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Serdal Kirmizialtin, Ph.D. - Publications

Affiliations: 
2007 Chemistry and Biochemistry University of Texas at Austin, Austin, Texas, U.S.A. 
Area:
Physical Chemistry, General Biophysics, Computer Science
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39 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2023 He W, San Emeterio J, Woodside MT, Kirmizialtin S, Pollack L. Atomistic structure of the SARS-CoV-2 pseudoknot in solution from SAXS-driven molecular dynamics. Nucleic Acids Research. PMID 37819014 DOI: 10.1093/nar/gkad809  0.3
2023 Liu C, Henning-Knechtel A, Österlund N, Wu J, Wang G, Gräslund RAO, Kirmizialtin S, Luo J. Oligomer Dynamics of LL-37 Truncated Fragments Probed by α-Hemolysin Pore and Molecular Simulations. Small (Weinheim An Der Bergstrasse, Germany). e2206232. PMID 37170734 DOI: 10.1002/smll.202206232  0.35
2022 He W, Henning-Knechtel A, Kirmizialtin S. Visualizing RNA Structures by SAXS-Driven MD Simulations. Frontiers in Bioinformatics. 2: 781949. PMID 36304317 DOI: 10.3389/fbinf.2022.781949  0.369
2022 Chen YL, He W, Kirmizialtin S, Pollack L. Insights into the structural stability of major groove RNA triplexes by WAXS-guided MD simulations. Cell Reports. Physical Science. 3. PMID 35936555 DOI: 10.1016/j.xcrp.2022.100971  0.327
2021 He W, Chen YL, Pollack L, Kirmizialtin S. The structural plasticity of nucleic acid duplexes revealed by WAXS and MD. Science Advances. 7. PMID 33893104 DOI: 10.1126/sciadv.abf6106  0.314
2020 Kirmizialtin S, Pitici F, Cardenas AE, Elber R, Thirumalai D. Dramatic Shape Changes Occur as Cytochrome Folds. The Journal of Physical Chemistry. B. PMID 32840372 DOI: 10.1021/Acs.Jpcb.0C05802  0.421
2020 Srivastava A, Timsina R, Heo S, Dewage SW, Kirmizialtin S, Qiu X. Structure-guided DNA-DNA attraction mediated by divalent cations. Nucleic Acids Research. PMID 32542319 DOI: 10.1093/Nar/Gkaa499  0.306
2020 Kleiman DE, Naleem N, Kirmizialtin S. Exploring the Ion-Mediated RNA Interactions of a Helix-Junction-Helix RNA Model through Well-Tempered Metadynamics Simulations Biophysical Journal. 118: 68a-69a. DOI: 10.1016/J.Bpj.2019.11.549  0.369
2019 Kim DN, Moriarty NW, Kirmizialtin S, Afonine PV, Poon B, Sobolev OV, Adams PD, Sanbonmatsu K. cryo_fit: Democratization of Flexible Fitting for Cryo-EM. Journal of Structural Biology. PMID 31279069 DOI: 10.1016/J.Jsb.2019.05.012  0.715
2018 Plumridge A, Katz AM, Calvey GD, Elber R, Kirmizialtin S, Pollack L. Revealing the distinct folding phases of an RNA three-helix junction. Nucleic Acids Research. PMID 29762712 DOI: 10.1093/Nar/Gky363  0.405
2018 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. Calix[4]arene-based Porous Organic Nanosheets. Acs Applied Materials & Interfaces. PMID 29687997 DOI: 10.1021/Acsami.8B03800  0.347
2018 Skorjanc T, Shetty D, Sharma S, Raya J, Traboulsi H, Han DS, Lalla J, Newlon R, Jagannathan R, Kirmizialtin S, Olsen JC, Trabolsi A. Redox-responsive Covalent Organic Nanosheets from Viologens and Calix[4]arene for Iodine and Toxic Dye Capture. Chemistry (Weinheim An Der Bergstrasse, Germany). PMID 29665187 DOI: 10.1002/Chem.201800623  0.322
2018 Plumridge A, Katz AM, Calvey GD, Elber R, Kirmizialtin S, Pollack L. Time-Resolved SAXS and Ensemble Modelling Reveal Magnesium Orchestration across an RNA Folding Landscape Biophysical Journal. 114: 433a. DOI: 10.1016/J.Bpj.2017.11.2399  0.353
2017 Gulay SP, Bista S, Varshney A, Kirmizialtin S, Sanbonmatsu KY, Dinman JD. Tracking fluctuation hotspots on the yeast ribosome through the elongation cycle. Nucleic Acids Research. PMID 28334755 DOI: 10.1093/Nar/Gkx112  0.689
2017 Kirmizialtin S, Yildiz BS, Yildiz I. A DFT-based mechanistic study on the formation of oximes Journal of Physical Organic Chemistry. 30: e3711. DOI: 10.1002/Poc.3711  0.312
2016 Rianasari I, Benyettou F, Sharma SK, Blanton T, Kirmizialtin S, Jagannathan R. A Chemical Template for Synthesis of Molecular Sheets of Calcium Carbonate. Scientific Reports. 6: 25393. PMID 27145699 DOI: 10.1038/Srep25393  0.313
2015 Kirmizialtin S, Johnson KA, Elber R. Enzyme Selectivity of HIV Reverse Transcriptase: Conformations, Ligands, and Free Energy Partition. The Journal of Physical Chemistry. B. PMID 26225641 DOI: 10.1016/J.Bpj.2015.11.410  0.318
2015 Kirmizialtin S, Loerke J, Behrmann E, Spahn CM, Sanbonmatsu KY. Using Molecular Simulation to Model High-Resolution Cryo-EM Reconstructions. Methods in Enzymology. 558: 497-514. PMID 26068751 DOI: 10.1016/Bs.Mie.2015.02.011  0.654
2015 Kirmizialtin S, Hennelly SP, Schug A, Onuchic JN, Sanbonmatsu KY. Integrating molecular dynamics simulations with chemical probing experiments using SHAPE-FIT. Methods in Enzymology. 553: 215-34. PMID 25726467 DOI: 10.1016/Bs.Mie.2014.10.061  0.723
2014 Jiang Y, Kirmizialtin S, Sanchez IC. Dynamic void distribution in myoglobin and five mutants. Scientific Reports. 4: 4011. PMID 24500195 DOI: 10.1038/Srep04011  0.369
2014 Seckler J, Kirmizialtin S, Johnson KA, Grossfield A. Covariance Ration Analysis of Molecular Dynamics Trajectories of Hiv-1 Reverse Transcriptase Biophysical Journal. 106: 653a. DOI: 10.1016/J.Bpj.2013.11.3611  0.39
2014 Kirmizialtin S, Sanbonmatsu KY. Molecular Dynamics Simulations of Ribosomes: Integrating Theory and Experiment Biophysical Journal. 106: 39a. DOI: 10.1016/J.Bpj.2013.11.288  0.688
2013 Meisburger SP, Sutton JL, Chen H, Pabit SA, Kirmizialtin S, Elber R, Pollack L. Polyelectrolyte properties of single stranded DNA measured using SAXS and single-molecule FRET: Beyond the wormlike chain model. Biopolymers. 99: 1032-45. PMID 23606337 DOI: 10.1002/Bip.22265  0.396
2012 Kirmizialtin S, Nguyen V, Johnson KA, Elber R. How conformational dynamics of DNA polymerase select correct substrates: experiments and simulations. Structure (London, England : 1993). 20: 618-27. PMID 22483109 DOI: 10.1016/J.Str.2012.02.018  0.377
2012 Kirmizialtin S, Silalahi AR, Elber R, Fenley MO. The ionic atmosphere around A-RNA: Poisson-Boltzmann and molecular dynamics simulations. Biophysical Journal. 102: 829-38. PMID 22385854 DOI: 10.1016/J.Bpj.2011.12.055  0.374
2012 Kirmizialtin S, Pabit SA, Meisburger SP, Pollack L, Elber R. RNA and its ionic cloud: solution scattering experiments and atomically detailed simulations. Biophysical Journal. 102: 819-28. PMID 22385853 DOI: 10.1016/J.Bpj.2012.01.013  0.414
2012 Kirmizialtin S, Elber R, Johnson KA. Antlion Strategy for Enzyme Specificity Biophysical Journal. 102: 273a. DOI: 10.1016/J.Bpj.2011.11.1502  0.416
2011 Kirmizialtin S, Elber R. Revisiting and computing reaction coordinates with Directional Milestoning. The Journal of Physical Chemistry. A. 115: 6137-48. PMID 21500798 DOI: 10.1021/Jp111093C  0.32
2010 Kirmizialtin S, Elber R. Computational exploration of mobile ion distributions around RNA duplex. The Journal of Physical Chemistry. B. 114: 8207-20. PMID 20518549 DOI: 10.1021/Jp911992T  0.367
2010 Kirmizialtin S, Elber R. Computational Exploration of Thermodynamics and Kinetics of Mobile Ions Around RNA Duplex Biophysical Journal. 98: 43a. DOI: 10.1016/J.Bpj.2009.12.245  0.346
2009 Kirmizialtin S, Elber R. Ionic Mixtures and Distributions Around RNA: Atomically Detailed Simulations with Replica Exchange Biophysical Journal. 96: 603a-604a. DOI: 10.1016/J.Bpj.2008.12.3187  0.327
2008 Kirmizialtin S, Makarov DE. Simulations of the untying of molecular friction knots between individual polymer strands. The Journal of Chemical Physics. 128: 094901. PMID 18331111 DOI: 10.1063/1.2835605  0.603
2007 Goodrich CP, Kirmizialtin S, Huyghues-Despointes BM, Zhu A, Scholtz JM, Makarov DE, Movileanu L. Single-molecule electrophoresis of beta-hairpin peptides by electrical recordings and Langevin dynamics simulations. The Journal of Physical Chemistry. B. 111: 3332-5. PMID 17388500 DOI: 10.1021/Jp071364H  0.576
2006 Kirmizialtin S, Huang L, Makarov DE. Computer simulations of protein translocation Physica Status Solidi (B) Basic Research. 243: 2038-2047. DOI: 10.1002/Pssb.200666812  0.602
2005 Huang L, Kirmizialtin S, Makarov DE. Computer simulations of the translocation and unfolding of a protein pulled mechanically through a pore. The Journal of Chemical Physics. 123: 124903. PMID 16392523 DOI: 10.1063/1.2008231  0.625
2005 Kirmizialtin S, Huang L, Makarov DE. Topography of the free-energy landscape probed via mechanical unfolding of proteins. The Journal of Chemical Physics. 122: 234915. PMID 16008495 DOI: 10.1063/1.1931659  0.601
2004 Kirmizialtin S, Ganesan V, Makarov DE. Translocation of a beta-hairpin-forming peptide through a cylindrical tunnel. The Journal of Chemical Physics. 121: 10268-77. PMID 15549903 DOI: 10.1063/1.1807832  0.581
2003 Kirmizialtin S, Menceloglu YZ, Baysal C. New surfactants design for CO2 applications: Molecular dynamics simulations of fluorocarbon-hydrocarbon oligomers Journal of Chemical Physics. 119: 4953-4961. DOI: 10.1063/1.1596873  0.345
2003 Kirmizialtin S, Baysal C, Erman B. Conformational properties of the bacterial polyester poly(3-hydroxy-5,8-decadienoate) Macromolecules. 36: 1132-1137. DOI: 10.1021/Ma021088Z  0.425
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