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 Yes

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 Yes

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Publications for Ligand Interacting Site Enriched

LISE in publications

 (3)
PMCID: 5020399
PMID: 27619067
DOI: 10.1038/srep33232

[…] methods, and then, the predicted ligand-binding site is determined according to the conservation of the residues in the cavity (e.g., ligsite-csc, surfnet-consurf, galaxysite, concavity, and lise). meta-pocket 1.0 and 2.0 (mpk1 and mpk2) combine the results of many methods to improve the prediction result., to identify a potential ligand-binding site, soga et al. developed an index known […]

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

[…] 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 […]

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

[…] 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 4, despite the fact that three well-defined pockets were found in bacillus subtilis yuei protein, the homologue structurally resolved closest to spr1035, the lack […]


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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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