Article ; Online: Accelerating Alchemical Free Energy Prediction Using a Multistate Method: Application to Multiple Kinases.
Journal of chemical information and modeling
2023 Volume 63, Issue 22, Page(s) 7133–7147
Abstract: Alchemical free-energy methods based on molecular dynamics (MD) simulations have become important tools to identify modifications of small organic molecules that improve their protein binding affinity during lead optimization. The routine application of ... ...
| Abstract | Alchemical free-energy methods based on molecular dynamics (MD) simulations have become important tools to identify modifications of small organic molecules that improve their protein binding affinity during lead optimization. The routine application of pairwise free-energy methods to rank potential binders from best to worst is impacted by the combinatorial increase in calculations to perform when the number of molecules to assess grows. To address this fundamental limitation, our group has developed replica-exchange enveloping distribution sampling (RE-EDS), a pathway-independent multistate method, enabling the calculation of alchemical free-energy differences between multiple ligands ( |
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| MeSH term(s) | Thermodynamics ; Entropy ; Molecular Dynamics Simulation ; Protein Binding ; Ligands | |||||
| Chemical Substances | Ligands | |||||
| Language | English | |||||
| Publishing date | 2023-11-10 | |||||
| Publishing country | United States | |||||
| Document type | Journal Article | |||||
| ZDB-ID | 190019-5 | |||||
| ISSN | 1549-960X ; 0095-2338 | |||||
| ISSN (online) | 1549-960X | |||||
| ISSN | 0095-2338 | |||||
| DOI | 10.1021/acs.jcim.3c01469 | |||||
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| Database | MEDical Literature Analysis and Retrieval System OnLINE |
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