LigASite statistics

Tool stats & trends

Looking to identify usage trends or leading experts?

LigASite specifications

Information


Unique identifier OMICS_08413
Name LigASite
Alternative name LIGand Attachment SITE
Restrictions to use None
Maintained No

Maintainer


This tool is not available anymore.

Publication for LIGand Attachment SITE

LigASite citations

 (5)
library_books

Target Prediction for an Open Access Set of Compounds Active against Mycobacterium tuberculosis

2013
PLoS Comput Biol
PMCID: 3789770
PMID: 24098102
DOI: 10.1371/journal.pcbi.1003253

[…] developed a new Random Forest classifier (RFS), which was trained with a dataset of “similar” and “non-similar” ligands. Two ligands were similar if they bind the same binding site as defined by the LigASite database, a gold-standard dataset of biologically relevant binding sites in protein structures . To avoid overestimation in the validation of our approach, all ligands in the database that we […]

library_books

Identification of Nucleotide Binding Sites in Protein Structures: A Novel Approach Based on Nucleotide Modularity

2012
PLoS One
PMCID: 3507729
PMID: 23209685
DOI: 10.1371/journal.pone.0050240

[…] to the removal of 115 structures reducing the size of the dataset to 924 nucleotide-binding protein structures (the complete list is provided in ).The second dataset is composed of proteins from the LigASite database that bind nucleotides and that have been crystallized in both their apo and holo forms. The LigASite database contains 391 non-redundant pairs of proteins (January 2012 release). Th […]

library_books

Identification of binding pockets in protein structures using a knowledge based potential derived from local structural similarities

2012
BMC Bioinformatics
PMCID: 3434446
PMID: 22536963
DOI: 10.1186/1471-2105-13-S4-S17

[…] gn a propensity value to each amino acid in the query structure. We optimized the score threshold on the training set of 1356 proteins using a leave-one-out procedure, and then tested PDBinder on the LigASite dataset, which comprises 239 apo/holo structure pairs.We obtained an MCC of 0.313 on the holo set, with a PPV of 0.413. Interestingly the performance on apo structures is quite similar to the […]

library_books

Phosphate binding sites identification in protein structures

2010
Nucleic Acids Res
PMCID: 3045618
PMID: 20974634
DOI: 10.1093/nar/gkq987

[…] To test the method we created a high-quality non-redundant test set, described in detail in the ‘Materials and Methods’ section. This data set was derived from the LigASite database () and consists of 52 proteins that bind ligands containing at least one phosphate group. Each protein was crystallized both in its apo and holo form.We applied Pfinder to the 52 hol […]

library_books

Analysis of substructural variation in families of enzymatic proteins with applications to protein function prediction

2010
BMC Bioinformatics
PMCID: 2885373
PMID: 20459833
DOI: 10.1186/1471-2105-11-242

[…] ], FEATURE [], FLORA []), computational scanning mutagenesis (SNAP []), evolutionary analysis (ET [], ConSurf []), expert knowledge (CSA []), and automatically curated databases (LigBase [], SFLD [], LigASite []). Substructures identified by these methods can be computationally represented, either in full or in part, by motifs that model both the geometric and physico-chemical properties of a give […]

Citations

Looking to check out a full list of citations?

LigASite institution(s)
Center for Structural Biology and Bioinformatics, Université Libre de Bruxelles (U L B), Bld du Triomphe, Bruxelles, Belgium

LigASite reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review LigASite