1,512
Views
1
CrossRef citations to date
0
Altmetric
Editorial

How do we further enhance 2D fingerprint similarity searching for novel drug discovery?

&
Pages 1173-1176 | Received 29 Jun 2022, Accepted 21 Sep 2022, Published online: 27 Sep 2022

References

  • Muegge I, Mukherjee P. An overview of molecular fingerprint similarity search in virtual screening. Expert Opin Drug Discov. 2016;11(2):137–148.
  • Ciriaco F, Gambacorta N, Alberga D, et al. Quantitative polypharmacology profiling based on a multifingerprint similarity predictive approach. J Chem Inf Model. 2021;61(10):4868–4876.
  • Janela T, Takeuchi K, Bajorath J. Introducing a chemically intuitive core-substituent fingerprint designed to explore structural requirements for effective similarity searching and machine learning. Molecules. 2022;27(7):2331.
  • Todeschini R, Consonni V, Xiang H, et al. Similarity coefficients for binary chemoinformatics data: overview and extended comparison using simulated and real data sets. J Chem Inf Model. 2012;52(11): 2884–2901.
  • Gao K, Nguyen DD, Sresht V, et al. Are 2D fingerprints still valuable for drug discovery? Phys Chem Chem Phys. 2020;22(16):8373–8390.
  • Axen SD, Huang XP, Caceres EL, et al. A simple representation of three-dimensional molecular structure. J Med Chem. 2017;60(17): 7393–7409.
  • Skuta C, Cortes-Ciriano I, Dehaen W, et al. QSAR-derived affinity fingerprints (part 1): fingerprint construction and modeling performance for similarity searching, bioactivity classification and scaffold hopping. J Cheminform. 2020;12(1):39.
  • Bragina ME, Daina A, Perez MAS, et al. The SwissSimilarity 2021 web tool: novel chemical libraries and additional methods for an enhanced ligand-based virtual screening experience. Int J Mol Sci. 2022;23(2): 811.
  • O’Boyle NM, Banck M, James CA, et al. Open babel: an open chemical toolbox. J Cheminform. 2011;3:33.
  • Yap CW. PaDEL-descriptor: an open source software to calculate molecular descriptors and fingerprints. J Comput Chem. 2011;32(7):1466–1474.
  • Venkatraman V. FP‑ADMET: a compendium of fingerprint‑based ADMET prediction models. J Cheminform. 2021;13(1):75.
  • Zhao Y, Wang XG, Ma ZY, et al. Systematic comparison of ligand-based and structure-based virtual screening methods on poly (ADP-ribose) polymerase-1 inhibitors. Brief Bioinform. 2021;22(6):1–13.
  • Zhang Q, Muegge I. Scaffold hopping through virtual screening using 2D and 3D similarity descriptors: ranking, voting, and consensus scoring. J Med Chem. 2006;49(5):1536–1548.
  • Mendolia I, Contino S, Perricone U, et al. Convolutional architectures for virtual screening. BMC Bioinformatics. 2020;21(Suppl 8):310.
  • Mendolia I, Contino S, De Simone G, et al. EMBER-embedding multiple molecular fingerprints for virtual screening. Int J Mol Sci. 2022;23(4):2156.
  • Zhao J, Ma Q, Zhang B, et al. Exploration of SARS-CoV-2 3CL(pro) inhibitors by virtual screening methods, FRET detection, and CPE assay. J Chem Inf Model. 2021;61(12):5763–5773.
  • Myint KZ, Wang L, Tong Q, et al. Molecular fingerprint-based artificial neural networks QSAR for ligand biological activity predictions. Mol Pharm. 2012;9(10):2912–2923.
  • Xie L, Xu L, Kong R, et al. Improvement of prediction performance with conjoint molecular fingerprint in deep learning. Front Pharmacol. 2020;11:606668.
  • Nasser M, Salim N, Hamza H, et al. Improved deep learning based method for molecular similarity searching using stack of deep belief networks. Molecules. 2020;26(1): 128.
  • Perron Q, Mirguet O, Tajmouati H, et al. Deep generative models for ligand-based de novo design applied to multi-parametric optimization. J Comput Chem. 2022;43(10):692–703.
  • Yang K, Swanson K, Jin W, et al. Analyzing learned molecular representations for property prediction. J Chem Inf Model. 2019;59(8):3370–3388.
  • Probst D, Reymond JL. A probabilistic molecular fingerprint for big data settings. J Cheminform. 2018;10(1):66.
  • Miranda-Quintana RA, Racz A, Bajusz D, et al. Extended similarity indices: the benefits of comparing more than two objects simultaneously. Part 2: speed, consistency, diversity selection. J Cheminform. 2021;13(1): 33.
  • Le T, Winter R, Noé F and Clevert D. (2020). Neuraldecipher – reverse-engineering extended-connectivity fingerprints (ECFPs) to their molecular structures. Chem. Sci., 11(38), 10378–10389. 10.1039/D0SC03115A

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.