End-Point Binding Free Energy Calculation with MM/PBSA and MM/GBSA: Strategies and Applications in Drug Design.
By Ercheng Wang, Huiyong Sun, Junmei Wang, Zhe Wang, Hui Liu, J. H. Zhang, Tingjun Hou. Chemical Reviews, 2019
1,862 citations recorded by the source corpus.
Molecular mechanics Poisson-Boltzmann surface area (MM/PBSA) and molecular mechanics generalized Born surface area (MM/GBSA) are arguably very popular methods for binding free energy prediction since they are more accurate than most scoring functions of molecular docking and less computationally demanding than alchemical free energy methods. MM/PBSA and MM/GBSA have been widely used in biomolecular studies such as protein folding, protein-ligand binding, protein-protein interaction, etc. In this review, methods to adjust the polar solvation energy and to improve the performance of MM/PBSA and MM/GBSA calculations are reviewed and discussed. The latest applications of MM/GBSA and MM/PBSA in drug design are also presented. This review intends to provide readers with guidance for practically applying MM/PBSA and MM/GBSA in drug design and related research fields.
Subfields: Computational Theory and Mathematics, Materials Chemistry, Molecular Biology
View Paper: https://www.semanticscholar.org/paper/adba1a42c43f8d5cf9fe68fdf71c9d10b4b825c4
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Citations in the corpus
- Fast Identification of Possible Drug Treatment of Coronavirus Disease −19 (COVID-19) Through Computational Drug Repurposing Study (2020, methodology): “…free energy calculation methods, such as the endpoint MM-PB/GBSA (molecular mechanics-Poisson Boltzmann/ Generalized Born Surface Area) methods 2, 3, 8-21 and the alchemical thermodynamic integration (TI) and free energy perturbation (FEP) methods, 22, 23 have been extensively applied in…”
- In silico methods and tools for drug discovery (2021, background): “…complexes can be calculated with the molecular mechanics/Poisson – Boltzmann surface area (MM/PBSA) and the molecular mechanics/generalized born surface area (MM/GBSA) because they are more accurate than most molecular docking scoring functions and less computationally expensive [193,194].”