List of Publications of Elena Lilkova

Journal Papers

1. L. Litov, P. Petkov, M. Rangelov, N. Ilieva, E. Lilkova, N. Todorova, E. Krachmarova, K. Malinova, A. Gospodinov, R. Hristova, I. Ivanov, G. Nacheva,, Molecular Mechanism of the Anti-Inflammatory Action of Heparin, International Journal of Molecular Sciences, 22,(19), 10730, (2021), DOI: 10.3390/ijms221910730
2. E. Lilkova, N. Ilieva, P. Petkov, E. Krachmarova, G. Nacheva and L. Litov, Molecular Dynamics Simulations of His 6-FLAG-hIFN 𝛾 Fusion Glycoproteins, In: Georgiev I., Kostadinov H., Lilkova E. (eds) Advanced Computing in Industrial Mathematics. BGSIAM 2018. Studies in Computational Intelligence, 961, pp. 256-267, (2021), DOI: 10.1007/978-3-030-71616-5_23
3. E. Lilkova, N. Ilieva, P. Petkov, M. Rangelov and L. Litov, In silico indications for human interferon gamma inhibition by heparin, AIP Conference Proceedings 2302, (2020), 020003, DOI: 10.1063/5.0033537, SJR = 0.19.
4. N. Ilieva, P. Petkov, E. Lilkova, T. Lazarova, A. Dolashki, L. Velkova, P. Dolashka and L. Litov, In Silico Study on the Structure of Novel Natural Bioactive Peptides., In: Large-Scale Scientific Computing. LSSC 2019. Lecture Notes in Computer Science, 11958, (2020), pp 332-339, DOI: 10.1007/978-3-030-41032-2_38
5. P. Petkov, E. Lilkova, N. Ilieva, and L. Litov, Self-Association of Antimicrobial Peptides: A Molecular Dynamics Simulation Study on Bombinin, International Journal of Molecular Sciences, 20(21), 5450, (2019), DOI: 10.3390/ijms20215450
6. E. Lilkova, P. Petkov, N. Ilieva, E. Krachmarova, G. Nacheva and L. Litov, Molecular modeling of the effects of glycosylation on the structure and dynamics of human interferon-gamma., Journal of Molecular Modeling, 25(5) 127 (2019), DOI: 10.1007/s00894-019-4013-8
7. R. Marinova, P. Petkov, N. Ilieva, E. Lilkova, and L. Litov, Molecular Dynamics Study of the Solution Behaviour of Antimicrobial Peptide Indolicidin, In: Georgiev K., Todorov M., Georgiev I. (eds) Advanced Computing in Industrial Mathematics. BGSIAM 2017. Studies in Computational Intelligence, 793(5), pp. 257-265, (2018), DOI: 10.1007/978-3-319-97277-0_21
8. P. Petkov, R. Marinova, V. Kochev, N. Ilieva, E. Lilkova, and L. Litov, Computational study of solution behavior of magainin 2 monomers, Journal of Biomolecular Structure and Dynamics, 37(5), pp. 1231-1240, (2019), DOI: 10.1080/07391102.2018.1454850
9. P. Petkov, E. Lilkova, N. Ilieva, G. Nacheva, I. Ivanov, and L. Litov, Computational modelling of the full length hIFN-γ homodimer., In: Large-Scale Scientific Computing. LSSC 2017. Lecture Notes in Computer Science, 10665, (2018), pp 544-551, DOI: 10.1007/978-3-319-73441-5_60
10. N. Ilieva, E. Lilkova, L. Litov, B. Pavlov, P. Petkov , On the Use of Large Intel Xeon Phi Clusters for GEANT4-based Simulations, Cybernetics and Information Technologies, 17(5), (2017), pp 101-109, DOI: 10.1515/cait-2017-0059
11. E. Krachmarova, M. Tileva, E. Lilkova, P. Petkov, K. Maskos, N. Ilieva, I. Ivanov, L. Litov and G. Nacheva, His-FLAG Tag as a Fusion Partner of Glycosylated Human Interferon-Gamma and Its Mutant: Gain or Loss?, BioMed Research International, vol. 2017, (2017), 3018608, DOI: 10.1155/2017/3018608
12. N. Ilieva, E. Lilkova, P. Petkov, and L. Litov, Semi-rigidity vs. flexibility in collective variables preselection for metadynamics studies of large proteins, AIP Conference Proceedings 1773, (2016), 110007, DOI: 10.1063/1.4965011
13. E. Lilkova, P. Petkov, N. Ilieva, and L. Litov, Towards molecular modeling of the impact of heparin-derived oligosaccharides on hIFN-γ binding, AIP Conference Proceedings 1684, (2015), 030008, DOI: 10.1063/1.4934292
14. G. Nacheva, E. Lilkova, P. Petkov, P. Petkov, N. Ilieva, I. Ivanov, and L. Litov, In silico studies on the stability of human interferon-gamma mutants, Biotechnology & Biotechnological Equipment 26(supp 1), (2012), pp 200-204, DOI: 10.5504/50YRTIMB.2011.0036
15. E. Lilkova, G. Nacheva, P. Petkov, P. Petkov, S. Markov, N. Ilieva, and L. Litov, Metadynamics study of mutant human interferon-gamma forms, Computers and Mathematics with Applications 64(3), (2012), pp 272-277, DOI: 10.1016/j.camwa.2012.01.061
16. E. Lilkova, L. Litov, P. Petkov, P. Petkov, S. Markov, and N. Ilieva, Computer simulations of human interferon gamma mutated forms, AIP Conference Proceedings 1203, (2010), pp. 914-919, DOI: 10.1063/1.3322582

Conference Papers

1. E. Lilkova, N. Ilieva, P. Petkov, L. Litov, Interaction of hIFNγ and Heparin-Derived Oligosaccharides(extended abstract), In: BGSIAM'21 Extended Abstracts, (2021), 21--23 December, 2021, Sofia, Bulgaria, (Fastumprint, Sofia, 2020; ISSN: 1313-3357), p. 37
2. N. Ilieva, P. Petkov, M. Rangelov, N. Todorova, E. Lilkova, L. Litov, Suggesting a new approach for management of the cytokine storm using computer modeling and simulations(extended abstract), In: BGSIAM'20 Extended Abstracts, (2020), 15--17 December, 2020, Sofia, Bulgaria, (Fastumprint, Sofia, 2020; ISSN: 1313-3357), p. 22
3. E. Lilkova, N. Ilieva, P. Petkov, L. Litov, Computational study of the aggregation behaviour of antimicrobial peptides(extended abstract), In: BGSIAM'20 Extended Abstracts, (2020), 15--17 December, 2020, Sofia, Bulgaria, (Fastumprint, Sofia, 2020; ISSN: 1313-3357), p. 34
4. T. Lazarova, P. Petkov, N. Ilieva, E. Lilkova, L. Litov, In silico study of the self-organisation process in mono-component solutions of antimicrobial peptides(extended abstract), In: BGSIAM'19 Extended Abstracts, (2019), 17--19 December, 2019, Sofia, Bulgaria, (Fastumprint, Sofia, 2019; ISSN: 1313-3357), p. 51
5. N. Ilieva, E. Lilkova, P. Petkov, L. Litov, Tracing point-mutation implications in human interferon-gamma variants (extended abstract), In: BGSIAM'18 Extended Abstracts, (2018), 18--20 December, 2018, Sofia, Bulgaria, (Fastumprint, Sofia, 2018; ISSN: 1313-3357), p. 48
6. E. Lilkova, N. Ilieva, P. Petkov, E. Krachmarova, G. Nacheva, L. Litov, Molecular dynamics simulations of His_6--FLAG--hIFNγ fusion glycoproteins (extended abstract), In: BGSIAM'18 Extended Abstracts, (2018), 18--20 December, 2018, Sofia, Bulgaria, (Fastumprint, Sofia, 2018; ISSN: 1313-3357), p. 71
7. E. Lilkova, N. Ilieva, P. Petkov, and L. Litov, Study of Human Interferon-Gamma Glycosilation by Molecular Dynamics Simulations, In: Proc. of the Int. Conf. NMSCAA'18, (2018), 28--31 May, 2018, Hissarya, Bulgaria, (Fastumprint, Sofia, 2018; ISBN: 978-954-91700-7-8), p. 60--64
8. N. Ilieva, P. Petkov, E. Lilkova, R. Marinova, A. J. Niemi, J. He, and L. Litov, Biomolecular studies in coarse-grain approaches: the good, the bad, and the beautiful (extended abstract), In: BGSIAM'17 Extended Abstracts, (2017), 20--22 December, 2017, Sofia, Bulgaria, (Fastumprint, Sofia, 2017; ISSN: 1313-3357), p. 48
9. E. Lilkova, N. Ilieva, P. Petkov, and L. Litov, Influence of glycosilation on human interferon gamma dynamics -- setting up the stage (extended abstract), In: BGSIAM'17 Extended Abstracts, (2017), 20--22 December, 2017, Sofia, Bulgaria, (Fastumprint, Sofia, 2017; ISSN: 1313-3357), p. 68
10. R. Marinova, P. Petkov, N. Ilieva, E. Lilkova, and L. Litov, Cluster formation from disordered peptides in water solution: a coarse-grain molecular dynamics approach (extended abstract), In: BGSIAM'17 Extended Abstracts, (2017), 20--22 December, 2017, Sofia, Bulgaria, (Fastumprint, Sofia, 2017; ISSN: 1313-3357), p. 71
11. N. Ilieva, E. Lilkova, P. Petkov, and L. Litov, Identification of structural units in large proteins for guided metadynamics investigations (extended abstract), In: BGSIAM'16 Proc., (2016), 20--22 December, 2016, Sofia, Bulgaria, (Fastumprint, Sofia, 2016; ISSN: 1313-3357), p. 35
12. N. Ilieva, E. Lilkova, P. Petkov, and L. Litov, Metadynamics of Large Proteins with Collective Variables Preselection by a Spatiotemporal Multistage Consensus Clustering (extended abstract), In: Proc. Int. Conf. NMSCAA'16, (2016), May 29 –- June 2, 2016, Hissarya, Bulgaria. , K. Georgiev (Ed.) (Fastumprint, Sofia, 2016; ISBN: 978-619-7223-18-7), p. 33
13. P. Petkov, E. Lilkova, D. Grancharov, S. Markov, N. Ilieva, and L. Litov, Libraries for treatment of electrostatic interactions for Intel Xeon Phi (extended abstract), In: Proc. Int. Conf. NMSCAA'14, (2014), May 19 – 22, 2014, Bansko, Bulgaria. K. Georgiev (Ed.) (Demetra Ltd, Sofia, 2014; ISBN: 978-954-91700-7-8), p. 93
14. D. Grancharov, E.Lilkova, N. Ilieva, P. Petkov, L. Litov, Open Problems in High-Performance Molecular-Dynamics Simulations, Information technologies and control 01/2012; Year X(2):23-29 (2012).
15. P. Petkov, E. Lilkova, P. Petkov, N. Ilieva, and L. Litov, Application of metadynamics for investigation of human interferon gamma mutated forms, Proc. 6th International Scientific Conference Computer Science 2011, (2011), ISBN: 978-954-438-914-7, pp. 347-352.
16. D. Grancharov, P. Petkov, E. Lilkova, N. Ilieva, and L. Litov, Investigation of Binding Affinity of hIFN-gamma Mutated Forms with the Rosetta Suite of Programs, Proc. 6th International Scientific Conference Computer Science 2011, (2011), ISBN: 978-954-438-914-7, pp. 353-357.

White Papers

1. P. Petkov, D. Grancharov, S. Markov, G. Georgiev, E. Lilkova, N. Ilieva, L. Litov, Massively parallel Poisson Equation Solver for hybrid Intel Xeon - Xeon Phi HPC Systems, PRACE whitepapers, (2017), DOI: 10.5281/zenodo.822701
2. P. Petkov, I. Todorov, D. Grancharov, N. Ilieva, E. Lilkova, L. Litov, and S. Markov, Development of an advanced implicit solvent model in DL_POLY, PRACE whitepapers, (2014), DOI: 10.5281/zenodo.823019
3. P. Petkov, I. Todorov, D. Grancharov, N. Ilieva, E. Lilkova, L. Litov, and S. Markov, Development of a Grid-based Electrostatics Model in a Memory-Distributed Manner for DL_POLY_4, PRACE whitepapers, (2014), DOI: 10.5281/zenodo.822960
4. P. Petkov, E. Lilkova, S. Markov, D. Grancharov, N. Ilieva, L. Litov, AGBNP2 Implicit Solvent Library for Intel® MIC Architecture, PRACE whitepapers, (2014), DOI: 10.5281/zenodo.822731
5. D. Grancharov, E. Lilkova, N. Ilieva1, P. Petkov, S. Markov and L. Litov, Analysis of symplectic integration algorithms with variable step size for petascale biomolecular simulations, PRACE whitepapers (2012)., DOI: 10.5281/zenodo.806923