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LISE specifications

Information


Unique identifier OMICS_04158
Name LISE
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

Information


Unique identifier OMICS_04158
Name LISE
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

 (4)
library_books

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

2016
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 http://lise.ibms.sinica.edu.tw, and PSI-BLAST was used to compute the PSSM files. The newest non-redundant protein sequence databases (04/23/2016) required by PSI-BL […]

library_books

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

2016
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 […]

library_books

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

2015
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 […]

library_books

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

2014
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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