The DOI matches its Crossref record; 5 of the 5 references it cites were found in a registry or an index.
Contribution of Conformer Focusing to the Uncertainty in Predicting Free Energies for Protein−Ligand Binding
Abstract
When a ligand binds to a protein, it is typically not in the lowest-energy conformation for the unbound ligand and there is also a loss of conformational degrees of freedom. The free-energy change for this "conformer focusing" is addressed here formally, and the associated errors with its estimation or neglect are considered in the context of scoring functions for protein-ligand docking and computation of absolute free energies of binding. Specific applications for inhibition of HIV-1 reverse transcriptase are reported. It is concluded that the uncertainties from this source alone are sufficient to preclude the viability of current docking methodology for rank-ordering of diverse compounds in high-throughput virtual screening.
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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
Drug Delivery Systems: Entering the Mainstream
Allen, T. M., & Cullis, P. R. (2004) · Science · doi:10.1126/science.1095833 · Cited by 4,552
Crystal structure at 3.5 A resolution of HIV-1 reverse transcriptase complexed with an inhibitor
Kohlstaedt, L. A., Wang, J., Friedman, J. M., Rice, P. A., & Steitz, T. A. (1992) · Science · doi:10.1126/science.1377403 · Cited by 1,914
Bissantz, C., Folkers, G., & Rognan, D. (2000) · Journal of Medicinal Chemistry · doi:10.1021/jm001044l · Cited by 740
Comparative evaluation of eight docking tools for docking and virtual screening accuracy
Kellenberger, E., Rodrigo, J., Muller, P., & Rognan, D. (2004) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.20149 · Cited by 577
Cited by
Ultra-large library docking for discovering new chemotypes
Lyu, J., Wang, S., Balius, T. E., Singh, I., Levit, A., Moroz, Y. S., O’Meara, M. J., Che, T., Algaa, E., Tolmachova, K., et al. (2019) · Nature · doi:10.1038/s41586-019-0917-9 · Cited by 998
Chen, Y.-C. (2015) · Trends in Pharmacological Sciences · doi:10.1016/j.tips.2014.12.001 · Cited by 611
A practical guide to large-scale docking
Bender, B. J., Gahbauer, S., Luttens, A., Lyu, J., Webb, C. M., Stein, R. M., Fink, E. A., Balius, T. E., Carlsson, J., Irwin, J. J., et al. (2021) · Nature Protocols · doi:10.1038/s41596-021-00597-z · Cited by 546
“Owing to these approximations and neglected terms, docking energies have known errors, and the method cannot even reliably rank order molecules from a large library screen 21,22 .”
MethodSmith, A. J. T., Zhang, X., Leach, A. G., & Houk, K. N. (2009) · Journal of Medicinal Chemistry · doi:10.1021/jm800498e · Cited by 193
Increasing the efficiency of ligands for FK506-binding protein 51 by conformational control
Wang, Y., Kirschner, A., Fabian, A.-K., Gopalakrishnan, R., Kress, C., Hoogeland, B., Koch, U., Kozany, C., Bracher, A., & Hausch, F. (2013) · Journal of Medicinal Chemistry · doi:10.1021/jm400087k · Cited by 60
Metadata
- Authors
- Tirado-Rives, J., & Jorgensen, W. L.
- Venue
- Journal of Medicinal Chemistry
- Publisher
- American Chemical Society (ACS)
- Published
- 2006-09-12
- Volume
- 49
- Issue
- 20
- Pages
- 5880-5884
- ISSN
- 0022-2623 (ISSN-L)
- 1520-4804
- OpenAlex
- W1990627326
- Cited by
- 270
- References
- 5
- FWCI
- 18.45
- Type
- journal article
- Language
- en
- Open access
- closed
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Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
