ArticleJournal of medicinal chemistry2023
A Distributional Model of Bound Ligand Conformational Strain: From Small Molecules up to Large Peptidic Macrocycles.
Article in Journal of medicinal chemistry, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- In Silico Isomerization Produces Apt Negative Data for VHTS Validation.Journal of chemical information and modeling · 2026Article
- The deformation energy gap in computational drug design: why interaction energy alone cannot rank drug candidates and a thermodynamic correction protocol.Journal of molecular modeling · 2026Article
- Isomer-Dependent Pharmacokinetic Behavior and VKOR Interactions of Second-Generation Anticoagulant Rodenticides: An Integrated In Vivo-In Vitro-In Silico Investigation.International journal of molecular sciences · 2026Article
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- Article
- Expanding Automated Multiconformer Ligand Modeling to Macrocycles and Fragments.bioRxiv : the preprint server for biology · 2025Article
- Structure-based pose prediction: Non-cognate docking extended to macrocyclic ligands.Journal of computer-aided molecular design · 2024Article
- Exploring protein-ligand binding affinity prediction with electron density-based geometric deep learning.RSC advances · 2024Article
- Complex peptide macrocycle optimization: combining NMR restraints with conformational analysis to guide structure-based and ligand-based design.Journal of computer-aided molecular design · 2023Article
- Unmasking the True Identity of Rapamycin's Minor Conformer.Journal of natural products · 2023Article
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The internal conformational strain incurred by ligands upon binding a target site has a critical impact on binding affinity, and expectations about the magnitude of ligand strain guide conformational search protocols. Estimates for bound ligand strain begin with modeled ligand atomic coordinates from X-ray co-crystal structures. By deriving low-energy conformational ensembles to fit X-ray diffraction data, calculated strain energies are substantially reduced compared with prior approaches. We show that the distribution of expected global strain energy values is dependent on molecular size in a superlinear manner. The distribution of strain energy follows a rectified normal distribution whose mean and variance are related to conformational complexity. The modeled strain distribution closely matches calculated strain values from experimental data comprising over 3000 protein-ligand complexes. The distributional model has direct implications for conformational search protocols as well as for directions in molecular design.
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