alvaDesc 2.0

alvaDesc is the next generation tool for the calculation of a wide range of molecular descriptors and a number of molecular fingerprints. It calculates more than 5000 descriptors independent of 3-dimensional information such as constitutional, topological, pharmacophore. It includes ETA and Atom-type E-state indices together with functional groups and fragment counts. Additionally, alvaDesc implements an extensive number of 3-dimensional descriptors such as 3D-autocorrelation, Weighted Holistic Invariant Molecular descriptors (WHIM) and GETAWAY. If needed, alvaDesc can calculate partial charges using the Gasteiger’s “Partial Equalization of Orbital Electronegativity” (PEOE).

alvaDesc provides the calculation of several model-based physicochemical properties such as molar refractivity, topological polar surface area (TPSA), molecular volume estimations, three LogP models (Moriguchi, Ghose-Chippen and Wildmann-Crippen octanol-water partition coefficient), a LogP consensus model (LOGPcons) and a LogS aqueous solubility model (ESOL). In order to get a quantitative estimation of synthetic accessibility of molecules, alvaDesc includes the synthetic accessibility score of drug-like molecules (SAscore).

There is a significative list of drug-like and lead-like alerts including the well-known Lipinski alert index. Considering the importance of drug-likeness when selecting compounds in the early stages of drug discovery, alvaDesc includes the calculation of the quantitative estimate of drug-likeness (QED).

alvaDesc carries out the calculation of MACCS166 fingerprint, Extended Connectivity Fingerprint (ECFP) and Path Fingerprint (PFP) and allows the customisation and calculation of the most used hashed molecular fingerprints. The calculation of hashed fingerprints can be tuned not only with respect to the fingerprint size, fragment type and dimensions but even by defining atom and bond parameters considered during fragment identifications (e.g. atom type, aromaticity, the number of attached hydrogen atoms, connectivity). alvaDesc provides the fragments identified during fingerprint calculation as SMARTS strings (SMARTS is a line notation developed by Daylight Chemical Information Systems for representing molecular substructures).

One of the most innovative features of alvaDesc is its capability to handle both full-connected and non-full-connected molecular structures, such as salts and ionic liquids. All of the molecular descriptor calculation algorithms provide different theoretical approaches for the calculation of molecular descriptors on such structures.

alvaDesc provides different tools to carry out a first exploration of your molecular dataset:

  • molecule structure verification using PubChem services
  • molecule structure visualisation and filtering
  • Principal Component Analysis (PCA), t-SNE and correlation analysis

Due to its capability of calculating large numbers of molecular descriptors, alvaDesc provides variable reduction tools, including the fast V-WSP method (variable reduction method adapted from space-filling designs).

Software Type
Standalone application with Graphical User Interface and Command Line version.
The software is 64 bit and it's available for Windows, Linux and macOS.
Academic and commercial licenses are available with different options. Check the underlying section for more details.

alvaDesc can be purchased on our website and the software is delivered by a safe download procedure. Contact us by email or with the form below, to request a quotation or for further details about licensing/pricing schemes.

alvaDesc is available with academic or commercial licenses.

Academic licenses are provided to universities and research institutions, under such licenses alvaDesc can be used for any research from which any resulting intellectual property remains in the public domain, but any commercial use is forbidden. Academic licenses are permanent, and the user has no access to any major software update, and access to minor updates only for the first year.

Commercial licenses are provided as rent licenses with two options:

  • Single: the software can be installed only on a single computer.
  • Site: the software can be installed on any computer at a specific research site.

Contact us for further details on licenses.

alvaDesc calculates 5,666 molecular descriptors, organized in different logical blocks. Blocks are further divided into sub-blocks to make management, selection, and analysis of descriptors easier. The complete list of all calculated descriptors is also available.