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