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Items: 1 to 20 of 26

1.

Comparative Computational Approach To Study Enzyme Reactions Using QM and QM-MM Methods.

Yildiz I, Yildiz BS, Kirmizialtin S.

ACS Omega. 2018 Nov 2;3(11):14689-14703. doi: 10.1021/acsomega.8b02638. eCollection 2018 Nov 30.

2.

Cryo_fit: Democratization of flexible fitting for cryo-EM.

Kim DN, Moriarty NW, Kirmizialtin S, Afonine PV, Poon B, Sobolev OV, Adams PD, Sanbonmatsu K.

J Struct Biol. 2019 Oct 1;208(1):1-6. doi: 10.1016/j.jsb.2019.05.012. Epub 2019 Jul 3.

PMID:
31279069
3.

Corrigendum: Redox-Responsive Covalent Organic Nanosheets from Viologens and Calix[4]arene for Iodine and Toxic Dye Capture.

Skorjanc T, Shetty D, Sharma SK, Raya J, Traboulsi H, Han DS, Lalla J, Newlon R, Jagannathan R, Kirmizialtin S, Olsen JC, Trabolsi A.

Chemistry. 2018 Oct 12;24(57):15392. doi: 10.1002/chem.201804498. Epub 2018 Sep 12. No abstract available.

PMID:
30311997
4.

Revealing the distinct folding phases of an RNA three-helix junction.

Plumridge A, Katz AM, Calvey GD, Elber R, Kirmizialtin S, Pollack L.

Nucleic Acids Res. 2018 Aug 21;46(14):7354-7365. doi: 10.1093/nar/gky363.

5.

Calix[4]arene-Based Porous Organic Nanosheets.

Shetty D, Skorjanc T, Raya J, Sharma SK, Jahovic I, Polychronopoulou K, Asfari Z, Han DS, Dewage S, Olsen JC, Jagannathan R, Kirmizialtin S, Trabolsi A.

ACS Appl Mater Interfaces. 2018 May 23;10(20):17359-17365. doi: 10.1021/acsami.8b03800. Epub 2018 May 10.

PMID:
29687997
6.

Redox-Responsive Covalent Organic Nanosheets from Viologens and Calix[4]arene for Iodine and Toxic Dye Capture.

Skorjanc T, Shetty D, Sharma SK, Raya J, Traboulsi H, Han DS, Lalla J, Newlon R, Jagannathan R, Kirmizialtin S, Olsen JC, Trabolsi A.

Chemistry. 2018 Jun 18;24(34):8648-8655. doi: 10.1002/chem.201800623. Epub 2018 May 22. Erratum in: Chemistry. 2018 Oct 12;24(57):15392.

PMID:
29665187
7.

The catalytic inactivation of the N-half of human hexokinase 2 and structural and biochemical characterization of its mitochondrial conformation.

Nawaz MH, Ferreira JC, Nedyalkova L, Zhu H, Carrasco-López C, Kirmizialtin S, Rabeh WM.

Biosci Rep. 2018 Feb 21;38(1). pii: BSR20171666. doi: 10.1042/BSR20171666. Print 2018 Feb 28.

8.

Tracking fluctuation hotspots on the yeast ribosome through the elongation cycle.

Gulay SP, Bista S, Varshney A, Kirmizialtin S, Sanbonmatsu KY, Dinman JD.

Nucleic Acids Res. 2017 May 5;45(8):4958-4971. doi: 10.1093/nar/gkx112.

9.

The in vitro selection world.

Jijakli K, Khraiwesh B, Fu W, Luo L, Alzahmi A, Koussa J, Chaiboonchoe A, Kirmizialtin S, Yen L, Salehi-Ashtiani K.

Methods. 2016 Aug 15;106:3-13. doi: 10.1016/j.ymeth.2016.06.003. Epub 2016 Jun 14. Review.

10.

A Chemical Template for Synthesis of Molecular Sheets of Calcium Carbonate.

Rianasari I, Benyettou F, Sharma SK, Blanton T, Kirmizialtin S, Jagannathan R.

Sci Rep. 2016 May 5;6:25393. doi: 10.1038/srep25393.

11.

Enzyme Selectivity of HIV Reverse Transcriptase: Conformations, Ligands, and Free Energy Partition.

Kirmizialtin S, Johnson KA, Elber R.

J Phys Chem B. 2015 Sep 3;119(35):11513-26. doi: 10.1021/acs.jpcb.5b05467. Epub 2015 Aug 14.

12.

Using Molecular Simulation to Model High-Resolution Cryo-EM Reconstructions.

Kirmizialtin S, Loerke J, Behrmann E, Spahn CMT, Sanbonmatsu KY.

Methods Enzymol. 2015;558:497-514. doi: 10.1016/bs.mie.2015.02.011. Epub 2015 May 9.

PMID:
26068751
13.

Integrating molecular dynamics simulations with chemical probing experiments using SHAPE-FIT.

Kirmizialtin S, Hennelly SP, Schug A, Onuchic JN, Sanbonmatsu KY.

Methods Enzymol. 2015;553:215-34. doi: 10.1016/bs.mie.2014.10.061. Epub 2015 Feb 7.

14.

Dynamic void distribution in myoglobin and five mutants.

Jiang Y, Kirmizialtin S, Sanchez IC.

Sci Rep. 2014 Feb 6;4:4011. doi: 10.1038/srep04011.

15.

Polyelectrolyte properties of single stranded DNA measured using SAXS and single-molecule FRET: Beyond the wormlike chain model.

Meisburger SP, Sutton JL, Chen H, Pabit SA, Kirmizialtin S, Elber R, Pollack L.

Biopolymers. 2013 Dec;99(12):1032-45. doi: 10.1002/bip.22265.

16.

Molecular machines.

Elber R, Kirmizialtin S.

Curr Opin Struct Biol. 2013 Apr;23(2):206-11. doi: 10.1016/j.sbi.2012.12.002. Epub 2013 Jan 8. Review.

PMID:
23305848
17.

How conformational dynamics of DNA polymerase select correct substrates: experiments and simulations.

Kirmizialtin S, Nguyen V, Johnson KA, Elber R.

Structure. 2012 Apr 4;20(4):618-27. doi: 10.1016/j.str.2012.02.018. Epub 2012 Apr 3.

18.

The ionic atmosphere around A-RNA: Poisson-Boltzmann and molecular dynamics simulations.

Kirmizialtin S, Silalahi AR, Elber R, Fenley MO.

Biophys J. 2012 Feb 22;102(4):829-38. doi: 10.1016/j.bpj.2011.12.055. Epub 2012 Feb 21.

19.

RNA and its ionic cloud: solution scattering experiments and atomically detailed simulations.

Kirmizialtin S, Pabit SA, Meisburger SP, Pollack L, Elber R.

Biophys J. 2012 Feb 22;102(4):819-28. doi: 10.1016/j.bpj.2012.01.013. Epub 2012 Feb 21.

20.

Revisiting and computing reaction coordinates with Directional Milestoning.

Kirmizialtin S, Elber R.

J Phys Chem A. 2011 Jun 16;115(23):6137-48. doi: 10.1021/jp111093c. Epub 2011 Apr 18.

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