The DOI matches its Crossref record; 3 of the 3 references it cites were found in a registry or an index.
Water at biomolecular binding interfaces
Abstract
Water molecules are often found at the binding interface of biomolecular complexes mediating the interaction between polar groups via hydrogen bonds, or simply filling space providing van der Waals interactions. Recent studies have demonstrated the importance of taking such water molecules into account in docking and binding affinity prediction. Here, we review the recent experimental and theoretical work aimed at quantifying the influence of interfacial water on the thermodynamic properties of binding. We highlight especially our recent results obtained by inhomogeneous fluid solvation theory in several systems and the prediction of the thermodynamic consequences of displacement of the bound water molecule by ligand modification. Finally, we discuss possible directions for further progress in this field.
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Cites
Friesner, R. A., Banks, J. L., Murphy, R. B., Halgren, T. A., Klicic, J. J., Mainz, D. T., Repasky, M. P., Knoll, E. H., Shelley, M., Perry, J. K., et al. (2004) · Journal of Medicinal Chemistry · doi:10.1021/jm0306430 · Cited by 10,057
Comparative evaluation of 11 scoring functions for molecular docking.
Wang, R., Lu, Y., & Wang, S. (2003) · Journal of Medicinal Chemistry · doi:10.1021/jm0203783 · Cited by 849
Orientational disorder and entropy of water in protein cavities
Denisov, V. P., Venu, K., Peters, J., Hörlein, H. D., & Halle, B. (1997) · The Journal of Physical Chemistry B · doi:10.1021/jp9712213 · Cited by 108
Cited by
Computations of Standard Binding Free Energies with Molecular Dynamics Simulations
Deng, Y., & Roux, B. (2009) · The Journal of Physical Chemistry B · doi:10.1021/jp807701h · Cited by 591
Moitessier, N., Englebienne, P., Lee, D., Lawandi, J., & Corbeil, C. R. (2008) · British Journal of Pharmacology · doi:10.1038/sj.bjp.0707515 · Cited by 514
Variability in docking success rates due to dataset preparation.
Corbeil, C. R., Williams, C. I., & Labute, P. (2012) · Journal of Computer-Aided Molecular Design · doi:10.1007/s10822-012-9570-1 · Cited by 469
Nguyen, C. N., Kurtzman Young, T., & Gilson, M. K. (2012) · The Journal of Chemical Physics · doi:10.1063/1.4733951 · Cited by 324
Water in Cavity−Ligand Recognition
Baron, R., Setny, P., & McCammon, J. A. (2010) · Journal of the American Chemical Society · doi:10.1021/ja1050082 · Cited by 274
Metadata
- Authors
- Li, Z., & Lazaridis, T.
- Venue
- Phys. Chem. Chem. Phys.
- Publisher
- Royal Society of Chemistry (RSC)
- Published
- 2007
- Volume
- 9
- Issue
- 5
- Pages
- 573-581
- ISSN
- 1463-9076 (ISSN-L)
- 1463-9084
- OpenAlex
- W1982030445
- Cited by
- 178
- References
- 3
- FWCI
- 5.80
- Type
- journal article
- Language
- en
- Open access
- closed
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- Li, Z., & Lazaridis, T. (2007). Water at biomolecular binding interfaces. Phys. Chem. Chem. Phys. https://doi.org/10.1039/b612449f
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Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
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