The DOI matches its Crossref record; 21 of the 21 references it cites were found in a registry or an index.
End-Point Binding Free Energy Calculation with MM/PBSA and MM/GBSA: Strategies and Applications in Drug Design
Abstract
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.
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gmx_MMPBSA: A New Tool to Perform End-State Free Energy Calculations with GROMACS
Valdés-Tresanco, M. S., Valdés-Tresanco, M. E., Valiente, P. A., & Moreno, E. (2021) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.1c00645 · Cited by 3,393
MISATO: machine learning dataset of protein–ligand complexes for structure-based drug discovery
Siebenmorgen, T., Menezes, F., Benassou, S., Merdivan, E., Didi, K., Mourão, A. S. D., Kitel, R., Liò, P., Kesselheim, S., Piraud, M., et al. (2024) · Nature Computational Science · doi:10.1038/s43588-024-00627-2 · Cited by 75
In Silico Modeling and Scoring of PROTAC-Mediated Ternary Complex Poses
Liao, J., Nie, X., Unarta, I. C., Ericksen, S. S., & Tang, W. (2022) · Journal of Medicinal Chemistry · doi:10.1021/acs.jmedchem.1c02155 · Cited by 62
Wang, J., Ishchenko, A., Zhang, W., Razavi, A., & Langley, D. (2022) · Scientific Reports · doi:10.1038/s41598-022-05875-8 · Cited by 55
Self-citationArf GTPase activates the WAVE regulatory complex through a distinct binding site
Yang, S., Tang, Y., Liu, Y., Brown, A. J., Schaks, M., Ding, B., Kramer, D. A., Mietkowska, M., Ding, L., Alekhina, O., et al. (2022) · Science Advances · doi:10.1126/sciadv.add1412 · Cited by 24
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Metadata
- Authors
- Wang, E., Sun, H., Wang, J., Wang, Z., Liu, H., Zhang, J. Z. H., & Hou, T.
- Venue
- Chemical Reviews
- Publisher
- American Chemical Society (ACS)
- Published
- 2019-06-24
- Volume
- 119
- Issue
- 16
- Pages
- 9478-9508
- ISSN
- 0009-2665 (ISSN-L)
- 1520-6890
- OpenAlex
- W2954094311
- Cited by
- 2,232
- References
- 21
- FWCI
- 8.45
- Type
- journal article
- Language
- en
- Open access
- closed
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- Wang, E., Sun, H., Wang, J., Wang, Z., Liu, H., Zhang, J. Z. H., & Hou, T. (2019). End-Point Binding Free Energy Calculation with MM/PBSA and MM/GBSA: Strategies and Applications in Drug Design. Chemical Reviews. https://doi.org/10.1021/acs.chemrev.9b00055
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