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Recent progress in molecular simulation methods for drug binding kinetics
- Publication Year :
- 2020
-
Abstract
- Due to the contribution of drug-target binding kinetics to drug efficacy, there is a high level of interest in developing methods to predict drug-target binding kinetic parameters. During the review period, a wide range of enhanced sampling molecular dynamics simulation-based methods has been developed for computing drug-target binding kinetics and studying binding and unbinding mechanisms. Here, we assess the performance of these methods considering two benchmark systems in detail: mutant T4 lysozyme-ligand complexes and a large set of N-HSP90-inhibitor complexes. The results indicate that some of the simulation methods can already be usefully applied in drug discovery or lead optimization programs but that further studies on more high-quality experimental benchmark datasets are necessary to improve and validate computational methods.<br />Comment: Figure 3 was improved. A definition of PIB was included. Reference to WE was added (ref. 20), reference to RAMD was corrected (ref. 43)
- Subjects :
- Quantitative Biology - Quantitative Methods
Quantitative Biology - Biomolecules
Subjects
Details
- Database :
- arXiv
- Publication Type :
- Report
- Accession number :
- edsarx.2002.08983
- Document Type :
- Working Paper
- Full Text :
- https://doi.org/10.1016/j.sbi.2020.06.022