4D Bioavailability (4DBA) Calculation¶

The bioavailability of compounds can be evaluated using 4D Bioavalability (4DBA) scores. Compounds with higher 4DBA scores are more likely to have oral drug-like characteristics. More details can be found in reference [26]. The 4DBA scores may facilitate lead optimization studies by indicating which compounds should be prioritized for chemical synthesis and biological testing.

The 4DBA score is calculated using four descriptors:

  1. MW (Molecular Weight)

  2. log P(o/w) (Logarithm of the octanol-water partition coefficient)

  3. HDO (Number of hydrogen bond donors)

  4. HAC (Number of hydrogen acceptors)

The SilcsBio software provides a utility through the command line interface (CLI) to calculate the four descriptors (MW, log P(o/w), HDO, HAC) and 4DBA scores. The 4DBA score can be calculated using the following command:

python $SILCSBIODIR/utils/python/calc_4dba.py --database <ligand SD file> --method <method for descriptors>

The calc_4dba.py code requires the following arguments:

  • Database of compounds in SD file format:

    --database <ligand SD file>

    The four descriptors and 4DBA scores will be calculated for all ligands in the SD file.

  • Method used to calculate the descriptors (optional):

    --method <method for descriptors; rdkit or moe; default=rdkit>

    Using the --method rdkit option will use RDKit to calculate the descriptors. By default the method will be set to rdkit.

    Using the --method moe option will use MOE to calculate the descriptors. This requires that the database provided in sdf format has been saved using MOE after calculating the descriptors.

  • Output file name (optional):

    --output <output file name; default=lgfe-4dba.csv>

    The output is a CSV file with the 4DBA score for each compound in the database. By default the output file name will be lgfe-4dba.csv.