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 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 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) 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.
A short video introduction:
alvaDesc is also available as:
- a set of KNIME nodes. Please check the alvaDesc KNIME Plugin page for more information.
- a Python module. Please check the alvaDescCLIWrapper page for more information.
BMFpred tool uses alvaDesc technology for the calculation of molecular descriptors included in the models for the estimation of fish Biomagnification Factor (BMF) of chemicals.