The DOI matches its Crossref record; 11 of the 11 references it cites were found in a registry or an index.
Advances and Challenges in Protein-Ligand Docking
Open accessAbstract
Molecular docking is a widely-used computational tool for the study of molecular recognition, which aims to predict the binding mode and binding affinity of a complex formed by two or more constituent molecules with known structures. An important type of molecular docking is protein-ligand docking because of its therapeutic applications in modern structure-based drug design. Here, we review the recent advances of protein flexibility, ligand sampling, and scoring functions—the three important aspects in protein-ligand docking. Challenges and possible future directions are discussed in the Conclusion.
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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
Development and validation of a genetic algorithm for flexible docking 1 1Edited by F. E. Cohen
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Benchmarking sets for molecular docking.
Huang, N., Shoichet, B. K., & Irwin, J. J. (2006) · Journal of Medicinal Chemistry · doi:10.1021/jm0608356 · Cited by 1,318
Principles of docking: An overview of search algorithms and a guide to scoring functions
Halperin, I., Ma, B., Wolfson, H., & Nussinov, R. (2002) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.10115 · Cited by 1,294
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
Implications of protein flexibility for drug discovery
Teague, S. J. (2003) · Nature Reviews Drug Discovery · doi:10.1038/nrd1129 · Cited by 755
Bissantz, C., Folkers, G., & Rognan, D. (2000) · Journal of Medicinal Chemistry · doi:10.1021/jm001044l · Cited by 740
Charifson, P. S., Corkery, J. J., Murcko, M. A., & Walters, W. P. (1999) · Journal of Medicinal Chemistry · doi:10.1021/jm990352k · Cited by 698
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
Scoring functions for protein-ligand docking.
Bentham Science Publisher, B. S. P. (2006) · Current Protein & Peptide Science · doi:10.2174/138920306778559395 · Cited by 258 · cited 1×
“The scoring function is a key element of a protein-ligand docking algorithm, because it directly determines the accuracy of the algorithm [78–82].”
Method
Cited by
Wang, Z., Sun, H., Yao, X., Li, D., Xu, L., Li, Y., Tian, S., & Hou, T. (2016) · Physical Chemistry Chemical Physics · doi:10.1039/c6cp01555g · Cited by 946
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
Docking Challenge: Protein Sampling and Molecular Docking Performance
Elokely, K. M., & Doerksen, R. J. (2013) · Journal of Chemical Information and Modeling · doi:10.1021/ci400040d · Cited by 287
Damm-Ganamet, K. L., Smith, R. D., Dunbar, J. B., Stuckey, J. A., & Carlson, H. A. (2013) · Journal of Chemical Information and Modeling · doi:10.1021/ci400025f · Cited by 133
New Aryl Hydrocarbon Receptor Homology Model Targeted To Improve Docking Reliability
Motto, I., Bordogna, A., Soshilov, A. A., Denison, M. S., & Bonati, L. (2011) · Journal of Chemical Information and Modeling · doi:10.1021/ci2001617 · Cited by 80
Metadata
- Authors
- Huang, S.-Y., & Zou, X.
- Venue
- International Journal of Molecular Sciences
- Publisher
- MDPI AG
- Published
- 2010-08-18
- Volume
- 11
- Issue
- 8
- Pages
- 3016-3034
- ISSN
- 1422-0067 (ISSN-L)
- OpenAlex
- W2005817231
- Cited by
- 639
- References
- 11
- FWCI
- 18.13
- Type
- journal article
- Language
- en
- Open access
- gold
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