The DOI matches its Crossref record; 8 of the 8 references it cites were found in a registry or an index.
Progress in molecular docking
Open accessAbstract
Background: In recent years, since the molecular docking technique can greatly improve the efficiency and reduce the research cost, it has become a key tool in computer‐assisted drug design to predict the binding affinity and analyze the interactive mode. Results: This study introduces the key principles, procedures and the widely‐used applications for molecular docking. Also, it compares the commonly used docking applications and recommends which research areas are suitable for them. Lastly, it briefly reviews the latest progress in molecular docking such as the integrated method and deep learning. Conclusion: Limited to the incomplete molecular structure and the shortcomings of the scoring function, current docking applications are not accurate enough to predict the binding affinity. However, we could improve the current molecular docking technique by integrating the big biological data into scoring function.
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Citations
Cites
Trott, O., & Olson, A. J. (2010) · Journal of Computational Chemistry · doi:10.1002/jcc.21334 · Cited by 38,412
The Cambridge Structural Database
Groom, C. R., Bruno, I. J., Lightfoot, M. P., & Ward, S. C. (2016) · Acta Crystallographica Section B Structural Science, Crystal Engineering and Materials · doi:10.1107/s2052520616003954 · Cited by 10,297
PubChem Substance and Compound databases
Kim, S., Thiessen, P. A., Bolton, E. E., Chen, J., Fu, G., Gindulyte, A., Han, L., He, J., He, S., Shoemaker, B. A., et al. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkv951 · Cited by 5,436
ZINC − A Free Database of Commercially Available Compounds for Virtual Screening
Irwin, J. J., & Shoichet, B. K. (2005) · Journal of Chemical Information and Modeling · doi:10.1021/ci049714+ · Cited by 4,058
ZDOCK: An initial‐stage protein‐docking algorithm
Chen, R., Li, L., & Weng, Z. (2003) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.10389 · Cited by 1,393 · cited 2×
“ZDOCK [37] Geometric complement-arity and molecular dynamics Molecular force field Medium Rigid docking.”
BackgroundMethodWang, 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
Deep Learning in Drug Discovery
Gawehn, E., Hiss, J. A., & Schneider, G. (2016) · Molecular Informatics · doi:10.1002/minf.201501008 · Cited by 723
Boosting docking-based virtual screening with deep learning.
Pereira, J. C., Caffarena, E. R., & dos Santos, C. N. (2016) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.6b00355 · Cited by 395
Cited by
A new paradigm for applying deep learning to protein–ligand interaction prediction
Wang, Z., Wang, S., Li, Y., Guo, J., Wei, Y., Mu, Y., Zheng, L., & Li, W. (2024) · Briefings in Bioinformatics · doi:10.1093/bib/bbae145 · Cited by 41
Park, M., Yi, J.-M., Kim, N. S., Lee, S.-Y., & Lee, H. (2024) · International Journal of Molecular Sciences · doi:10.3390/ijms25094636 · Cited by 11
Large Language Model Agent for Modular Task Execution in Drug Discovery
Ock, J., Meda, R. S., Badrinarayanan, S., Aluru, N. S., Chandrasekhar, A., & Barati Farimani, A. (2026) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.5c02454 · Cited by 5
Metadata
- Authors
- Fan, J., Fu, A., & Zhang, L.
- Venue
- Quantitative Biology
- Publisher
- Wiley
- Published
- 2019-06
- Volume
- 7
- Issue
- 2
- Pages
- 83-89
- ISSN
- 2095-4689 (ISSN-L)
- 2095-4697
- OpenAlex
- W2943893168
- Cited by
- 611
- References
- 8
- FWCI
- 15.39
- Type
- journal article
- Language
- en
- Open access
- diamond
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