Computational methods in drug discovery

Scholarly Works

• Matore, B. W.; Murmu, A.; Banjare, P.; Vishvakarma, N. K.; Roy, P. P.; Singh, J. Discovery of newer 1,3,4-Oxadiazole clubbed Isoindoline-1,3-dione derivatives as potential anticancer agents: Design, machine learning, synthesis, molecular docking, ADMET, DFT and MD simulation. Computational biology and chemistry 2025, 118, 108492. doi:10.1016/j.compbiolchem.2025.108492
• Ei, Z. Z.; Racha, S.; Chunhacha, P.; Yokoya, M.; Moriue, S.; Zou, H.; Chanvorachote, P. Substituents introduction of methyl and methoxy functional groups on resveratrol stabilizes mTOR binding for autophagic cell death induction. Scientific reports 2025, 15, 14675. doi:10.1038/s41598-025-98616-6
• Jadhav, S.; Vaidya, G.; Vora, A. A review on computational tools for antidiabetic herbs research. Discover Chemistry 2025, 2. doi:10.1007/s44371-025-00135-w
• Agoni, C.; Fernández-Díaz, R.; Timmons, P. B.; Adelfio, A.; Gómez, H.; Shields, D. C. Molecular Modelling in Bioactive Peptide Discovery and Characterisation. Biomolecules 2025, 15, 524. doi:10.3390/biom15040524
• Majumder, S.; Panigrahi, G. K. Advancements in contemporary pharmacological innovation: Mechanistic insights and emerging trends in drug discovery and development. Intelligent Pharmacy 2025, 3, 118–126. doi:10.1016/j.ipha.2024.10.001
• Gadkari, A.; Daigavhane, M.; Arghode, A.; Verma, P.; Gundewar, S. A Review on the Applications of Machine Learning, Predictive Modeling and Virtual Screening for Drug Discovery. Lecture Notes in Networks and Systems; Springer Nature Singapore, 2025; pp 359–370. doi:10.1007/978-981-97-9529-1_31
• Mohamed, A.; Brooks, B. R.; Amin, M. Leveraging-Induced Polarization for Drug Discovery: Efficient IC50 Prediction Using Minimal Features. Journal of chemical information and modeling 2025, 65, 3715–3722. doi:10.1021/acs.jcim.5c00076
• McMillan, J.; Bester, M. J.; Apostolides, Z. In silico docking and ADMET studies on clinical targets for type 2 diabetes correlated to in vitro inhibition of pancreatic alpha-amylase and alpha-glucosidase by rutin, caffeic acid, p-coumaric acid, and vanillin. In silico pharmacology 2025, 13, 42. doi:10.1007/s40203-025-00324-6
• Yousif, R.; Mohamed, H. M.; Almogaddam, M. A.; Elamin, K. M.; Ibrahim, S. R.; Ainousah, B. E.; Alraddadi, A. M.; Awad, E. A.; Alzain, A. A. Computational screening campaign reveal natural candidates as potential ASK1 inhibitors: Pharmacophore modeling, molecular docking, MMGBSA calculations, ADMET prediction, and molecular dynamics simulation studies. Scientific African 2025, 28, e02634. doi:10.1016/j.sciaf.2025.e02634
• Paiva, V. A.; Pires, D. E. V.; Bressan, G. C.; Izidoro, S. C.; Silveira, S. A. BENDER DB: a database of protein binding sites across neglected disease proteomes. Cold Spring Harbor Laboratory 2025. doi:10.1101/2025.02.18.638856
• Rabeek, S. M.; Belagalla, N.; Khare, K.; Kodadi, S. K.; Reddy, J. S.; Shaik, M. B. Computational Approaches to Molecular Dynamics Simulation for Drug Design and Discovery. In 2025 First International Conference on Advances in Computer Science, Electrical, Electronics, and Communication Technologies (CE2CT), IEEE, 2025; pp 724–728. doi:10.1109/ce2ct64011.2025.10940022
• Mandujano-Lázaro, G.; Torres-Rojas, M. F.; Ramírez-Moreno, E.; Marchat, L. A. Virtual screening combined with molecular docking for the !identification of new anti-adipogenic compounds. Science progress 2025, 108, 368504251320313. doi:10.1177/00368504251320313
• Luo, J.; Zhu, Z.; Xu, Z.; Xiao, C.; Wei, J.; Shen, J. GS-DTA: integrating graph and sequence models for predicting drug-target binding affinity. BMC genomics 2025, 26, 105. doi:10.1186/s12864-025-11234-4
• Chen, S.; Hu, X.; Chen, F.; Liu, J.; Su, J.; Chen, R.; Wei, W.; Yuan, Z.; An, S.; Ye, L.; Liang, H.; Jiang, J. Forsythoside B activates Siglec-14 to inhibit HIV-1 replication via the JAK1/STAT1 pathway. International journal of biological macromolecules 2025, 303, 140632. doi:10.1016/j.ijbiomac.2025.140632
• Pereira, T. O.; Abbasi, M.; Arrais, J. P. ABIET: An explainable transformer for identifying functional groups in biological active molecules. Computers in biology and medicine 2025, 187, 109740. doi:10.1016/j.compbiomed.2025.109740
• Yue, Q.; Hua-Juan, J.; Yu-Shun, Y.; Xiao-Qin, H.; Xue-Wen, Z. Review of the crystallized structures of the SARS-CoV-2 papain-like protease. Journal of Molecular Structure 2025, 1333, 141730. doi:10.1016/j.molstruc.2025.141730
• Vijayalakshmi, G.; Perianayagi, L.; Kores, J. J.; Nayagam, B. R. D.; Jeyamalar, J. I. Unveiling the anticancer potential: Exploring 4-fluoro benzoic acid and piperazine through spectroscopic, X-ray diffraction, DFT and molecular docking analysis. Journal of Molecular Structure 2025, 1322, 140507. doi:10.1016/j.molstruc.2024.140507
• Sharma, S.; Darlami, J. QSAR Modeling and Its Application in Veterinary Drug Design. Bioinformatics in Veterinary Science; Springer Nature Singapore, 2025; pp 367–385. doi:10.1007/978-981-97-7395-4_15
• Mohamed, A.; Brooks, B. R.; Amin, M. The role of induced polarization in drug discovery applications. Cold Spring Harbor Laboratory 2025. doi:10.1101/2025.01.14.632933
• Dos Santos, G. P.; Coelho, A. C.; Reimão, J. Q. The latest progress in assay development in leishmaniasis drug discovery: a review of the available papers on PubMed from the past year. Expert opinion on drug discovery 2025, 20, 177–192. doi:10.1080/17460441.2025.2450787

Explore citations to this article at