| Year |
Citation |
Score |
| 2023 |
Bahar I, Banerjee A, Mathew S, Naqvi M, Yilmaz S, Zachoropoulou M, Doruker P, Kumita J, Yang SH, Gur M, Itzhaki L, Gordon R. Influence of Point Mutations on PR65 Conformational Adaptability: Insights from Nanoaperture Optical Tweezer Experiments and Molecular Simulations. Research Square. PMID 38014259 DOI: 10.21203/rs.3.rs-3599809/v1 |
0.767 |
|
| 2023 |
Kumar A, Kaynak BT, Dorman KS, Doruker P, Jernigan RL. Predicting Allosteric Pockets in Protein Biological Assemblages. Bioinformatics (Oxford, England). PMID 37115636 DOI: 10.1093/bioinformatics/btad275 |
0.326 |
|
| 2023 |
Kaynak BT, Dahmani ZL, Doruker P, Banerjee A, Yang SH, Gordon R, Itzhaki LS, Bahar I. Cooperative mechanics of PR65 scaffold underlies the allosteric regulation of the phosphatase PP2A. Structure (London, England : 1993). PMID 36948205 DOI: 10.1016/j.str.2023.02.012 |
0.53 |
|
| 2022 |
Todd NK, Huang Y, Lee JY, Doruker P, Krieger JM, Salisbury R, MacDonald M, Bahar I, Thathiah A. GPCR kinases generate an APH1A phosphorylation barcode to regulate amyloid-β generation. Cell Reports. 40: 111110. PMID 35858570 DOI: 10.1016/j.celrep.2022.111110 |
0.449 |
|
| 2022 |
Wingert B, Doruker P, Bahar I. Activation and Speciation Mechanisms in Class A GPCRs. Journal of Molecular Biology. 167690. PMID 35728652 DOI: 10.1016/j.jmb.2022.167690 |
0.568 |
|
| 2022 |
Kaynak BT, Krieger JM, Dudas B, Dahmani ZL, Costa MGS, Balog E, Scott AL, Doruker P, Perahia D, Bahar I. Sampling of Protein Conformational Space Using Hybrid Simulations: A Critical Assessment of Recent Methods. Frontiers in Molecular Biosciences. 9: 832847. PMID 35187088 DOI: 10.3389/fmolb.2022.832847 |
0.707 |
|
| 2021 |
Sutkeviciute I, Lee JY, White AD, Maria CS, Peña KA, Savransky S, Doruker P, Li H, Lei S, Kaynak B, Tu C, Clark LJ, Sanker S, Gardella TJ, Chang W, et al. Precise druggability of the PTH type 1 receptor. Nature Chemical Biology. PMID 34949836 DOI: 10.1038/s41589-021-00929-w |
0.51 |
|
| 2021 |
Kaynak BT, Zhang S, Bahar I, Doruker P. ClustENMD: Efficient sampling of biomolecular conformational space at atomic resolution. Bioinformatics (Oxford, England). PMID 34240100 DOI: 10.1093/bioinformatics/btab496 |
0.778 |
|
| 2021 |
Zhang S, Krieger JM, Zhang Y, Kaya C, Kaynak B, Mikulska-Ruminska K, Doruker P, Li H, Bahar I. ProDy 2.0: Increased Scale and Scope after 10 Years of Protein Dynamics Modelling with Python. Bioinformatics (Oxford, England). PMID 33822884 DOI: 10.1093/bioinformatics/btab187 |
0.765 |
|
| 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 |
0.625 |
|
| 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 |
0.541 |
|
| 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/J.Sbi.2020.05.013 |
0.704 |
|
| 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 |
0.605 |
|
| 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/J.Sbi.2019.11.002 |
0.786 |
|
| 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 |
0.441 |
|
| 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 |
0.395 |
|
| 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 |
0.372 |
|
| 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 |
0.796 |
|
| 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 |
0.791 |
|
| 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 |
0.738 |
|
| 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 |
0.37 |
|
| 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 |
0.776 |
|
| 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 |
0.796 |
|
| 2015 |
Yesiltepe Y, Uyar A, Turgut D, Haliloglu T, Doruker P, Ozisik R. Targeted Conformational Transitions of Multimeric Proteins by Monte Carlo Simulations Combined with Collective Anisotropic Network Model Modes Biophysical Journal. 108: 211a. DOI: 10.1016/J.Bpj.2014.11.1169 |
0.434 |
|
| 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 |
0.418 |
|
| 2014 |
Uyar A, Pande V, Mura C, McCammon JA, Doruker P, Nilsson L. Assessing Dynamic Features of NF-κB via Molecular Dynamics Simulations and Elastic Network Model Biophysical Journal. 106: 252a. DOI: 10.1016/J.Bpj.2013.11.1482 |
0.432 |
|
| 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 |
0.423 |
|
| 2013 |
Kurkcuoglu Z, Doruker P. Substrate Effect on Catalytic Loop and Global Dynamics of Triosephosphate Isomerase Entropy. 15: 1085-1099. DOI: 10.3390/E15031085 |
0.784 |
|
| 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 |
0.779 |
|
| 2012 |
Alakent B, Kurkcuoglu Z, Doruker P. Functional Dynamics of Proteins Elucidated by Statistical Analysis of Simulation Data Current Physical Chemistry. 2: 443-451. DOI: 10.2174/1877946811202040443 |
0.76 |
|
| 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 |
0.755 |
|
| 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 |
0.447 |
|
| 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 |
0.498 |
|
| 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 |
0.486 |
|
| 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 |
0.466 |
|
| 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 |
0.773 |
|
| 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 |
0.65 |
|
| 2008 |
Kantarci-Carsibasi N, Haliloglu T, Doruker P. Conformational transition pathways explored by Monte Carlo simulation integrated with collective modes. Biophysical Journal. 95: 5862-73. PMID 18676657 DOI: 10.1529/Biophysj.107.128447 |
0.405 |
|
| 2008 |
Cansu S, Doruker P. Dimerization affects collective dynamics of triosephosphate isomerase. Biochemistry. 47: 1358-68. PMID 18189421 DOI: 10.1021/Bi701916B |
0.516 |
|
| 2006 |
Kantarci N, Doruker P, Haliloglu T. Cooperative fluctuations point to the dimerization interface of p53 core domain. Biophysical Journal. 91: 421-32. PMID 16807229 DOI: 10.1529/Biophysj.106.077800 |
0.352 |
|
| 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 DOI: 10.1080/07391102.2006.10507093 |
0.456 |
|
| 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 |
0.458 |
|
| 2005 |
Alakent B, Camurdan MC, Doruker P. Hierarchical structure of the energy landscape of proteins revisited by time series analysis. II. Investigation of explicit solvent effects. The Journal of Chemical Physics. 123: 144911. PMID 16238428 DOI: 10.1063/1.2042408 |
0.404 |
|
| 2005 |
Alakent B, Camurdan MC, Doruker P. Hierarchical structure of the energy landscape of proteins revisited by time series analysis. I. Mimicking protein dynamics in different time scales. The Journal of Chemical Physics. 123: 144910. PMID 16238427 DOI: 10.1063/1.2042407 |
0.417 |
|
| 2005 |
Kantarci N, Tamerler C, Sarikaya M, Haliloglu T, Doruker P. Molecular dynamics simulations on constraint metal binding peptides Polymer. 46: 4307-4313. DOI: 10.1016/J.Polymer.2005.03.016 |
0.367 |
|
| 2005 |
Kurkcuoglu O, Jernigan R, Doruker P. Collective Dynamics of Large Proteins from Mixed Coarse-Grained Elastic Network Model Qsar & Combinatorial Science. 24: 443-448. DOI: 10.1002/Qsar.200430922 |
0.477 |
|
| 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 |
0.45 |
|
| 2004 |
Alakent B, Doruker P, Camurdan MC. Application of time series analysis on molecular dynamics simulations of proteins: a study of different conformational spaces by principal component analysis. The Journal of Chemical Physics. 121: 4759-69. PMID 15332910 DOI: 10.1063/1.1778377 |
0.463 |
|
| 2004 |
Alakent B, Doruker P, Camurdan MC. Time series analysis of collective motions in proteins. The Journal of Chemical Physics. 120: 1072-88. PMID 15267944 DOI: 10.1063/1.1630793 |
0.408 |
|
| 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 |
0.469 |
|
| 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 |
0.456 |
|
| 2003 |
Kucukpinar E, Doruker P. Molecular simulations of small gas diffusion and solubility in copolymers of styrene Polymer. 44: 3607-3620. DOI: 10.1016/S0032-3861(03)00166-6 |
0.311 |
|
| 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 |
0.61 |
|
| 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 |
0.58 |
|
| 2002 |
Doruker P, Bahar I, Baysal C, Erman B. Collective deformations in proteins determined by a mode analysis of molecular dynamics trajectories Polymer. 43: 431-439. DOI: 10.1016/S0032-3861(01)00424-4 |
0.698 |
|
| 2002 |
Doruker P, Jernigan RL, Navizet I, Hernandez R. Important fluctuation dynamics of large protein structures are preserved upon coarse-grained renormalization International Journal of Quantum Chemistry. 90: 822-837. DOI: 10.1002/Qua.955 |
0.438 |
|
| 2000 |
Doruker P, Atilgan AR, Bahar I. Dynamics of proteins predicted by molecular dynamics simulations and analytical approaches: application to alpha-amylase inhibitor. Proteins. 40: 512-24. PMID 10861943 DOI: 10.1002/1097-0134(20000815)40:3<512::Aid-Prot180>3.0.Co;2-M |
0.644 |
|
| 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 |
0.3 |
|
| 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 |
0.303 |
|
| 2000 |
Baschnagel J, Binder K, Doruker P, Gusev AA, Hahn O, Kremer K, Mattice WL, Müller-Plathe F, Murat M, Paul W, Santos S, Suter UW, Tries V. Bridging the gap between atomistic and coarse-grained models of polymers: Status and perspectives Advances in Polymer Science. 152: 41-156. DOI: 10.1007/3-540-46778-5_2 |
0.304 |
|
| 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. DOI: 10.1002/(Sici)1521-3919(19990901)8:5<463::Aid-Mats463>3.0.Co;2-0 |
0.367 |
|
| 1998 |
Doruker P, Mattice WL. Dynamics of bulk polyethylene on a high coordination lattice Macromolecular Symposia. 133: 47-70. DOI: 10.1002/Masy.19981330107 |
0.372 |
|
| 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 |
0.542 |
|
| 1997 |
Bahar I, Cho J, Doruker P, Erman B, Haliloglu T, Kim E, Mattice W, Monnerie L, Rapold R. Three approaches that may permit more efficient simulation of the dynamics of atomistic models of polymers Trends in Polymer Science. 5: 155-160. DOI: 10.5072/Zenodo.19294 |
0.698 |
|
| 1997 |
Doruker P, Mattice WL. Reverse mapping of coarse-grained polyethylene chains from the second nearest neighbor diamond lattice to an atomistic model in continuous space Macromolecules. 30: 5520-5526. DOI: 10.1021/Ma970297U |
0.356 |
|
| 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. DOI: 10.1063/1.471563 |
0.33 |
|
| 1993 |
Bahar I, Badur B, Doruker P. Solvent effect on translational diffusivity and orientational mobility of polymers in solution: A molecular dynamics study The Journal of Chemical Physics. 99: 2235-2246. DOI: 10.1063/1.465233 |
0.543 |
|
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