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Publication for LigBase
Neighborhood Properties Are Important Determinants of Temperature Sensitive Mutations
[…] 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 […]
Analysis of substructural variation in families of enzymatic proteins with applications to protein function prediction
[…] 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 […]
A Kernel for Open Source Drug Discovery in Tropical Diseases
[…] 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 […]
Structural descriptor database: a new tool for sequence based functional site prediction
[…] 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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