An Application of InterCriteria Analysis Approach to Assess the AMMOS Software Platform Outcomes
DOI:
https://doi.org/10.55630/j.biomath.2022.03.068Keywords:
decision making, intercriteria analysis, post-docking optimization,Abstract
The experimental procedures of drug design, proven to be time-consuming and costly, are successfully complemented with computer-aided (in silico) approaches nowadays. Virtual ligand screening (VLS) is one of the most promising approaches when searching for new hit compounds. The efficiency of VLS procedures might be improved via post-docking optimization. In the focus of this investigation is AMMOS (Automatic Molecular Mechanics Optimization for in silico Screening) developed as multi-step structure-based procedure for efficient computational refinement of protein-ligand complexes at different levels of protein flexibility. Their performance has been assessed by the recently developed InterCriteria Analysis (ICrA), elaborated as multi-criterion decision-making approach to reveal possible relations in the behavior of pairs of criteria when multiple objects are considered. The capacity of ICrA as a supporting tool to assess the effect of applying different levels of protein flexibility in the post-docking optimization via AMMOS has been investigated and analyzed.
References
[1] Atanassov, K., Mavrov, D., Atanassova, V.: Intercriteria decision making: a new approach for multicriteria decision making, based on index matrices and intuitionistic fuzzy sets. Issues IFSs and GNs 11, 1-8 (2014).
[2] Atanassov, K.: Intuitionistic fuzzy sets, VII ITKR Session, Sofia, 20-23 June 1983, Reprinted: Int. J. Bioautomation, 20(S1), S1-S6 (2016).
[3] Atanassov, K. On intuitionistic fuzzy sets theory, Springer, Cham (2012).
[4] Atanassov, K. Index matrices: Towards an augmented matrix calculus, Springer, Berlin (2014).
[5] Atanassov, K., Atanassova, V., Gluhchev, G.: InterCriteria Analysis: Ideas and problems, Notes on IFSs, 21(1), 81-88 (2015).
[6] Atanassova, V., Doukovska, L., Atanassov, K., Mavrov, D.: InterCriteria decision making approach to EU member states competitiveness analysis. In: Proceedings of the International Symposium on Business Modeling and Software Design – BMSD’14, 289-294 (2014).
[7] Georgieva, V., Angelova, N., Roeva, O., Pencheva, T.: Intercriteria analysis of wastewater treatment quality. Journal of Int Scientific Publications: Ecology & Safety, 10, 365-376 (2016).
[8] Todinova, S., Mavrov, D., Krumova, S., Marinov, P., Atanassova, V., Atanassov, K., Taneva, S. G.: Blood Plasma Thermograms Dataset Analysisby Means of InterCriteria and Correlation Analyses for the Case of Colorectal Cancer. Int. J. Bioautomation 20(1), 115-124 (2016).
[9] Zaharieva, B., Doukovska, L., Ribagin, S., Radeva, I.: InterCriteria Analysis of Data Obtained from Patients with Behterev’s Disease. Int. J. Bioautomation, 24(1), 5-14 (2020), DOI: 10.7546/ijba.2020.24.1.000507.
[10] Sotirov, S., Sotirova, E., Atanassova, V., Atanassov, K., Castillo, O., Melin, P., Petkov, T., Surchev, S.: A Hybrid Approach for Modular Neural Network Design Using InterCriteria Analysis and Intuitionistic Fuzzy Logic. Complexity, 2018, Art. ID 3927951, (2018), DOI: 10.1155/2018/3927951.
[11] Pencheva, T., Roeva, O., Angelova, M.: Investigation of Genetic Algorithm Performance Based on Different Algorithms for InterCriteria Relations Calculation. Lecture Notes in Computer Science, 10665, 390-398 (2018), DOI: 10.1007/978-3-319-73441-5_42.
[12] Roeva, O., Fidanova, S.: Comparison of different metaheuristic algorithms based on InterCriteria Analysis. Journal of Computational and Applied Mathematics, 340, 615-628 (2018), DOI: 10.1016/j.cam.2017.07.028.
[13] Jereva, D., Pencheva, T., Tsakovska, I., Alov, P., Pajeva, I.: Exploring applicability of intercriteria analysis to evaluate the performance of MOE and GOLD scoring functions. Studies in Computational Intelligence, in press (2020)
[14] Tsakovska, I., Alov, P., Ikonomov, N., Atanassova, V., Vassilev, P., Roeva, O., Jereva, D., Atanassov, K., Pajeva, I., Pencheva, T.: InterCriteria Analysis Implementation for Exploration of the Performance of Various Docking Scoring Functions. Studies in Computational Intelligence, 902, 88-98 (2021), DOI: 10.1007/978-3-030-55347-0_8.
[15] Ikonomov, N., Vassilev, P., Roeva, O.: ICrAData – Software for InterCriteria Analysis, Int. J. Bioautomation 22(1), 1-10 (2018), DOI: 10.7546/ijba.2018.22.1.1-10.
[16] Sauton, N., Lagorce, D., Villoutreix, B.O., Miteva, M.A.: MS-DOCK: Accurate multiple conformation generator and rigid docking protocol for multi-step virtual ligand screening, BMC Bioinformatics 9:184 (2008), DOI: 10.1186/1471-2105-9-184.
[17] Moustakas, D.T., Lang, P.T., Pegg, S., Pettersen, E., Kuntz, I.D., Brooijmans, N., Rizzo, R.C.: Development and validation of a modular, extensible docking program: DOCK 5. J. Comput. Aided Mol. Des. 20, 601-619 (2006), DOI: 10.1007/s10822-006-9060-4.
[18] Pencheva, T., Lagorce, D., Pajeva, I., Villoutreix, B.O., Miteva, M.A.: AMMOS: automated molecular mechanics optimization tool for in silico screening. BMC Bioinform. 9:438 (2008), DOI: 10.1186/1471-2105-9-438.
[19] Labbé, C.M., Pencheva, T., Jereva, D., Desvillechabrol, D., Becot, J., Villoutreix, B.O., Pajeva, I., Miteva, M.A.: AMMOS2: A web server for protein-ligand-water complexes refinement via molecular mechanics. Nucleic Acids Res. 45 (W1), W350-W355 (2017), DOI: 10.1093/nar/gkx397.
[20] Pencheva, T., Soumana, O., Pajeva, I., Miteva, M.: Post-docking virtual screening of diverse binding pockets: comparative study using DOCK, AMMOS, X-Score and FRED scoring functions, Eur J Med Chem. 45 (6), 2622-2628 (2010), DOI: 10.1016/j.ejmech.2009.12.025.
[21] Pencheva, T., Alov, P., Jereva, D., Pajeva, I., Miteva, M.A.: Post-docking optimization and analysis of protein-ligand interactions with AMMOS Free Software, Topics in Chemistry and Material Science, Vol. 5 of Current Issues in Organic Chemistry 2 (Proceedings of the Third International Symposium on Organic Chemistry with Satellite Meeting on NMR in Life Sciences, October 30 - November 2, 2010, Sofia, Bulgaria, Eds. Nikolova R. D., S. Simova, P. Denkova, G. N. Vayssilov), 43-51 (2011).
[22] Jia, M., Dahlman-Wright, K., Gustafsson, J.: Estrogen receptor alpha and beta in health and disease. Best Pract Res Clin Endocrinol Metab. 29(4), 557-68 (2015), DOI: 10.1016/j.beem.2015.04.008.
[23] Eyster, K.M.: The estrogen receptors: an overview from different perspectives. Methods Mol Biol. 1366, 1-10 (2016), DOI: 10.1007/978-1-4939-3127-9_1.
[24] Bassetti, M., Castaldo, N., Carnelutti, A.: Neuraminidase inhibitors as a strategy for influenza treatment: pros, cons and future perspectives. Exp Opin Pharmacother. 20(14), 1711-18 (2019), DOI: 10.1080/14656566.2019.1626824.
[25] Jagadesh, A., Salam, A.A., Mudgal, P.P., Arunkumar, G.: Influenza virus neuraminidase (NA): a target for antivirals and vaccines. Arch Virol. 161(8), 2087-94 (2016), DOI: 10.1007/s00705-016-2907-7.
[26] Pajeva, I., Tsakovska, I., Pencheva, T., Alov, P., Al Sharif, M., Lesigiarska, I., Jereva, D., Diukendjieva, A.: In silico Studies of Biologically Active Molecules, In: Research in Computer Science in the Bulgarian Academy of Sciences (Atanassov K., Ed.), Studies in Computational Intelligence 934, 421-451 (2021).
Downloads
Published
Issue
Section
License
Copyright (c) 2022 Dessislava Jereva, Maria Angelova, Ivanka Tsakovska, Petko Alov, Ilza Pajeva, Maria Miteva, Tania Pencheva
This work is licensed under a Creative Commons Attribution 4.0 International License.
The journal Biomath is an open access journal. All published articles are immeditely available online and the respective DOI link activated. All articles can be access for free and no reader registration of any sort is required. No fees are charged to authors for article submission or processing. Online publications are funded through volunteer work, donations and grants.
Authors who publish with this journal agree to the following terms:
- Authors retain copyright and grant the journal right of first publication with the work simultaneously licensed under a Creative Commons Attribution License 4.0 that allows others to share the work with an acknowledgement of the work's authorship and initial publication in this journal.
- Authors are able to enter into separate, additional contractual arrangements for the non-exclusive distribution of the journal's published version of the work (e.g., post it to an institutional repository or publish it in a book), with an acknowledgement of its initial publication in this journal.
- Authors are permitted and encouraged to post their work online (e.g., in institutional repositories or on their website) prior to and during the submission process, as it can lead to productive exchanges, as well as earlier and greater citation of published work (See The Effect of Open Access).
