Sieradzan AK - Search Results

1

Molecular dynamics insights into protein-glycosaminoglycan systems from microsecond-scale simulations.

Bojarski KK, Sieradzan AK, Samsonov SA. Bojarski KK, et al. Among authors: sieradzan ak. Biopolymers. 2019 Jul;110(7):e23252. doi: 10.1002/bip.23252. Epub 2019 Jan 22. Biopolymers. 2019. PMID: 30667535

2

Studies of conformational changes of an arginine-binding protein from Thermotoga maritima in the presence and absence of ligand via molecular dynamics simulations with the coarse-grained UNRES force field.

Lipska AG, Sieradzan AK, Krupa P, Mozolewska MA, D'Auria S, Liwo A. Lipska AG, et al. Among authors: sieradzan ak. J Mol Model. 2015 Mar;21(3):64. doi: 10.1007/s00894-015-2609-1. Epub 2015 Mar 3. J Mol Model. 2015. PMID: 25731877

3

UNRES server for physics-based coarse-grained simulations and prediction of protein structure, dynamics and thermodynamics.

Czaplewski C, Karczynska A, Sieradzan AK, Liwo A. Czaplewski C, et al. Among authors: sieradzan ak. Nucleic Acids Res. 2018 Jul 2;46(W1):W304-W309. doi: 10.1093/nar/gky328. Nucleic Acids Res. 2018. PMID: 29718313 Free PMC article.

4

The molecular mechanism of structural changes in the antimicrobial peptide CM15 upon complex formation with drug molecule suramin: a computational analysis.

Kohut G, Sieradzan A, Zsila F, Juhász T, Bősze S, Liwo A, Samsonov SA, Beke-Somfai T. Kohut G, et al. Phys Chem Chem Phys. 2019 May 28;21(20):10644-10659. doi: 10.1039/c9cp00471h. Epub 2019 May 13. Phys Chem Chem Phys. 2019. PMID: 31080973

5

Evaluation of the scale-consistent UNRES force field in template-free prediction of protein structures in the CASP13 experiment.

Lubecka EA, Karczyńska AS, Lipska AG, Sieradzan AK, Ziȩba K, Sikorska C, Uciechowska U, Samsonov SA, Krupa P, Mozolewska MA, Golon Ł, Giełdoń A, Czaplewski C, Ślusarz R, Ślusarz M, Crivelli SN, Liwo A. Lubecka EA, et al. Among authors: sieradzan ak. J Mol Graph Model. 2019 Nov;92:154-166. doi: 10.1016/j.jmgm.2019.07.013. Epub 2019 Jul 26. J Mol Graph Model. 2019. PMID: 31376733

6

Improved Consensus-Fragment Selection in Template-Assisted Prediction of Protein Structures with the UNRES Force Field in CASP13.

Karczyńska AS, Ziȩba K, Uciechowska U, Mozolewska MA, Krupa P, Lubecka EA, Lipska AG, Sikorska C, Samsonov SA, Sieradzan AK, Giełdoń A, Liwo A, Ślusarz R, Ślusarz M, Lee J, Joo K, Czaplewski C. Karczyńska AS, et al. Among authors: sieradzan ak. J Chem Inf Model. 2020 Mar 23;60(3):1844-1864. doi: 10.1021/acs.jcim.9b00864. Epub 2020 Feb 11. J Chem Inf Model. 2020. PMID: 31999919 Free PMC article.

7

Truncation of Huia versabilis Bowman-Birk inhibitor increases its selectivity, matriptase-1 inhibitory activity and proteolytic stability.

Gitlin-Domagalska A, Dębowski D, Gucwa K, Starego D, Ptaszyńska N, Sieradzan A, Karczyńska A, Samsonov SA, Mangold M, Gütschow M, Łęgowska A, Rolka K. Gitlin-Domagalska A, et al. Biochimie. 2020 Apr-May;171-172:178-186. doi: 10.1016/j.biochi.2020.03.006. Epub 2020 Mar 10. Biochimie. 2020. PMID: 32169666

8

Investigation of Phosphorylation-Induced Folding of an Intrinsically Disordered Protein by Coarse-Grained Molecular Dynamics.

Sieradzan AK, Korneev A, Begun A, Kachlishvili K, Scheraga HA, Molochkov A, Senet P, Niemi AJ, Maisuradze GG. Sieradzan AK, et al. J Chem Theory Comput. 2021 May 11;17(5):3203-3220. doi: 10.1021/acs.jctc.1c00155. Epub 2021 Apr 28. J Chem Theory Comput. 2021. PMID: 33909430 Free PMC article.

9

Modeling protein structures with the coarse-grained UNRES force field in the CASP14 experiment.

Antoniak A, Biskupek I, Bojarski KK, Czaplewski C, Giełdoń A, Kogut M, Kogut MM, Krupa P, Lipska AG, Liwo A, Lubecka EA, Marcisz M, Maszota-Zieleniak M, Samsonov SA, Sieradzan AK, Ślusarz MJ, Ślusarz R, Wesołowski PA, Ziȩba K. Antoniak A, et al. Among authors: sieradzan ak. J Mol Graph Model. 2021 Nov;108:108008. doi: 10.1016/j.jmgm.2021.108008. Epub 2021 Aug 17. J Mol Graph Model. 2021. PMID: 34419932

10

Theory and Practice of Coarse-Grained Molecular Dynamics of Biologically Important Systems.

Liwo A, Czaplewski C, Sieradzan AK, Lipska AG, Samsonov SA, Murarka RK. Liwo A, et al. Among authors: sieradzan ak. Biomolecules. 2021 Sep 11;11(9):1347. doi: 10.3390/biom11091347. Biomolecules. 2021. PMID: 34572559 Free PMC article.

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