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Structure. 2018 Apr 3;26(4):565-571.e3. doi: 10.1016/j.str.2018.02.009. Epub 2018 Mar 15.

Ranking Enzyme Structures in the PDB by Bound Ligand Similarity to Biological Substrates.

Author information

1
EMBL-EBI, Wellcome Genome Campus, Hinxton CB10 1SD, UK. Electronic address: tyzack@ebi.ac.uk.
2
EMBL-EBI, Wellcome Genome Campus, Hinxton CB10 1SD, UK.

Abstract

There are numerous applications that use the structures of protein-ligand complexes from the PDB, such as 3D pharmacophore identification, virtual screening, and fragment-based drug design. The structures underlying these applications are potentially much more informative if they contain biologically relevant bound ligands, with high similarity to the cognate ligands. We present a study of ligand-enzyme complexes that compares the similarity of bound and cognate ligands, enabling the best matches to be identified. We calculate the molecular similarity scores using a method called PARITY (proportion of atoms residing in identical topology), which can conveniently be combined to give a similarity score for all cognate reactants or products in the reaction. Thus, we generate a rank-ordered list of related PDB structures, according to the biological similarity of the ligands bound in the structures.

KEYWORDS:

PDB; biological; bound; cognate; enzyme; ligand; native; relevance; similarity

PMID:
29551288
PMCID:
PMC5890617
DOI:
10.1016/j.str.2018.02.009
[Indexed for MEDLINE]
Free PMC Article

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