alvaMolecule is a software tool to visualise, analyse, curate and standardize your molecular dataset. alvaMolecule is free for academic and non-commercial use. alvaMolecule is conceived as a molecular worksheet where molecular datasets can be visualised both as a molecule grid or as a spreadsheet; additional data provided within SMILES and MDL files is automatically imported and can be used to sort and filter the molecular dataset, as well as using the calculated descriptors and physicochemical properties.

alvaMolecule provides 10 predefined checkers that can help the identification of erroneous structure or for filtering specific structural feature:

  • Multiple structures
  • Unusual valence
  • Covalent/Ionic bond
  • Total charge
  • Isotope
  • Charged atom
  • None carbon atoms
  • Non-standard atom set (H,C,N,O,P,S,F,Cl,Br,I)
  • Aromaticity
  • Radical atom

Additionally, alvaMolecule provides the molecule structure verification using PubChem services. alvaMolecule provides 12 predefined standardizers that can be used to fix erroneous representation of molecules, to remove specific features from molecules or to standardize specific structural features:

  • Convert unusual covalent bonds to ionic bonds
  • Add charge to quaternary nitrogen
  • Remove exceeding hydrogens
  • Add missing hydrogens
  • Remove monoatomic fragments
  • Retain biggest fragment
  • Standardize nitro group
  • Standardize azide group
  • Standardize diazo group
  • Clear isotopes
  • Clear chirality
  • Clear bond direction

alvaMolecule calculates 88 molecular descriptors and physicochemical properties. Specifically alvaMolecule calculates a wide set of structural descriptors belonging to the constitutional and ring descriptors as implemented in alvaDesc. Additionally, alvaMolecule calculates many physicochemical properties, drug-like and lead-like scores, among them alvaMolecule provides the calculation of several model-based physicochemical properties such as molar refractivity, topological polar surface area (TPSA), molecular volume estimations and two LogP models (Moriguchi and Ghose-Chippen octanol-water partition coefficient). There is a significative list of drug-like and lead-like scores including the well-known Lipinski alert index, that can be used to filter drug- and lead-like compounds.
You can sort and filter molecules using:

  • data loaded from molecule files
  • calculated molecular descriptors
  • calculated physicochemical properties
Software Type
Standalone application with Graphical User Interface
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.

alvaMolecule 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.

alvaMolecule 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.