Sieradzan A - Search Results

1

On the need to introduce environmental characteristics in ab initio protein structure prediction using a coarse-grained UNRES force field.

Roterman I, Sieradzan A, Stapor K, Fabian P, Wesołowski P, Konieczny L. Roterman I, et al. Among authors: sieradzan a. J Mol Graph Model. 2022 Jul;114:108166. doi: 10.1016/j.jmgm.2022.108166. Epub 2022 Mar 18. J Mol Graph Model. 2022. PMID: 35325843 Free article.

2

Folding and self-assembly of a small heterotetramer.

Yaşar F, Sieradzan AK, Hansmann UH. Yaşar F, et al. J Chem Phys. 2014 Mar 14;140(10):105103. doi: 10.1063/1.4868140. J Chem Phys. 2014. PMID: 24628212 Free PMC article.

3

A unified coarse-grained model of biological macromolecules based on mean-field multipole-multipole interactions.

Liwo A, Baranowski M, Czaplewski C, Gołaś E, He Y, Jagieła D, Krupa P, Maciejczyk M, Makowski M, Mozolewska MA, Niadzvedtski A, Ołdziej S, Scheraga HA, Sieradzan AK, Slusarz R, Wirecki T, Yin Y, Zaborowski B. Liwo A, et al. Among authors: sieradzan ak. J Mol Model. 2014 Aug;20(8):2306. doi: 10.1007/s00894-014-2306-5. Epub 2014 Jul 15. J Mol Model. 2014. PMID: 25024008 Free PMC article.

4

Physics-based potentials for the coupling between backbone- and side-chain-local conformational states in the UNited RESidue (UNRES) force field for protein simulations.

Sieradzan AK, Krupa P, Scheraga HA, Liwo A, Czaplewski C. Sieradzan AK, et al. J Chem Theory Comput. 2015 Feb 10;11(2):817-31. doi: 10.1021/ct500736a. J Chem Theory Comput. 2015. PMID: 25691834 Free PMC article.

5

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

6

Introduction of periodic boundary conditions into UNRES force field.

Sieradzan AK. Sieradzan AK. J Comput Chem. 2015 May 5;36(12):940-6. doi: 10.1002/jcc.23864. Epub 2015 Mar 8. J Comput Chem. 2015. PMID: 25753584

7

Performance of protein-structure predictions with the physics-based UNRES force field in CASP11.

Krupa P, Mozolewska MA, Wiśniewska M, Yin Y, He Y, Sieradzan AK, Ganzynkowicz R, Lipska AG, Karczyńska A, Ślusarz M, Ślusarz R, Giełdoń A, Czaplewski C, Jagieła D, Zaborowski B, Scheraga HA, Liwo A. Krupa P, et al. Among authors: sieradzan ak. Bioinformatics. 2016 Nov 1;32(21):3270-3278. doi: 10.1093/bioinformatics/btw404. Epub 2016 Jul 4. Bioinformatics. 2016. PMID: 27378298 Free PMC article.

8

Shielding effect in protein folding.

Sieradzan AK, Lipska AG, Lubecka EA. Sieradzan AK, et al. J Mol Graph Model. 2018 Jan;79:118-132. doi: 10.1016/j.jmgm.2017.10.018. Epub 2017 Nov 1. J Mol Graph Model. 2018. PMID: 29161634

9

Extension of coarse-grained UNRES force field to treat carbon nanotubes.

Sieradzan AK, Mozolewska MA. Sieradzan AK, et al. J Mol Model. 2018 Apr 26;24(5):121. doi: 10.1007/s00894-018-3656-1. J Mol Model. 2018. PMID: 29700628 Free PMC article.

10

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.

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