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AlvaDesc is a software application for the calculation and analysis of molecular descriptors, fingerprints, and structural patterns. Developed by Alvascience, alvaDesc is widely used in cheminformatics and Quantitative Structure-Activity Relationship (QSAR) modeling to numerically describe molecular structures, aiding in chemical property prediction and machine learning applications.

Overview

Molecular descriptors and fingerprints serve as mathematical representations of chemical compounds, enabling computational models to predict properties such as bioactivity, toxicity, and solubility.

The software is used widely in drug discovery, materials science, and environmental chemistry, allowing researchers to process large chemical datasets, extract key molecular features, and integrate results into machine learning workflows.

Features

AlvaDesc supports the calculation of descriptors and fingerprints across multiple categories:

• 0D–3D molecular descriptors: including Constitutional indices, topological indices, connectivity indices, geometrical descriptors, pharmacophore descriptors, charge descriptors, and more.
• Molecular properties: including LogP (octanol-water partition coefficient), molar refractivity, polar surface area (PSA), solvent-accessible surface area (SASA), and hydrogen bond donors/acceptors.
• Molecular fingerprints: including MACCS keys, Extended Connectivity Fingerprints (ECFP), Path-based fingerprints.
• Descriptor analysis tools: including Principal Component Analysis (PCA), t-SNE analysis, correlation analysis, variable reduction.
• Support for disconnected structures: Handles salts, mixtures, ionic liquids, and metal complexes.
• Cross-platform compatibility: Available for Windows, macOS, and Linux, supporting both graphical user interface (GUI) and command-line interface (CLI).
• KNIME and Python integration: alvaDesc can be integrated into cheminformatics workflows using the KNIME analytics platform and Python scripting.

Scientific Contributions

AlvaDesc has been referenced in numerous peer-reviewed scientific publications, particularly in QSAR and Quantitative Structure-Property Relationship (QSPR) research

See also

• Molecular descriptor
• Topological index
• QSAR

References

1. Mauri, Andrea (2020). "alvaDesc: A Tool to Calculate and Analyze Molecular Descriptors and Fingerprints". Methods in Pharmacology and Toxicology. New York, NY: Springer US. pp. 801–820. doi:10.1007/978-1-0716-0150-1_32. ISBN 978-1-0716-0149-5. ISSN 1557-2153. S2CID 213896490.
2. Mauri, Andrea; Bertola, Matteo (2022). "Alvascience: A New Software Suite for the QSAR Workflow Applied to the Blood–Brain Barrier Permeability". International Journal of Molecular Sciences. 23 (12882): 12882. doi:10.3390/ijms232112882. PMC 9655980. PMID 36361669.
3. Todeschini, Roberto; Consonni, Viviana (2000). Handbook of Molecular Descriptors. Methods and Principles in Medicinal Chemistry. Wiley. doi:10.1002/9783527613106. ISBN 978-3-527-29913-3.

• Computational chemistry software
• Cheminformatics