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LiSiCA specifications


Unique identifier OMICS_24925
Name LiSiCA
Alternative name Ligand Similarity using Clique Algorithm
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input data A reference and the target compound files.
Input format MOL2
Operating system Unix/Linux, Mac OS, Windows
Computer skills Advanced
Version 1.0.1
Stability Stable
Source code URL
Maintained Yes




No version available


  • person_outline Dusanka Janezic
  • person_outline Janez Konc

Publication for Ligand Similarity using Clique Algorithm

LiSiCA citations


BoBER: web interface to the base of bioisosterically exchangeable replacements

J Cheminform
PMCID: 5727005
PMID: 29234984
DOI: 10.1186/s13321-017-0251-x

[…] lead structures. We showed how the BoBER web server could be used on an inhibitor of MurF enzyme. In the future, the BoBER approach will be implemented in the ligand-based virtual screening software LiSiCA [] to enable searching databases for similar ligands not only on the basis of atom type similarity but also based on possible bioisosteric or scaffold hopping replacements. […]


Trypanocidal Effect of Isotretinoin through the Inhibition of Polyamine and Amino Acid Transporters in Trypanosoma cruzi

PLoS Negl Trop Dis
PMCID: 5371382
PMID: 28306713
DOI: 10.1371/journal.pntd.0005472

[…] earching in a database that comprises a total of 2924 worldwide commercially available drugs and nutraceuticals approved by U.S. Food and Drug Administration (FDA). This screening was performed using LiSiCA v1.0 (Ligand Similarity using Clique Algorithm) software [], and similarities were expressed using the Tanimoto coefficient []. The structural data of compounds retrieved from similarity screen […]


Ligand based virtual screening interface between PyMOL and LiSiCA

J Cheminform
PMCID: 5013575
PMID: 27606012
DOI: 10.1186/s13321-016-0157-z
call_split See protocol

[…] The general requirement for the LiSiCA plugin is an installed PyMOL program (version >1.4) with plugin support. LiSiCA software executable used by the plugin runs under Linux and Windows operating systems. The plugin uses the native […]


Direct Characterization of Transcription Elongation by RNA Polymerase I

PLoS One
PMCID: 4959687
PMID: 27455049
DOI: 10.1371/journal.pone.0159527

[…] In this experimental setup, both our measurement and the estimate by Viktorovskaya et al. [] yield an in vitro average elongation rate of 18–20 nt/s. A recent in vitro study using optical tweezers by Lisica et al. [] reported, instead, a similar average and maximum elongation rate (~32 nt/s and ~39 nt/s, respectively). Their experimental conditions differed from those used in our work in that they […]


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LiSiCA institution(s)
National Institute of Chemistry, Ljubljana, Slovenia; Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, Koper, Slovenia; Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia

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