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LiSiCA Software

lisica image
LiSiCA (Ligand Similarity using Clique Algorithm) is a ligand-based virtual screening software that searches for 2D and 3D similarities between a reference compound and a database of target compounds which should be represented in a Mol2 format. The similarities are expressed using the Tanimoto coefficients and the target compounds are ranked accordingly.

LiSiCA Command Line

Download the current version:

Example Input Files

Release Notes

1.0.1

  • Reads gzipped mol2 files (mol2.gz) for target molecules
Windows: No installation is required.
Linux: Mark the file as executable:
  1. chmod +x lisica

Linux from source: Unzip the source code, change the current directory to the 'lisica' folder and compile LiSiCA by typing 'make'.
  1. unzip lisica.zip
  2. cd lisica
  3. make

General Use

Windows:
  1. LiSiCA{x86|x64}.exe -R <path to reference molecule> -T <path to target molecules> [parameters]
Linux:
  1. ./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 "@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).

Input Parameters

LiSiCA uses the following optional parameters:
  • -n
    Description: number of CPU threads to use
    Default value: the default is to try to detect the number of CPUs and use all of them or, failing that, use 1
  • -d
    Description: product graph dimension
    Possible input: 2, 3
    Default value: 2
  • -m
    Description: maximum allowed atom spatial distance difference for the 3D product graph measured in angstroms
    Default value: 1.0
  • -s
    Description: maximum allowed shortest path difference for the 2D product graph measured in the number of covalent bonds between atoms
    Default value: 1
  • -h
    Description: consider hydrogens.
    Default value: False
  • -w
    Description: number of highest ranked molecules to write to output
    Default value: 0
  • -c
    Description: maximum allowed number of highest scoring conformations to be outputed
    Default value: 1
  • --help
    Description: print LiSiCA parameters

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.

Examples

  • 1. 2D screening with default options where the final results are saved to the results_2D.dat file:
  • ./lisica -R reference.mol2 -T database.mol2[.gz] > results_2D.dat

  • 2. 3D screening with default options where the final results are saved to the results_3D.dat:
  • ./lisica -R reference.mol2 -T database.mol2[.gz] -d 3 > results_3D.dat

  • 3. Rigorous 3D screening where results are send to the standard output only:
  • ./lisica -R reference.mol2 -T database.mol2[.gz] -d 3 -m 0.5

  • 4. 3D screening where 30 highest scoring target molecules are written in mol2 files with their matching atoms (to the ones in the reference molecule) displayed in the comment section of the mol2 file. Two mol2 files of the best scoring conformers for each molecule are allowed to be written.
  • ./lisica -R reference.mol2 -T database.mol2[.gz] -d 3 -w 30 -c 2

Related Publications

pdf S. Lesnik, T. Stular, B. Brus, D. Knez, S. Gobec, D. Janezic, J. Konc, LiSiCA: A Software for Ligand-Based Virtual Screening and Its Application for the Discovery of Butyrylcholinesterase Inhibitors, J. Chem. Inf. Model., 2015, 55, 1521–1528.
Lešnik, Samo, et al. "LiSiCA: A Software for Ligand-Based Virtual Screening and Its Application for the Discovery of Butyrylcholinesterase Inhibitors." Journal of chemical information and modeling 55.8 (2015): 1521-1528.
Lešnik, S., Štular, T., Brus, B., Knez, D., Gobec, S., Janežič, D., & Konc, J. (2015). LiSiCA: A Software for Ligand-Based Virtual Screening and Its Application for the Discovery of Butyrylcholinesterase Inhibitors. Journal of chemical information and modeling, 55(8), 1521-1528.
LEŠNIK, Samo, et al. LiSiCA: A Software for Ligand-Based Virtual Screening and Its Application for the Discovery of Butyrylcholinesterase Inhibitors. Journal of chemical information and modeling, 2015, 55.8: 1521-1528.
@article{lešnik2015lisica,
 title={LiSiCA: A Software for Ligand-Based Virtual Screening and Its Application for the Discovery of Butyrylcholinesterase Inhibitors},
 author={Lešnik, Samo and Štular, Tanja and Brus, Boris and Knez, Damijan and Gobec, Stanislav and Janežič, Dušanka and Konc, Janez},
 journal={Journal of chemical information and modeling},
 volume={55},
 number={8},
 pages={1521--1528},
 year={2015},
 publisher={ACS Publications}
}
%0 Journal Article
%T LiSiCA: A Software for Ligand-Based Virtual Screening and Its Application for the Discovery of Butyrylcholinesterase Inhibitors
%A Lešnik, Samo
%A Štular, Tanja
%A Brus, Boris
%A Knez, Damijan
%A Gobec, Stanislav
%A Janežič, Dušanka
%A Konc, Janez
%J Journal of chemical information and modeling
%V 55
%N 8
%P 1521-1528
%@ 1549-9596
%D 2015
%I ACS Publications
TY - JOUR
T1 - LiSiCA: A Software for Ligand-Based Virtual Screening and Its Application for the Discovery of Butyrylcholinesterase Inhibitors
A1 - Lešnik, Samo
A1 - Štular, Tanja
A1 - Brus, Boris
A1 - Knez, Damijan
A1 - Gobec, Stanislav
A1 - Janežič, Dušanka
A1 - Konc, Janez
JO - Journal of chemical information and modeling
VL - 55
IS - 8
SP - 1521
EP - 1528
SN - 1549-9596
Y1 - 2015
PB - ACS Publications
ER -