Autors: Sapundzhi, F., Prodanova, K. S., Lazarova, M. D.
Title: Survey of the scoring functions for protein-ligand docking (Open Access)
Keywords: -

Abstract: Molecular docking algorithms predict the binding of a macromolecule (receptor) and a small molecule (ligand). Virtual screening by molecular docking has become established as a method for drug lead discovery and optimization. All docking algorithms make use of a scoring function in combination with a method of search. Presuming adequate search strategies, a scoring function's location performance will dominate behavior with respect to docking accuracy: the degree to which a predicted pose of a ligand matches experimental observation. Approaches to the development of scoring functions have varied widely, with a number of functions yielding similarly high levels of performance relating to the location issue. In this paper a survey of scoring functions for protein-ligand docking is presented

References

    Issue

    AIP Conference Proceedings. 45th International Conference on Application of Mathematics in Engineering and Economics, AMEE 2019; Sozopol; Bulgaria; 7 June 2019 through 13 June 2019, vol. 2172, pp. Article number 100008, 2019, Bulgaria, American Institute of Physics Inc., DOI 10.1063/1.5133601

    Copyright Author(s)

    Цитирания (Citation/s):
    1. Pant, S. and Jena, N.R., 2021. Inhibition of the RNA-dependent RNA Polymerase of the SARS-CoV-2 by Short Peptide Inhibitors. European Journal of Pharmaceutical Sciences, 167, p.106012 - 2021 - в издания, индексирани в Scopus или Web of Science
    2. Olujide O. Olubiyi, Suman Samantray, Alexander-Maurice Illig, Advances in structure-based virtual screening for drug discovery, In book: Advances in Protein Molecular and Structural Biology Methods, January 2022, DOI: 10.1016/B978-0-323-90264-9.00024-6 - 2022 - от чужди автори в чужди издания, неиндексирани в Scopus или Web of Science
    3. Vikas Kumar,Shraddha Parate,Gunjan Thakur,Gihwan Lee, Keun Woo Lee, Identification of CDK7 Inhibitors from Natural Sourses Using Pharmacoinformatics and Molecular Dynamics Simulations, Biomedicines, September 2021, 9(9), 1197. ISSN 22279059, Swetzeland. (SJR 2019=1.511; Q1); DOI: 10.3390/biomedicines9091197 - 2021 - в издания, индексирани в Scopus или Web of Science
    4. Jongkon, N.; Seaho, B.; Tayana, N.; Prateeptongkum, S.; Duangdee, N.; Jaiyong, P. Computational Analysis and Biological Activities of Oxyresveratrol Analogues, the Putative Cyclooxygenase-2 Inhibitors. Molecules 2022, 27, 2346. https:// doi.org/10.3390/molecules27072346 (SJR=0.78; Q1); - 2022 - в издания, индексирани в Scopus или Web of Science
    5. Thakur, P., Atway, J., Limbach, P.A. and Addepalli, B., 2022. RNA Cleavage Properties of Nucleobase-Specific RNase MC1 and Cusativin Are Determined by the Dinucleotide-Binding Interactions in the Enzyme-Active Site. International Journal of Molecular Sciences, 23(13), p.7021. ISSN: 1422-0067 ; SJR (2021)=0,21 (Q1) - 2022 - в издания, индексирани в Scopus или Web of Science
    6. 1. Olujide O. Olubiyi, Suman Samantray, Alexander-Maurice Illig, Advances in structure-based virtual screening for drug discovery, In book: Advances in Protein Molecular and Structural Biology Methods, January 2022, DOI: 10.1016/B978-0-323-90264-9.00024-6 - 2022 - в издания, индексирани в Scopus или Web of Science
    7. 3. Khalil, A., El-Khouly, A.S., Elkaeed, E.B. and Eissa, I.H., 2022. The Inhibitory Potential of 2′-dihalo Ribonucleotides against HCV: Molecular Docking, Molecular Simulations, MM-BPSA, and DFT Studies. Molecules, 27(14), p.4530.(SJR 2019=0.71; Q1); - 2022 - в издания, индексирани в Scopus или Web of Science
    8. Mohammed Salha at al, Bioactivity of the cannabigerol cannabinoid and its analogues - the role of 3-dimensional conformation, Organic & Biomolecular Chemistry 21(22), May 2023, DOI: 10.1039/d3ob00383c (IF 2022=3,2; Q2) - 2023 - в издания, индексирани в Scopus или Web of Science
    9. Rogala, P.; Jabło ́nska-Wawrzycka, A.; Czerwonka, G.;Kazimierczuk, K.; Gałczy ́nska, K.;Michałkiewicz, S.; Kalinowska-Tłu ́scik, J.; Karpiel, M.; Klika, K.D.Synthesis, Characterization and Biological Investigations of Half-Sandwich Ruthenium(II) Complexes Containing Benzimidazole Moiety, Molecules, 2023, 28, 40, pp. 1-25. https://doi.org/10.3390/molecules28010040 (SJR 2022=0,7; Q1) - 2023 - в издания, индексирани в Scopus или Web of Science
    10. Phengsakun, G., Boonyarit, B., Rungrotmongkol, T. and Suginta, W., 2023. Structure-based virtual screening for potent inhibitors of GH-20 β-N-acetylglucosaminidase: classical and machine learning scoring functions, and molecular dynamics simulations. Computational Biology and Chemistry, p.107856. (IF 2022=3,688) - 2023 - в издания, индексирани в Scopus или Web of Science
    11. Idrees, M., Kumar, V., Khan, A.M., Joo, M.D., Lee, K.W., Sohn, S.H. and Kong, I.K., 2023. Cycloastragenol activation of telomerase improves β-Klotho protein level and attenuates age-related malfunctioning in ovarian tissues. Mechanisms of Ageing and Development, 209, p.111756. (SJR 2022=1,38; Q1) - 2023 - в издания, индексирани в Scopus или Web of Science
    12. Christabel Ming Ming Koh, Lilian Siaw Yung Ping, Christopher Ha Heng Xuan, Lau Bee Theng, Hwang Siaw San, Enzo A. Palombo & Xavier Chee Wezen (2023) A data-driven machine learning approach for discovering potent LasR inhibitors, Bioengineered, 14:1, 2243416, DOI: 10.1080/21655979.2023.2243416 IF(2023)=6.832 - 2023 - в издания, индексирани в Scopus или Web of Science
    13. Kavinda Kashi Juliyan Gunasinghe at all, Discovery of MDM2 Inhibitors Against Nasopharyngeal Cancer: An In-Silico Investigation, Journal of Smart Science and Technology 3(2):44-56, 2023 DOI: 10.24191/jsst.v3i2.55 SJR(2022)=0.301 - 2023 - в издания, индексирани в Scopus или Web of Science
    14. Charles S, Edgar MP, Mahapatra RK. Artificial intelligence based virtual screening study for competitive and allosteric inhibitors of the SARS-CoV-2 main protease. J Biomol Struct Dyn. 2023 Mar 21:1-19. Epub ahead of print. DOI: 10.1080/07391102.2023.2188419 ; SJR(2022)=0.67 (Q2); Im F (2021)= 5.235 (2021) (Q1) - 2023 - в издания, индексирани в Scopus или Web of Science
    15. S. Pant & N. R. Jena (2023) Repurposing of antiparasitic drugs against the NS2B-NS3 protease of the Zika virus, Journal of Biomolecular Structure and Dynamics, DOI: 10.1080/07391102.2023.2255648 SJR=0.67 (Q2) - 2023 - в издания, индексирани в Scopus или Web of Science
    16. Ssemuyiga, C., Ssemanda, P., Pius, E.M., Kasoma, A.N. and Ntambi, S., 2023. The Hunt for antipox compounds against Monkeypox Virus Thymidylate Kinase and scaffolding protein leveraging Pharmacophore modeling, molecular docking, ADMET Studies, and molecular dynamics simulation studies. DOI: 10.21203/rs.3.rs-3306551/v1 SJR=0.31 (Q2) - 2023 - в издания, индексирани в Scopus или Web of Science
    17. Ssemuyiga Charles, Mulumba Pius Edgar & Rajani Kanta Mahapatra (2023) Artificial intelligence based virtual screening study for competitive and allosteric inhibitors of the SARS-CoV-2 main protease, Journal of Biomolecular Structure and Dynamics, (SJR=0.56;Q3) DOI: 10.1080/07391102.2023.2188419 - 2023 - в издания, индексирани в Scopus или Web of Science
    18. Jena, N.R. and Pant, S., 2023. Peptide inhibitors derived from the nsp7 and nsp8 cofactors of nsp12 targeting different substrate binding sites of nsp12 of the SARS-CoV-2. Journal of Biomolecular Structure and Dynamics, pp.1-13. https://doi.org/10.1021/acs.jpcb.0c04198 (SJR=0.67;Q2) - 2023 - в издания, индексирани в Scopus или Web of Science
    19. Koh, C.M.M., Ping, L.S.Y., Xuan, C.H.H., Theng, L.B., San, H.S., Palombo, E.A. and Wezen, X.C., 2023. A data-driven machine learning approach for discovering potent LasR inhibitors. Bioengineered, 14(1), p.2243416. ImF(2022)=4.9; Q1 - 2023 - в издания, индексирани в Scopus или Web of Science
    20. . M. Chaudhary1 and K. Tyagi, 2024,REVIEW ON MOLECULAR DOCKING AND IT’S APPLICATION, J. Adv. Res., 12(03), 1141-1153. DOI: 10.21474/IJAR01/185055 (SJR 2023=1,91; Q1) - 2024 - в издания, индексирани в Scopus или Web of Science
    21. Aziana Abu Hassan, Marko Hanževački, Anca Pordea, Computational investigation of cis-1,4-polyisoprene binding to the latex-clearing protein LcpK30, May 2024, PLOS ONE 19(5). DOI: 10.1371/journal.pone.0302398 SJR(2023)=0.84 (Q1); Im. F. (2023)=3.7 - 2024 - в издания, индексирани в Scopus или Web of Science
    22. M. Dimova-Gabrovska, M. Stamenova, M. Yankova, The Modern Digital Intraoral Scanning Systems: A Review, 2024, Acta Medica Bulgarica 51(2):58-64. DOI: 10.2478/amb-2024-0021 (SJR 2023=0,12; Q4) - 2024 - в издания, индексирани в Scopus или Web of Science

    Вид: пленарен доклад в международен форум, публикация в издание с импакт фактор, публикация в реферирано издание, индексирана в Scopus