Pemra Doruker - Publications

Chemical Engineering Bogazici University, Istanbul, Turkey 

40 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
2020 Kaynak BT, Bahar I, Doruker P. Essential site scanning analysis: A new approach for detecting sites that modulate the dispersion of protein global motions. Computational and Structural Biotechnology Journal. 18: 1577-1586. PMID 32637054 DOI: 10.1016/j.csbj.2020.06.020  0.8
2020 Clark LJ, Krieger J, White AD, Bondarenko V, Lei S, Fang F, Lee JY, Doruker P, Böttke T, Jean-Alphonse F, Tang P, Gardella TJ, Xiao K, Sutkeviciute I, Coin I, et al. Allosteric interactions in the parathyroid hormone GPCR-arrestin complex formation. Nature Chemical Biology. PMID 32632293 DOI: 10.1038/s41589-020-0567-0  0.8
2020 Krieger JM, Doruker P, Scott AL, Perahia D, Bahar I. Towards gaining sight of multiscale events: utilizing network models and normal modes in hybrid methods. Current Opinion in Structural Biology. 64: 34-41. PMID 32622329 DOI: 10.1016/  0.8
2020 Li H, Doruker P, Hu G, Bahar I. Modulation of Toroidal Proteins Dynamics in Favor of Functional Mechanisms upon Ligand Binding. Biophysical Journal. PMID 32130874 DOI: 10.1016/j.bpj.2020.01.046  0.8
2019 Zhang Y, Doruker P, Kaynak B, Zhang S, Krieger J, Li H, Bahar I. Intrinsic dynamics is evolutionarily optimized to enable allosteric behavior. Current Opinion in Structural Biology. 62: 14-21. PMID 31785465 DOI: 10.1016/  0.8
2019 Kaynak BT, Doruker P. Protein-Ligand Complexes as Constrained Dynamical Systems. Journal of Chemical Information and Modeling. PMID 30912658 DOI: 10.1021/acs.jcim.8b00946  0.52
2019 Dilcan G, Doruker P, Akten ED. Ligand-Binding Affinity of Alternative Conformers of Human β -adrenergic Receptor in the Presence of Intracellular Loop 3 (ICL3) and Their Potential Use in Virtual Screening Studies. Chemical Biology & Drug Design. PMID 30637937 DOI: 10.1111/cbdd.13478  0.4
2017 Kaynak BT, Findik D, Doruker P. RESPEC Incorporates Residue Specificity and Ligand Effect into Elastic Network Model. The Journal of Physical Chemistry. B. PMID 29268615 DOI: 10.1021/acs.jpcb.7b10325  0.52
2017 Can MT, Kurkcuoglu Z, Ezeroglu G, Uyar A, Kurkcuoglu O, Doruker P. Conformational dynamics of bacterial trigger factor in apo and ribosome-bound states. Plos One. 12: e0176262. PMID 28437479 DOI: 10.1371/journal.pone.0176262  1
2016 Kurkcuoglu Z, Bahar I, Doruker P. ClustENM: ENM-based sampling of essential conformational space at full atomic resolution. Journal of Chemical Theory and Computation. PMID 27494296 DOI: 10.1021/acs.jctc.6b00319  1
2016 Kurkcuoglu Z, Doruker P. Correction: Ligand Docking to Intermediate and Close-To-Bound Conformers Generated by an Elastic Network Model Based Algorithm for Highly Flexible Proteins. Plos One. 11: e0160130. PMID 27441374 DOI: 10.1371/journal.pone.0160130  1
2016 Ozgur C, Doruker P, Akten ED. Investigation of allosteric coupling in human β2-adrenergic receptor in the presence of intracellular loop 3. Bmc Structural Biology. 16: 9. PMID 27368374 DOI: 10.1186/s12900-016-0061-9  0.8
2016 Kurkcuoglu Z, Doruker P. Ligand Docking to Intermediate and Close-To-Bound Conformers Generated by an Elastic Network Model Based Algorithm for Highly Flexible Proteins. Plos One. 11: e0158063. PMID 27348230 DOI: 10.1371/journal.pone.0158063  1
2015 Kurkcuoglu Z, Findik D, Akten ED, Doruker P. How an Inhibitor Bound to Subunit Interface Alters Triosephosphate Isomerase Dynamics. Biophysical Journal. 109: 1169-78. PMID 26190635 DOI: 10.1016/j.bpj.2015.06.031  0.8
2014 Uyar A, Kantarci-Carsibasi N, Haliloglu T, Doruker P. Features of large hinge-bending conformational transitions. Prediction of closed structure from open state Biophysical Journal. 106: 2656-2666. PMID 24940783 DOI: 10.1016/j.bpj.2014.05.017  0.8
2013 Ozcan O, Uyar A, Doruker P, Akten ED. Effect of intracellular loop 3 on intrinsic dynamics of human β2-adrenergic receptor Bmc Structural Biology. 13. PMID 24206668 DOI: 10.1186/1472-6807-13-29  0.8
2012 Kurkcuoglu Z, Bakan A, Kocaman D, Bahar I, Doruker P. Coupling between catalytic loop motions and enzyme global dynamics. Plos Computational Biology. 8: e1002705. PMID 23028297 DOI: 10.1371/journal.pcbi.1002705  0.8
2011 Kurkcuoglu Z, Ural G, Demet Akten E, Doruker P. Blind Dockings of Benzothiazoles to Multiple Receptor Conformations of Triosephosphate Isomerase from Trypanosoma cruzi and Human. Molecular Informatics. 30: 986-95. PMID 27468153 DOI: 10.1002/minf.201100109  1
2011 Uyar A, Kurkcuoglu O, Nilsson L, Doruker P. The elastic network model reveals a consistent picture on intrinsic functional dynamics of type II restriction endonucleases. Physical Biology. 8: 056001. PMID 21791727 DOI: 10.1088/1478-3975/8/5/056001  0.8
2011 Alakent B, Baskan S, Doruker P. Effect of ligand binding on the intraminimum dynamics of proteins Journal of Computational Chemistry. 32: 483-496. PMID 20730777 DOI: 10.1002/jcc.21636  0.8
2009 Kurkcuoglu O, Turgut OT, Cansu S, Jernigan RL, Doruker P. Focused functional dynamics of supramolecules by use of a mixed-resolution elastic network model. Biophysical Journal. 97: 1178-87. PMID 19686666 DOI: 10.1016/j.bpj.2009.06.009  0.8
2009 Akten ED, Cansu S, Doruker P. A docking study using atomistic conformers generated via elastic network model for cyclosporin A/cyclophilin A complex. Journal of Biomolecular Structure & Dynamics. 27: 13-26. PMID 19492859 DOI: 10.1080/07391102.2009.10507292  0.8
2009 Kurkcuoglu O, Kurkcuoglu Z, Doruker P, Jernigan RL. Collective dynamics of the ribosomal tunnel revealed by elastic network modeling. Proteins. 75: 837-45. PMID 19004020 DOI: 10.1002/prot.22292  1
2008 Kurkcuoglu O, Doruker P, Sen TZ, Kloczkowski A, Jernigan RL. The ribosome structure controls and directs mRNA entry, translocation and exit dynamics. Physical Biology. 5: 046005. PMID 19029596 DOI: 10.1088/1478-3975/5/4/046005  0.76
2006 Doruker P, Nilsson L, Kurkcuoglu O. Collective dynamics of EcoRI-DNA complex by elastic network model and molecular dynamics simulations Journal of Biomolecular Structure and Dynamics. 24: 1-15. PMID 16780370  0.8
2006 Kurkcuoglu O, Jernigan RL, Doruker P. Loop motions of triosephosphate isomerase observed with elastic networks. Biochemistry. 45: 1173-82. PMID 16430213 DOI: 10.1021/bi0518085  0.76
2004 Yildirim Y, Doruker P. Collective motions of RNA polymerases. Analysis of core enzyme, elongation complex and holoenzyme Journal of Biomolecular Structure and Dynamics. 22: 267-280. PMID 15473702 DOI: 10.1080/07391102.2004.10507000  0.8
2004 Kurkcuoglu O, Jernigan RL, Doruker P. Mixed levels of coarse-graining of large proteins using elastic network model succeeds in extracting the slowest motions Polymer. 45: 649-657. DOI: 10.1016/J.POLYMER.2003.10.071  0.32
2003 Doruker P, Jernigan RL. Functional motions can be extracted from on-lattice construction of protein structures. Proteins. 53: 174-81. PMID 14517969 DOI: 10.1002/prot.10486  0.56
2002 Doruker P, Jernigan RL, Bahar I. Dynamics of large proteins through hierarchical levels of coarse-grained structures. Journal of Computational Chemistry. 23: 119-27. PMID 11913377 DOI: 10.1002/jcc.1160  0.8
2002 Isin B, Doruker P, Bahar I. Functional motions of influenza virus hemagglutinin: a structure-based analytical approach. Biophysical Journal. 82: 569-81. PMID 11806902 DOI: 10.1016/S0006-3495(02)75422-2  0.8
2001 Doruker P, Mattice WL. Effect of surface roughness on structure and dynamics in thin films Macromolecular Theory and Simulations. 10: 363-367. DOI: 10.1002/1521-3919(20010401)10:4<363::AID-MATS363>3.0.CO;2-V  0.8
2000 Doruker P, Wang Y, Mattice WL. Simulation of the random scission of C-C bonds in the initial stage of the thermal degradation of polyethylene Computational and Theoretical Polymer Science. 11: 155-166. DOI: 10.1016/S1089-3156(99)00078-1  0.8
2000 Ozisik R, Doruker P, Mattice WL, Von Meerwall ED. Translational diffusion in Monte Carlo simulations of polymer melts: Center of mass displacement vs. integrated velocity autocorrelation function Computational and Theoretical Polymer Science. 10: 411-418. DOI: 10.1016/S1089-3156(00)00008-8  0.8
2000 Vao-soongnern V, Doruker P, Mattice WL. Simulation of an amorphous polyethylene nanofiber on a high coordination lattice Macromolecular Theory and Simulations. 9: 1-13. DOI: 10.1002/(SICI)1521-3919(20000101)9:1<1::AID-MATS1>3.0.CO;2-R  0.8
1999 Doruker P, Mattice WL. Segregation of chain ends is a weak contributor to increased mobility at free polymer surfaces Journal of Physical Chemistry B. 103: 178-183.  0.8
1999 Doruker P, Mattice WL. A second generation of mapping/reverse mapping of coarse-grained and fully atomistic models of polymer melts Macromolecular Theory and Simulations. 8: 463-478.  0.8
1999 Doruker P, Mattice WL. Mobility of the surface and interior of thin films composed of amorphous polyethylene Macromolecules. 32: 194-198.  0.8
1997 Doruker P, Bahar I. Role of water on unfolding kinetics of helical peptides studied by molecular dynamics simulations. Biophysical Journal. 72: 2445-56. PMID 9168021 DOI: 10.1016/S0006-3495(97)78889-1  0.48
1996 Doruker P, Rapold RF, Mattice WL. Rotational Isomeric State models for polyoxyethylene and polythiaethylene on a high coordination lattice Journal of Chemical Physics. 104: 8742-8749.  0.8
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