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LISE specifications


Unique identifier OMICS_04158
Alternative name Ligand Interacting Site Enriched
Interface Web user interface
Restrictions to use Academic or non-commercial use
Input data A PDB ID
Input format PDB
Output data 3 predicted sites (3 groups of grids) and 10 predicted sites (10 representing points) are available for presentation and download.
Computer skills Basic
Stability Stable
Maintained No


Unique identifier OMICS_04158
Alternative name Ligand Interacting Site Enriched
Software type Application/Script
Interface Command line interface
Restrictions to use Academic or non-commercial use
Input data A PDB ID or a protein structure
Input format PDB
Output data Predicted ligand binding sites
Output format PDB
Operating system Unix/Linux, Mac OS
Programming languages Perl
Computer skills Advanced
Version 3.0
Stability Stable
Maintained No




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Publications for Ligand Interacting Site Enriched

LISE citations


Improving the performance of the PLB index for ligand binding site prediction using dihedral angles and the solvent accessible surface area

Sci Rep
PMCID: 5020399
PMID: 27619067
DOI: 10.1038/srep33232

[…] Python scripts, which are shown in Tables S1, S2, and S3, to upload the pdb files, set the parameters from the three above-mentioned web servers and download the prediction results automatically. The LISE Perl script was obtained from, and PSI-BLAST was used to compute the PSSM files. The newest non-redundant protein sequence databases (04/23/2016) required by PSI-BL […]


Predicting Ligand Binding Sites on Protein Surfaces by 3 Dimensional Probability Density Distributions of Interacting Atoms

PLoS One
PMCID: 4981321
PMID: 27513851
DOI: 10.1371/journal.pone.0160315

[…] mmarized in – Tables respectively. compares the success rate for top 1 predicted site by ISMBLab-LIG with other methods for S48b and S48ub sets. ISMBLab-LIG’s performance (85%) was second to that of LISE (92%) in S48b and equal to VICE and MPK2, and was equally top with VICE (83%) in S48ub [, , ]. In the S210 testing set (), the success rate of ISMBLab-LIG is 84%, which ranks as the first among 9 […]


Proteins and Their Interacting Partners: An Introduction to Protein–Ligand Binding Site Prediction Methods

Int J Mol Sci
PMCID: 4691145
PMID: 26694353
DOI: 10.3390/ijms161226202

[…] predict the location of the ligand binding site and/or the putative ligand binding site residues. Such methods can be further sub-categorised into: 1. Geometric-based methods (FINDSITE [], LigDig [], LISE [], PatchSurfer2.0 [], Surflex-PSIM [], EvolutionaryTrace [], PRANK [], a Two-dimensional replica-exchange method [], FMO-RESP [], MapReduce approach [], TIFP [], ProGolem [], a Chemogenomics app […]


Inspecting the potential physiological and biomedical value of 44 conserved uncharacterised proteins of Streptococcus pneumoniae

BMC Genomics
PMCID: 4143570
PMID: 25096389
DOI: 10.1186/1471-2164-15-652

[…] tructures, and the different chemical properties of their natural ligands, a consensus of nine independent strategies was used: the seven algorithms of Metapocket 2.0 [], and the DoGSiteScorer [] and LISE [] algorithms (Figure B).Figure 4Despite the fact that three well-defined pockets were found in Bacillus subtilis YueI protein, the homologue structurally resolved closest to Spr1035, the lack of […]

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LISE institution(s)
Institute of Biomedical Informatics, National Yang-Ming University, Taipei, Taiwan; Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
LISE funding source(s)
Support for this project (NSC 96-2627-B-001-004) and a post-doctoral research fellowship (NSC 100-2811-B- 001-067) were provided by the National Science Council of Taiwan

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