alvaDesc is the next generation tool for the calculation of a wide range of molecular descriptors and a number of molecular fingerprints. Specifically it calculates almost 4000 descriptors independent of 3-dimensional information such as constitutional, topological, phamacophore. 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.

alvaDesc

alvaDesc provides the calculation of several model-based physicochemical properties such as molar refractivity, topological polar surface area (TPSA), molecular volume estimations, two LogP models (Moriguchi and Ghose-Chippen octanol-water partition coefficient). There is a significative list of drug-like and lead-like alerts including the well-known Lipinski alert index.

alvaDesc carries out the calculation of MACCS166 fingerprint, Extended Connectivity Fingerprint and Path Fingerprint 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 fragment 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) 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) proposed in "Ballabio, D., Consonni, V., Mauri, A., Claeys-Bruno, M., Sergent, M., & Todeschini, R. (2014). A novel variable reduction method adapted from space-filling designs. CHEMOMETRICS AND INTELLIGENT LABORATORY SYSTEMS, 136, 147-154".

The software is available for Windows, Linux and macOS platforms and it is provided both as an easy to use command line tool and as an intuitive graphical interface.

ALVADESC 1.0

Software type
Standalone application for Windows, Linux and MacOS platforms

Requirements
Supported platforms: Microsoft Windows (7 or above), Linux (Ubuntu 14.04 or above, Fedora 29 or above), macOS Sierra (10.12 or above).

License
Academic and commercial licenses are available with different options. Check the underlying section for more details.

How to get it
Ask a quotation from your private area (requires registration) or contact us directly by email. The purchased software is delivered by a safe download procedure from our website.

alvaDesc 1.0 calculates 5,305 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 5,305 calculated descriptors is also available.

alvaDesc 1.0 provides the calculation of hashed molecular fingerprints. It calculates path based and extended connectivity fingerprints (ECFP). Path based fingerprints are generated identifying all linear paths of the molecule while ECFP are generated exhaustively identifying all circular fragments grown radially from each heavy atom of the molecule. Both fingerprint types are calculated defining a set of options like the fingerprint size, the minimum and maximum length of the identified fragments and an extensive list of atom properties to be considered in order to differentiate fragments (e.g. atom type, aromaticity, formal charge, connectivity and bond order). The full customization of fingerprints allows to obtain the most suitable solutions for any task (modelling, similarity screening etc.).

alvaDesc 1.0 also includes its implementation of MACCS 166 fingerprint. MACCS 166 fingerprint is a fixed size structural key comprising a dictionary of 166 well-defined molecular features, every bit of the fingerprint indicates the presence or absence of a specific molecular feature.

alvaDesc 1.0 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 or request a quotation in your private area for further details on licenses.

alvaDesc can be purchased on our website (payment by bank transfer or directly on-line with credit cards) and the software is delivered by a safe download procedure. Please register on our website and log in, a form for quotation request is available in your private area. If you wish you can contact us directly by email to request a quotation or further details about licensing/pricing schemes.