ArticleComputational and structural biotechnology journal2025
Predicting fragment binding modes using customized Lennard-Jones potentials in short molecular dynamics simulations.
Article in Computational and structural biotechnology journal, 2025. 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.
- Design, synthesis and anti-glioblastoma multiforme activity of N-methoxy-2-(pyrimidin-4-ylamino)benzamide derivatives as focal adhesion kinase inhibitors.Molecular diversity · 2026Article
- Stability-Driven Pose Prediction and Ligand Design via Contact Persistence Analysis from Molecular Dynamics Simulations.Computational and structural biotechnology journal · 2026Article
- Solvent-Site Prediction for Fragment Docking and Its Implication on Fragment-Based Drug Discovery.Journal of chemical information and modeling · 2025Article
- Boosting Drug Discovery: Expanding the Applicability of Fragment Dissolved Molecular Dynamics to Accelerate Binding Mode Elucidation.Journal of chemical information and modeling · 2025Article
- How many crystal structures do you need to trust your docking results?bioRxiv : the preprint server for biology · 2025Article
- CrypToth: Cryptic Pocket Detection through Mixed-Solvent Molecular Dynamics Simulations-Based Topological Data Analysis.Journal of chemical information and modeling · 2025Article
- CrypTothML: An Integrated Mixed-Solvent Molecular Dynamics Simulation and Machine Learning Approach for Cryptic Site Prediction.International journal of molecular sciences · 2025Article
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3 authors.
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Abstract
Reliable in silico prediction of fragment binding modes remains a challenge in current drug design research. Due to their small size and generally low binding affinity, fragments can potentially interact with their target proteins in different ways. In the current study, we propose a workflow aimed at predicting favorable fragment binding sites and binding poses through multiple short molecular dynamics simulations. Tailored Lennard-Jones potentials enable the simulation of systems with high concentrations of identical fragment molecules surrounding their respective target proteins. In the present study, descriptors and binding free energy calculations were implemented to filter out the desired fragment position. The proposed method was tested for its performance using four epigenetic target proteins and their respective fragment binders and showed high accuracy in identifying the binding sites as well as predicting the native binding modes. The approach presented here represents an alternative method for the prediction of fragment binding modes and may be useful in fragment-based drug discovery when the corresponding experimental structural data are limited.
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