LiSiCA

LiSiCA{x86|x64}.exe -R <path to reference molecule> -T <path to target molecules> [parameters]

./lisica -R <path to reference molecule> -T <path to target molecules> [parameters]

Both the reference and the target compound files must be in the Tripos mol2 format. Alternatively, the target database file can be a mol2 file compressed with gzip [mol2.gz]. The LiSiCA similarity search depends on comparing SYBYL atom types (e.g., C.2, C.3, O.3), therefore this data must me present in the fifth column. The reference file should contain only one (reference) compound; the target file may contain many compounds. If the reference file contains more than one compound, the first molecule is used as a reference. Molecules in the target file having the same name (the line after the "@<TRIPOS>MOLECULE" line) are considered as different conformers of the same molecule. Only the best-scoring (by Tanimoto coefficient) conformer will be shown by default in the final output for the 3D screening option. To save the final output (ranked list by Tanimoto coefficient) to a file in Linux, use the bash standard output redirection function (see examples below).

The -d option tells LiSiCA which screening option to use. The 2D option is based on finding similarities between ligands which have the same (-s option = 0) or similar (-s option > 0) number of covalent bond between the same type of atoms. Accordingly, the 3D option is based on finding similarities between ligands where spatial distance between the same type of atoms is similar (or the same if the -m option = 0.0).

The -m option corresponds to the maximum allowed difference in spatial distances between atoms of the two compared product graph vertices. Lesser values correspond to a more rigorous screening. This option can only be used in combination with the -d 3 (3D screening option) option.

The -s option corresponds to the maximum allowed difference in shortest-path lengths between atoms of the two compared product graph vertices. Lesser values correspond to a more rigorous screening. This option can only be used in combination with the -d 2 (2D screening) option.

If the -w option is set to a value higher than 0, LiSiCA will create mol2 files of the highest scoring target molecules with a comment section at the end of the file where the matching atom pairs are displayed.

The -c option corresponds to the maximum number of outputted files of one molecule in different conformations.

The -h option lets the user choose if the hydrogen atoms are to be considered for the calculation of the similarity using the maximum clique algorithm. By default, hydrogen atoms are not considered in finding the largest substructure common to the reference and target molecules, so as to obtain faster results.