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Sefika B. Ozkan - Publications

Affiliations: 
Physics Arizona State University, Tempe, AZ, United States 
Area:
General Biophysics, Biochemistry
Website:
http://ozkanlab.physics.asu.edu/banuozkan.html
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41 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
2021 Zou T, Woodrum BW, Halloran N, Campitelli P, Bobkov AA, Ghirlanda G, Ozkan SB. Local Interactions That Contribute Minimal Frustration Determine Foldability. The Journal of Physical Chemistry. B. PMID 33687216 DOI: 10.1021/acs.jpcb.1c00364  0.619
2020 Modi T, Campitelli P, Kazan IC, Ozkan SB. Protein folding stability and binding interactions through the lens of evolution: a dynamical perspective. Current Opinion in Structural Biology. 66: 207-215. PMID 33388636 DOI: 10.1016/j.sbi.2020.11.007  0.493
2020 Campitelli P, Modi T, Kumar S, Ozkan SB. The Role of Conformational Dynamics and Allostery in Modulating Protein Evolution. Annual Review of Biophysics. PMID 32075411 DOI: 10.1146/annurev-biophys-052118-115517  0.434
2020 Modi T, Ozkan SB, Pressé S. Information propagation in time through allosteric signaling Physical Review Research. 2. DOI: 10.1103/Physrevresearch.2.023367  0.562
2018 Butler BM, Kazan IC, Kumar A, Ozkan SB. Coevolving residues inform protein dynamics profiles and disease susceptibility of nSNVs. Plos Computational Biology. 14: e1006626. PMID 30496278 DOI: 10.1371/Journal.Pcbi.1006626  0.452
2018 Modi T, Huihui J, Ghosh K, Ozkan SB. Ancient thioredoxins evolved to modern-day stability-function requirement by altering native state ensemble. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 373. PMID 29735738 DOI: 10.1098/rstb.2017.0184  0.421
2018 Risso VA, Sanchez-Ruiz JM, Ozkan SB. Biotechnological and protein-engineering implications of ancestral protein resurrection. Current Opinion in Structural Biology. 51: 106-115. PMID 29660672 DOI: 10.1016/j.sbi.2018.02.007  0.431
2018 Ozkan SB. Allostery and Conformational Dynamics in Protein Evolution Biophysical Journal. 114: 400a-401a. DOI: 10.1016/j.bpj.2017.11.2217  0.444
2017 Campitelli P, Zhou H, Ghirlanda G, Ozkan SB. Dynamic Flexibility Index Sheds Light on Pin1 Allostery Biophysical Journal. 112: 317a. DOI: 10.1016/J.Bpj.2016.11.1720  0.328
2015 Kumar A, Butler BM, Kumar S, Ozkan SB. Integration of structural dynamics and molecular evolution via protein interaction networks: a new era in genomic medicine. Current Opinion in Structural Biology. PMID 26684487 DOI: 10.1016/J.Sbi.2015.11.002  0.377
2015 Kumar A, Campitelli P, Thorpe MF, Ozkan SB. Partial Unfoldingand Refolding for Structure Refinement: A Unified Approach of Geometric Simulations and Molecular Dynamics. Proteins. PMID 26476100 DOI: 10.1002/Prot.24947  0.461
2015 Kumar A, Glembo TJ, Ozkan SB. The Role of Conformational Dynamics and Allostery in the Disease Development of Human Ferritin. Biophysical Journal. PMID 26255589 DOI: 10.1016/J.Bpj.2015.06.060  0.397
2015 Zou T, Kumar A, Butler BM, Ozkan SB. 174 Mechanism of protein evolution: conformational dynamics and allostery. Journal of Biomolecular Structure & Dynamics. 33: 114. PMID 26103384 DOI: 10.1080/07391102.2015.1032811  0.66
2015 Kim H, Zou T, Modi C, Dörner K, Grunkemeyer TJ, Chen L, Fromme R, Matz MV, Ozkan SB, Wachter RM. A hinge migration mechanism unlocks the evolution of green-to-red photoconversion in GFP-like proteins. Structure (London, England : 1993). 23: 34-43. PMID 25565105 DOI: 10.1016/J.Bpj.2014.11.2086  0.644
2015 Butler BM, Gerek ZN, Kumar S, Ozkan SB. Conformational dynamics of nonsynonymous variants at protein interfaces reveals disease association. Proteins. 83: 428-35. PMID 25546381 DOI: 10.1002/prot.24748  0.388
2015 Zou T, Risso VA, Gavira JA, Sanchez-Ruiz JM, Ozkan SB. Evolution of conformational dynamics determines the conversion of a promiscuous generalist into a specialist enzyme. Molecular Biology and Evolution. 32: 132-43. PMID 25312912 DOI: 10.1093/Molbev/Msu281  0.593
2014 Zou T, Williams N, Ozkan SB, Ghosh K. Proteome folding kinetics is limited by protein halflife. Plos One. 9: e112701. PMID 25393560 DOI: 10.1371/Journal.Pone.0112701  0.639
2014 Dutta P, O'Connell KE, Ozkan SB, Sailer AW, Dev KK. The protein interacting with C-kinase (PICK1) interacts with and attenuates parkin-associated endothelial-like (PAEL) receptor-mediated cell death. Journal of Neurochemistry. 130: 360-73. PMID 24749734 DOI: 10.1111/Jnc.12741  0.334
2014 Bolia A, Woodrum BW, Cereda A, Ruben MA, Wang X, Ozkan SB, Ghirlanda G. A flexible docking scheme efficiently captures the energetics of glycan-cyanovirin binding Biophysical Journal. 106: 1142-1151. PMID 24606938 DOI: 10.1016/J.Bpj.2014.01.040  0.306
2014 Bolia A, Gerek ZN, Ozkan SB. BP-Dock: a flexible docking scheme for exploring protein-ligand interactions based on unbound structures. Journal of Chemical Information and Modeling. 54: 913-25. PMID 24380381 DOI: 10.1021/ci4004927  0.322
2014 Zou T, Risso VA, Gavira JA, Sanchez-Ruiz JM, Ozkan SB. Mechanistic Insights of β-Lactmases Evolution Biophysical Journal. 106: 663a. DOI: 10.1016/J.Bpj.2013.11.3669  0.579
2014 Butler BM, Kumar S, Ozkan SB. Biophysical Insights of Neutral and Non-Neutral Sequence Variants in the Human Proteome Biophysical Journal. 106: 462a. DOI: 10.1016/J.Bpj.2013.11.2616  0.407
2013 Knight AM, Culviner PH, Kurt-Yilmaz N, Zou T, Ozkan SB, Cavagnero S. Electrostatic effect of the ribosomal surface on nascent polypeptide dynamics. Acs Chemical Biology. 8: 1195-204. PMID 23517476 DOI: 10.1021/Cb400030N  0.639
2012 Glembo TJ, Farrell DW, Gerek ZN, Thorpe MF, Ozkan SB. Collective dynamics differentiates functional divergence in protein evolution. Plos Computational Biology. 8: e1002428. PMID 22479170 DOI: 10.1371/Journal.Pcbi.1002428  0.464
2011 Zou T, Ozkan SB. Local and non-local native topologies reveal the underlying folding landscape of proteins. Physical Biology. 8: 066011. PMID 22146659 DOI: 10.1088/1478-3975/8/6/066011  0.626
2011 Gerek ZN, Ozkan SB. Change in allosteric network affects binding affinities of PDZ domains: analysis through perturbation response scanning. Plos Computational Biology. 7: e1002154. PMID 21998559 DOI: 10.1371/journal.pcbi.1002154  0.302
2010 Atilgan C, Gerek ZN, Ozkan SB, Atilgan AR. Manipulation of conformational change in proteins by single-residue perturbations. Biophysical Journal. 99: 933-43. PMID 20682272 DOI: 10.1016/J.Bpj.2010.05.020  0.508
2010 Glembo TJ, Ozkan SB. Union of geometric constraint-based simulations with molecular dynamics for protein structure prediction. Biophysical Journal. 98: 1046-54. PMID 20303862 DOI: 10.1016/j.bpj.2009.11.031  0.427
2010 Gerek ZN, Ozkan SB. A flexible docking scheme to explore the binding selectivity of PDZ domains. Protein Science : a Publication of the Protein Society. 19: 914-28. PMID 20196074 DOI: 10.1002/pro.366  0.368
2010 Zou T, Ozkan SB. A Physics-Based Approach for Understanding Foldability Biophysical Journal. 98: 637a-638a. DOI: 10.1016/J.Bpj.2009.12.3492  0.648
2010 Glembo T, Thorpe M, Ozkan SB. Recreating the Structure and Dynamics of Ancestral Proteins Biophysical Journal. 98: 460a. DOI: 10.1016/J.Bpj.2009.12.2499  0.611
2009 Gerek ZN, Keskin O, Ozkan SB. Identification of specificity and promiscuity of PDZ domain interactions through their dynamic behavior. Proteins. 77: 796-811. PMID 19585657 DOI: 10.1002/Prot.22492  0.339
2009 Shell MS, Ozkan SB, Voelz V, Wu GA, Dill KA. Blind test of physics-based prediction of protein structures. Biophysical Journal. 96: 917-24. PMID 19186130 DOI: 10.1016/J.Bpj.2008.11.009  0.739
2009 Ozkan SB, Ni X, Gee J, Shell MS. Protein Structure Refinement Using Physics-Based Models And Sampling Biophysical Journal. 96: 653a-654a. DOI: 10.1016/j.bpj.2008.12.3451  0.336
2008 Dill KA, Ozkan SB, Shell MS, Weikl TR. The protein folding problem. Annual Review of Biophysics. 37: 289-316. PMID 18573083 DOI: 10.1063/1.881371  0.637
2007 Ghosh K, Ozkan SB, Dill KA. The ultimate speed limit to protein folding is conformational searching. Journal of the American Chemical Society. 129: 11920-7. PMID 17824609 DOI: 10.1021/Ja066785B  0.55
2007 Ozkan SB, Wu GA, Chodera JD, Dill KA. Protein folding by zipping and assembly. Proceedings of the National Academy of Sciences of the United States of America. 104: 11987-92. PMID 17620603 DOI: 10.1073/Pnas.0703700104  0.745
2007 Dill KA, Ozkan SB, Weikl TR, Chodera JD, Voelz VA. The protein folding problem: when will it be solved? Current Opinion in Structural Biology. 17: 342-6. PMID 17572080 DOI: 10.1016/J.Sbi.2007.06.001  0.756
2003 Ozkan SB, Dill KA, Bahar I. Computing the transition state populations in simple protein models. Biopolymers. 68: 35-46. PMID 12579578 DOI: 10.1002/Bip.10280  0.546
2002 Ozkan SB, Dill KA, Bahar I. Fast-folding protein kinetics, hidden intermediates, and the sequential stabilization model. Protein Science : a Publication of the Protein Society. 11: 1958-70. PMID 12142450 DOI: 10.1110/Ps.0207102  0.539
2001 Ozkan SB, Bahar I, Dill KA. Transition states and the meaning of Phi-values in protein folding kinetics. Nature Structural Biology. 8: 765-9. PMID 11524678 DOI: 10.1038/Nsb0901-765  0.494
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