ArticleStructure (London, England : 1993)2018
Ranking Enzyme Structures in the PDB by Bound Ligand Similarity to Biological Substrates.
Article in Structure (London, England : 1993), 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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15 citing papers in PubMed.
- Methods for the establishment of enzymatic mechanisms - from QM to ML.Chemical science · 2026Review
- Atom-level enzyme active site scaffolding using RFdiffusion2.Nature methods · 2026Article
- Ten rules for a structural bioinformatic analysis.PLoS computational biology · 2025Article
- PDBe tools for an in-depth analysis of small molecules in the Protein Data Bank.Protein science : a publication of the Protein Society · 2025Article
- Design, synthesis, and pharmacological evaluation of indazole carboxamides of N-substituted pyrrole derivatives as soybean lipoxygenase inhibitors.Molecular diversity · 2024Article
- Large-scale annotation of biochemically relevant pockets and tunnels in cognate enzyme-ligand complexes.Journal of cheminformatics · 2024Article
- ChannelsDB 2.0: a comprehensive database of protein tunnels and pores in AlphaFold era.Nucleic acids research · 2024Article
- ProCogGraph: a graph-based mapping of cognate ligand domain interactions.Bioinformatics advances · 2024Article
- Enzyme function and evolution through the lens of bioinformatics.The Biochemical journal · 2023Review
- EzMechanism: an automated tool to propose catalytic mechanisms of enzyme reactions.Nature methods · 2023Article
- Annotation of biologically relevant ligands in UniProtKB using ChEBI.Bioinformatics (Oxford, England) · 2023Article
- Conformational Variation in Enzyme Catalysis: A Structural Study on Catalytic Residues.Journal of molecular biology · 2022Article
- Clustering FunFams using sequence embeddings improves EC purity.Bioinformatics (Oxford, England) · 2021Article
- CATH functional families predict functional sites in proteins.Bioinformatics (Oxford, England) · 2021Article
- Finding enzyme cofactors in Protein Data Bank.Bioinformatics (Oxford, England) · 2019Article
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5 authors.
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No grant is acknowledged in the PubMed record.
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.
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