The DOI matches its Crossref record; 121 of the 121 references it cites were found in a registry or an index.
A Structure-Based Drug Discovery Paradigm
Open accessAbstract
Structure-based drug design is becoming an essential tool for faster and more cost-efficient lead discovery relative to the traditional method. Genomic, proteomic, and structural studies have provided hundreds of new targets and opportunities for future drug discovery. This situation poses a major problem: the necessity to handle the “big data” generated by combinatorial chemistry. Artificial intelligence (AI) and deep learning play a pivotal role in the analysis and systemization of larger data sets by statistical machine learning methods. Advanced AI-based sophisticated machine learning tools have a significant impact on the drug discovery process including medicinal chemistry. In this review, we focus on the currently available methods and algorithms for structure-based drug design including virtual screening and de novo drug design, with a special emphasis on AI- and deep-learning-based methods used for drug discovery.
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Cites
Breiman, L. (2001) · Machine Learning · doi:10.1023/a:1010933404324 · Cited by 133,538
LeCun, Y., Bengio, Y., & Hinton, G. (2015) · Nature · doi:10.1038/nature14539 · Cited by 84,126
Cortes, C., & Vapnik, V. (1995) · Machine Learning · doi:10.1007/bf00994018 · Cited by 59,421
Machine learning for molecular and materials science
Butler, K. T., Davies, D. W., Cartwright, H., Isayev, O., & Walsh, A. (2018) · Nature · doi:10.1038/s41586-018-0337-2 · Cited by 4,968 · cited 1×
“In a GAN (Figure 3), two ANN models—the generator and discriminator—are trained simultaneously and generate a new molecule from scratch by optimizing a different and opposing objective function in a zero-sum game [123].”
BackgroundDocking and scoring in virtual screening for drug discovery: methods and applications
Kitchen, D. B., Decornez, H., Furr, J. R., & Bajorath, J. (2004) · Nature Reviews Drug Discovery · doi:10.1038/nrd1549 · Cited by 4,150
Molecular Docking: A Powerful Approach for Structure-Based Drug Discovery
Meng, X.-Y., Zhang, H.-X., Mezei, M., & Cui, M. (2011) · Current Computer Aided-Drug Design · doi:10.2174/157340911795677602 · Cited by 3,771
A Fast Flexible Docking Method using an Incremental Construction Algorithm
Rarey, M., Kramer, B., Lengauer, T., & Klebe, G. (1996) · Journal of Molecular Biology · doi:10.1006/jmbi.1996.0477 · Cited by 2,827
Molecular Docking and Structure-Based Drug Design Strategies
Ferreira, L., Dos Santos, R., Oliva, G., & Andricopulo, A. (2015) · Molecules · doi:10.3390/molecules200713384 · Cited by 2,528
Quantifying the chemical beauty of drugs
Bickerton, G. R., Paolini, G. V., Besnard, J., Muresan, S., & Hopkins, A. L. (2012) · Nature Chemistry · doi:10.1038/nchem.1243 · Cited by 2,242
A Critical Assessment of Docking Programs and Scoring Functions
Warren, G. L., Andrews, C. W., Capelli, A.-M., Clarke, B., LaLonde, J., Lambert, M. H., Lindvall, M., Nevins, N., Semus, S. F., Senger, S., et al. (2006) · Journal of Medicinal Chemistry · doi:10.1021/jm050362n · Cited by 1,814
Research works printed but not linked: 8
- 2007, Drug evaluation: Prx-00023, a selective 5-ht1a receptor agonist for depression, Curr. Opin. Investig. Drugs, 8, 78
- Grant, 2009, Protein structure prediction in structure-based ligand design and virtual screening, Comb. Chem. High Throughput Screen., 12, 940, 10.2174/138620709789824718 · doi:10.2174/138620709789824718
- Lameijer, 2007, Designing active template molecules by combining computational de novo design and human chemist’s expertise, J. Med. Chem, 50, 1925, 10.1021/jm061356+ · doi:10.1021/jm061356+
- Tang, 2006, New technologies in computer-aided drug design: Toward target identification and new chemical entity discovery, Drug Discov. Today Technol., 3, 307, 10.1016/j.ddtec.2006.09.004 · doi:10.1016/j.ddtec.2006.09.004
- Roy, K. (2019). Chapter 2—computational drug design methods—current and future perspectives. In silico drug design, Academic Press.
- Secchi, 2018, On the role of statistics in the era of big data: A call for a debate, Stat. Probab. Lett., 136, 10, 10.1016/j.spl.2018.02.041 · doi:10.1016/j.spl.2018.02.041
- Kuritzkes, 2008, Maraviroc, Nat. Rev. Drug Discov., 7, 15, 10.1038/nrd2490 · doi:10.1038/nrd2490
- Suthaharan, S. (2016). Support vector machine. Machine Learning Models and Algorithms for Big Data Classification: Thinking with Examples for Effective Learning, Springer US.
Cited by
Varadi, M., Anyango, S., Deshpande, M., Nair, S., Natassia, C., Yordanova, G., Yuan, D., Stroe, O., Wood, G., Laydon, A., et al. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkab1061 · Cited by 7,850
In silico methods and tools for drug discovery
Shaker, B., Ahmad, S., Lee, J., Jung, C., & Na, D. (2021) · Computers in Biology and Medicine · doi:10.1016/j.compbiomed.2021.104851 · Cited by 607
Targeting RNA structures with small molecules
Childs-Disney, J. L., Yang, X., Gibaut, Q. M. R., Tong, Y., Batey, R. T., & Disney, M. D. (2022) · Nature Reviews Drug Discovery · doi:10.1038/s41573-022-00521-4 · Cited by 587
Chai-1: Decoding the molecular interactions of life
Discovery, C., Boitreaud, J., Dent, J., McPartlon, M., Meier, J., Reis, V., Rogozhnikov, A., & Wu, K. (2024) · doi:10.1101/2024.10.10.615955 · Cited by 517
Ren, F., Ding, X., Zheng, M., Korzinkin, M., Cai, X., Zhu, W., Mantsyzov, A., Aliper, A., Aladinskiy, V., Cao, Z., et al. (2023) · Chemical Science · doi:10.1039/d2sc05709c · Cited by 365
Metadata
- Authors
- Batool, M., Ahmad, B., & Choi, S.
- Venue
- International Journal of Molecular Sciences
- Publisher
- MDPI AG
- Published
- 2019-06-06
- Volume
- 20
- Issue
- 11
- Pages
- 2783
- ISSN
- 1422-0067 (ISSN-L)
- OpenAlex
- W2948831670
- Cited by
- 744
- References
- 121
- FWCI
- 41.25
- Type
- journal article
- Language
- en
- Open access
- gold
- Funders
- National Research Foundation of Korea (2019R1H1A2039674)
- Ministry of Science and ICT (2018K000369)
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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.