ArticleJournal of chemical theory and computation2023
Protein-Ligand CH-π Interactions: Structural Informatics, Energy Function Development, and Docking Implementation.
Article in Journal of chemical theory and computation, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed, 31 citations in OpenAlex.
- Investigations of Intramolecular and Intermolecular Noncovalent Interactions in Alkaline Earth Metal Complexes ofInorganic chemistry · 2026Article
- Reproducibility, validation, and failure modes across classical and AI-driven molecular docking.Journal of computer-aided molecular design · 2026Review
- Structural modification of oxazolidinone antibiotics alters nascent peptide stalling preference and peptide trajectory through the ribosome.bioRxiv : the preprint server for biology · 2026Article
- Parallels between the chloro and methoxy groups for potency optimization.RSC medicinal chemistry · 2026Article
- Computational Pipeline for Accelerating the Design of Glycomimetics.Journal of chemical information and modeling · 2025Article
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- Role of Active Site Residues and Weak Noncovalent Interactions in Substrate Positioning inBiochemistry · 2025Article
- Development of Bioactive Cotton, Wool, and Silk Fabrics Functionalized withPharmaceutics · 2025Article
- NMR-driven structure-based drug discovery by unveiling molecular interactions.Communications chemistry · 2025Review
- The structural basis for the broad aldehyde specificity of the aminoaldehyde dehydrogenase PauC from the human pathogen Pseudomonas aeruginosa.Protein science : a publication of the Protein Society · 2025Article
- Three-Dimensional CH/π and CH/N Interactions from Quantum-Mechanical and Database Analyses.Journal of chemical information and modeling · 2025Article
- Molecular Determinants for Guanine Binding in GTP-Binding Proteins: A Data Mining and Quantum Chemical Study.International journal of molecular sciences · 2024Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
Here, we develop an empirical energy function based on quantum mechanical data for the interaction between methane and benzene that captures the contribution from CH-π interactions. Such interactions are frequently observed in protein-ligand crystal structures, particularly for carbohydrate ligands, but have been hard to quantify due to the absence of a model for CH-π interactions in typical molecular mechanical force fields or docking scoring functions. The CH-π term was added to the AutoDock Vina (AD VINA) scoring function enabling its performance to be evaluated against a cohort of more than 1600 occurrences in 496 experimental structures of protein-ligand complexes. By employing a conformational grid search algorithm, inclusion of the CH-π term was shown to improve the prediction of the preferred orientation of flexible ligands in protein-binding sites and to enhance the detection of carbohydrate-binding sites that display CH-π interactions. Last but not least, this term was also shown to improve docking performance for the CASF-2016 benchmark set and a carbohydrate set.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.