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

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.

SUBMITTER: Tyzack JD

PROVIDER: S-EPMC5890617 | biostudies-literature | 2018 Apr

REPOSITORIES: biostudies-literature

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

Tyzack Jonathan D JD Fernando Laurent L Ribeiro Antonio J M AJM Borkakoti Neera N Thornton Janet M JM

Structure (London, England : 1993) 20180315 4

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 matche ...[more]

PMID: 29551288

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Dataset Information

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

Publications

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

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