ArticleInternational journal of molecular sciences2021
Dissimilar Ligands Bind in a Similar Fashion: A Guide to Ligand Binding-Mode Prediction with Application to CELPP Studies.
Article in International journal of molecular sciences, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 citing papers in PubMed.
- Docking-based virtual screening: Past, present, and future.Biophysical journal · 2026Review
- Augmented BindingNet dataset for enhanced ligand binding pose predictions using deep learning.npj drug discovery · 2025Article
- Docking strategies for predicting protein-ligand interactions and their application to structure-based drug design.Communications in information and systems · 2024Article
- Novel Genetic and Biochemical Insights into the Spectrum of NEFL-Associated Phenotypes.Journal of neuromuscular diseases · 2024Review
- Template-guided method for protein-ligand complex structure prediction: Application to CASP15 protein-ligand studies.Proteins · 2023Article
- CoDock-Ligand: combined template-based docking and CNN-based scoring in ligand binding prediction.BMC bioinformatics · 2023Article
- CSAlign and CSAlign-Dock: Structure alignment of ligands considering full flexibility and application to protein-ligand docking.Computational and structural biotechnology journal · 2023Article
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2 authors.
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Abstract
The molecular similarity principle has achieved great successes in the field of drug design/discovery. Existing studies have focused on similar ligands, while the behaviors of dissimilar ligands remain unknown. In this study, we developed an intercomparison strategy in order to compare the binding modes of ligands with different molecular structures. A systematic analysis of a newly constructed protein-ligand complex structure dataset showed that ligands with similar structures tended to share a similar binding mode, which is consistent with the Molecular Similarity Principle. More importantly, the results revealed that dissimilar ligands can also bind in a similar fashion. This finding may open another avenue for drug discovery. Furthermore, a template-guiding method was introduced for predicting protein-ligand complex structures. With the use of dissimilar ligands as templates, our method significantly outperformed the traditional molecular docking methods. The newly developed template-guiding method was further applied to recent CELPP studies.
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