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LigBase specifications

Information


Unique identifier OMICS_05437
Name LigBase
Restrictions to use None
Maintained Yes

Publication for LigBase

LigBase citations

 (4)
call_split

Neighborhood Properties Are Important Determinants of Temperature Sensitive Mutations

2011
PLoS One
PMCID: 3229608
PMID: 22164302
DOI: 10.1371/journal.pone.0028507
call_split See protocol

[…] tant residues , , . A binary feature was developed to assess whether the wild type or mutant residue was buried and charged . Residues involved in ligand binding were identified from three databases: LigBase, ModBase, and PDBsum , , . We also developed features to examine the relationship between mutation site and the secondary structure. Thermal factor measures residue rigidity. We calculated the […]

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

[…] pproach to further analyze and understand the role of these substructures. In future work, several substructure selection methods and databases, such as CASTp, ET [], ConSurf [], CSA [], SNAP [], and LigBase [], will be used as sources for large numbers of motifs. This work used only residues deemed to be functionally important by experimentalists, as defined by literature references, in order to […]

library_books

A Kernel for Open Source Drug Discovery in Tropical Diseases

2009
PLoS Negl Trop Dis
PMCID: 2667270
PMID: 19381286
DOI: 10.1371/journal.pntd.0000418

[…] alignments generated by an all-against-all comparison of known protein structures, was used to identify structure relationships between our modeling templates and other known protein structures; (iv) LigBase , which contains 232,852 structurally defined ligand-binding sites in PDB, was used as a resource for AnnoLyze to predict ligand binding sites on pathogen protein models; (v) MSDChem , which c […]

library_books

Structural descriptor database: a new tool for sequence based functional site prediction

2008
BMC Bioinformatics
PMCID: 2612011
PMID: 19032768
DOI: 10.1186/1471-2105-9-492

[…] iscovery development [].Protein-ligand interactions can be solved by assessing the co-crystallized ligand structure. Nowadays, there are several applications for this purpose. One such application is LigBase [], a 3D ligand-binding database derived from the Protein Data Bank (PDB) []. In LigBase, a ligand-binding site is an amino acid with at least one atom within 5 Å from a ligand atom. There are […]

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LigBase institution(s)
Laboratories of Molecular Biophysics, Pels Family Center for Biochemistry and Structural Biology, The Rockefeller University, New York, NY, USA

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