaning functionalities  
     5. Does not allow selection of local-fragments  
     6. Does not allow selection of atom weighting schemes  
Model 98 None 1. Web-based graphic user interface 1. No parallel processing Use of MODEL for commercial purposes is not allowed
    2. Accepts the formats: PDB, MDL, MOL2,COR 2. No data cleaning tasks http://jing.cz3.nus.edu.sg/cgi-bin/model/model.cgi
     3. Does not allow selection of local-fragments  
     4. Does not allow selection of atom weighting schemes  
     5. For academic purposes only  
Mol2 20 None 1. Command line interface 1. No graphic user interface http://www.fda.gov/ScienceResearch/BioinformaticsTools/Mold2/ucm144528.htm
    2. Free of charge download request 2. Only Windows platform  
     3. Only accepts SDfile format  
     4. No parallel processing  
     5. No data cleaning functionalities  
     6. Does not allow selection of local-fragments  
     7. Does not allow selection of atom weighting schemes  
MOE None 1. Graphic user interface 1. Only accepts SDfile format http://www.chemcomp.com/MOE-Cheminformatics_and_QSAR.htm
    2. Command line interface 2. No parallel processing  
    3. Data cleaning tasks 3. Does not allow selection of local-fragment  
    4. Fully cross-platform 4. Does not allow selection of atom weighting schemes  
VolSurf 22 None 1. Graphic user interface 1. Commercial http://www.moldiscovery.com/soft_volsurf.php
    2. Command line interface 2. Only Linux platform  
    3. Accepts several formats: MDL SDF, Sybyl, Mol2, Multi Mol2, GRID kout 3. Only compute 2D MDs  
     4. No parallel processing  
     5. Does not allow selection of local-fragment  
     6. Does not allow selection of atom weighting schemes  
Adriana. Code 5 None 1. Graphic user interface 1. Commercial A demo version is available on request free of charge
    2. Command line interface 2. Only Windows and Linux platforms http://www.molecular-networks.com/products/adrianacode
    3. Batch mode processing 3. No parallel processing  
    4. Accepts any organic molecule 4. No data cleaning functionalities  
    5. Several input and output formats 5. Does not allow selection of local-fragment  
     6. Does not allow selection of atom weighting schemes  
CODESSA PRO 8 None 1. Graphic user interface 1. Commercial http://www.codessa-pro.com/
     2. Only for Windows platform  
     3. No parallel processing  
     4. No batch mode processing  
     5. Does not allow selection of local-fragment  
     6. Does not allow selection of atom weighting schemes  
PowerMV None 1. Graphic user interface 1. Only for Windows platform Requires Microsoft.Net 1.1 or above
     2. No parallel processing http://nisla05.niss.org/PowerMV
     3. No batch mode processing  
     4. Does not allow selection of local-fragment  
     5. Does not allow selection of atom weighting schemes  
Molconn-Z v4.10 79   Multi-platform SGI Irix, Linux, Solaris, Mac OS-X and Windows. 12 months free Support No GUI, Commercial Minimum price US$750 for a Single Educational Node/User license
      http://www.edusoft-lc.com/molconn
Pre ADMET Descriptor 34   GUI, Free web-based Limited application and Commercial PC version. Maintenance and Upgrade free of charge Commercial. Runs on Windows. Only accepts MDL files (MOL or SDF) as input formats Requires Microsoft.NET Framework 2.0 and minimum price is US$1 000 for 1 year Academic license
      http://preadmet.bmdrc.org
Toxicity Estimation Software Tool (T.E.S.T.) v4.1 13 (628)   GUI, Open source and multi-platform Platform specific distributions. Only accepts MOL or SMILES as input formats Based on CDK library. Requires Java JRE 1.6
      http://www.epa.gov/ordntrnt/ORD/NRMRL/std/qsar/qsar.html
ADAPT 27   Non-Commercial Runs on Unix. Heavy-atom limitations up to 255 atoms. Only accepts MOL as input formats Written in Fortran and is installed on a DEC alpha workstation
      http://research.chem.psu.edu/pcjgroup/adapt.html
ChemAxon Calculator Plugins v5.11 12 27 Free for non-commercial, freely accessible web pages s http://www.chemaxon.com/marvin/help/calculations/calculator-plugins.html
    GUI, Batch execution from command line   
    Multi-platform Windows, HP, MacOS X, Solaris and Linux   
JOELib2   40 Free, Open Source, Redistributable. Multi-platform   http://www.ra.cs.uni-tuebingen.de/software/joelib/introduction.html
TOPS-MODE & MODes Lab   Several (mainly edge-based) topological indices GUI Runs on Windows http://www.modeslab.com/
    Non-Commercial No Batch execution