Patterns in Protein-Ligand Interactions
Author Information
Author(s): Chen Ke, Kurgan Lukasz
Primary Institution: University of Alberta
Hypothesis
The study investigates the role of covalent and non-covalent bonds in protein-small ligand interactions using a comprehensive dataset of 2,320 complexes.
Conclusion
The majority of protein-ligand interactions are repetitive and can be summarized with several simple atomic-level patterns.
Supporting Evidence
- 73% of investigated covalent bonds were summarized with just three patterns.
- 66% of hydrogen bonds in protein-organic compound complexes are formed between NH- group of protein residues and oxygen atom of ligands.
- The extracted patterns can improve predictions of binding sites.
Takeaway
This study looks at how proteins and small molecules stick together and finds that there are common ways they do this, which can help in designing new drugs.
Methodology
The study analyzed a dataset of 2,320 protein-ligand complexes to identify interaction patterns based on different types of bonds.
Limitations
The study may not cover all types of protein-ligand interactions, particularly those involving van der Waals contacts.
Digital Object Identifier (DOI)
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