Sponer J - Search Results

1

Molecular Simulations to Investigate the Impact of N6-Methylation in RNA Recognition: Improving Accuracy and Precision of Binding Free Energy Prediction.

Piomponi V, Krepl M, Sponer J, Bussi G. Piomponi V, et al. Among authors: sponer j. J Phys Chem B. 2024 Sep 19;128(37):8896-8907. doi: 10.1021/acs.jpcb.4c03397. Epub 2024 Sep 6. J Phys Chem B. 2024. PMID: 39240243

2

Leading RNA tertiary interactions: structures, energies, and water insertion of A-minor and P-interactions. A quantum chemical view.

Sponer JE, Réblova K, Mokdad A, Sychrovský V, Leszczynski J, Sponer J. Sponer JE, et al. Among authors: sponer j. J Phys Chem B. 2007 Aug 2;111(30):9153-64. doi: 10.1021/jp0704261. Epub 2007 Jun 29. J Phys Chem B. 2007. PMID: 17602515

3

Trans Hoogsteen/sugar edge base pairing in RNA. Structures, energies, and stabilities from quantum chemical calculations.

Mládek A, Sharma P, Mitra A, Bhattacharyya D, Sponer J, Sponer JE. Mládek A, et al. Among authors: sponer j, sponer je. J Phys Chem B. 2009 Feb 12;113(6):1743-55. doi: 10.1021/jp808357m. J Phys Chem B. 2009. PMID: 19152254

4

Dependence of A-RNA simulations on the choice of the force field and salt strength.

Besseová I, Otyepka M, Réblová K, Sponer J. Besseová I, et al. Among authors: sponer j. Phys Chem Chem Phys. 2009 Dec 7;11(45):10701-11. doi: 10.1039/b911169g. Epub 2009 Sep 24. Phys Chem Chem Phys. 2009. PMID: 20145814

5

Structural dynamics of the box C/D RNA kink-turn and its complex with proteins: the role of the A-minor 0 interaction, long-residency water bridges, and structural ion-binding sites revealed by molecular simulations.

Spacková N, Réblová K, Sponer J. Spacková N, et al. Among authors: sponer j. J Phys Chem B. 2010 Aug 19;114(32):10581-93. doi: 10.1021/jp102572k. J Phys Chem B. 2010. PMID: 20701388

6

A-minor tertiary interactions in RNA kink-turns. Molecular dynamics and quantum chemical analysis.

Réblová K, Šponer JE, Špačková N, Beššeová I, Šponer J. Réblová K, et al. Among authors: sponer j, sponer je. J Phys Chem B. 2011 Dec 1;115(47):13897-910. doi: 10.1021/jp2065584. Epub 2011 Nov 7. J Phys Chem B. 2011. PMID: 21999672

7

Simulations of A-RNA duplexes. The effect of sequence, solute force field, water model, and salt concentration.

Beššeová I, Banáš P, Kührová P, Košinová P, Otyepka M, Šponer J. Beššeová I, et al. Among authors: sponer j. J Phys Chem B. 2012 Aug 23;116(33):9899-916. doi: 10.1021/jp3014817. Epub 2012 Aug 9. J Phys Chem B. 2012. PMID: 22809319

8

Reference simulations of noncanonical nucleic acids with different χ variants of the AMBER force field: quadruplex DNA, quadruplex RNA and Z-DNA.

Krepl M, Zgarbová M, Stadlbauer P, Otyepka M, Banáš P, Koča J, Cheatham TE 3rd, Jurečka P, Sponer J. Krepl M, et al. Among authors: sponer j. J Chem Theory Comput. 2012 Jul 10;8(7):2506-2520. doi: 10.1021/ct300275s. Epub 2012 Jun 5. J Chem Theory Comput. 2012. PMID: 23197943 Free PMC article.

9

Effect of guanine to inosine substitution on stability of canonical DNA and RNA duplexes: molecular dynamics thermodynamics integration study.

Krepl M, Otyepka M, Banáš P, Šponer J. Krepl M, et al. Among authors: sponer j. J Phys Chem B. 2013 Feb 14;117(6):1872-9. doi: 10.1021/jp311180u. Epub 2013 Feb 5. J Phys Chem B. 2013. PMID: 23350675

10

Bioinformatics and molecular dynamics simulation study of L1 stalk non-canonical rRNA elements: kink-turns, loops, and tetraloops.

Krepl M, Réblová K, Koča J, Sponer J. Krepl M, et al. Among authors: sponer j. J Phys Chem B. 2013 May 9;117(18):5540-55. doi: 10.1021/jp401482m. Epub 2013 Apr 24. J Phys Chem B. 2013. PMID: 23534440

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