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ProBiS-ligands specifications

Information


Unique identifier OMICS_04130
Name ProBiS-ligands
Interface Web user interface
Restrictions to use None
Input data One protein structure or binding site
Input format PDB
Output data Ligand 3D Viewer and a table with predicted small-molecule ligands clustered according to their predicted location on the query protein and transposed from different binding sites
Computer skills Basic
Stability Stable
Maintained Yes

Documentation


Publication for ProBiS-ligands

ProBiS-ligands citations

 (3)
library_books

Protein ligand specific binding residue predictions by an ensemble classifier

2016
BMC Bioinformatics
PMCID: 5114821
PMID: 27855637
DOI: 10.1186/s12859-016-1348-3

[…] ically and structurally different. The assessment of binding site residue predictions in CASP9 [] suggests that the assessment should be made according to the chemo-type categories of the ligand. The ProBiS-ligands server [] predicts the types of ligands that can be bound to a given structure. Recently, researchers have paid attention to the differences in ligands, and many ligand-specific methods […]

library_books

Identification of Ecdysone Hormone Receptor Agonists as a Therapeutic Approach for Treating Filarial Infections

2016
PLoS Negl Trop Dis
PMCID: 4907521
PMID: 27300294
DOI: 10.1371/journal.pntd.0004772

[…] for these 25 compounds are shown in . Of particular note, two compounds found to be active were isolated without using the ligand’s structural information (i.e., were obtained via ProBis CHARMMing / ProBis Ligands). Out of these 25 compounds, four (AM580, BMS493, 22-R-Hydroxycholesterol, TTNPB) were commercially available. When tested on the cell-based assay, AM580 and BMS493 were active agonists […]

library_books

Modeling enzyme ligand binding in drug discovery

2015
J Cheminform
PMCID: 4594084
PMID: 26457119
DOI: 10.1186/s13321-015-0096-0

[…] lar range (for dihydropholate reductase from E.coli and two mammalian protein tyrosine phosphatases).Also a recently developed, freely-available web server, which enables ligand homology modeling, is ProBiS-ligands (Fig. ) [], a method that uses a fast maximum clique algorithm [] to screen the non-redundant PDB database, to find structurally similar target binding sites to user provided input quer […]


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ProBiS-ligands institution(s)
National Institute of Chemistry, Ljubljana, Slovenia; University of Primorska, Faculty of Mathematics, Natural Sciences and Information Technologies, Koper, Slovenia
ProBiS-ligands funding source(s)
This project was funded by the Ministry of Higher Education, Science and Technology of Slovenia and the Slovenian Research Agency [P1-0002, J1-5455].

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