| Year |
Citation |
Score |
| 2024 |
Demirtaş K, Erman B, Haliloğlu T. Dynamic correlations: Exact and approximate methods for mutual information. Bioinformatics (Oxford, England). PMID 38341647 DOI: 10.1093/bioinformatics/btae076 |
0.552 |
|
| 2022 |
Haliloglu T, Hacisuleyman A, Erman B. Prediction of Allosteric Communication Pathways in Proteins. Bioinformatics (Oxford, England). PMID 35674396 DOI: 10.1093/bioinformatics/btac380 |
0.729 |
|
| 2022 |
Altintel B, Acar B, Erman B, Haliloglu T. Subsets of Slow Dynamic Modes Reveal Global Information Sources as Allosteric Sites. Journal of Molecular Biology. 167644. PMID 35644497 DOI: 10.1016/j.jmb.2022.167644 |
0.544 |
|
| 2020 |
Acar B, Rose J, Aykac Fas B, Ben-Tal N, Lewinson O, Haliloglu T. Distinct Allosteric Networks Underlie Mechanistic Speciation of ABC Transporters. Structure (London, England : 1993). PMID 32320672 DOI: 10.1016/J.Str.2020.03.014 |
0.737 |
|
| 2019 |
Sayılgan JF, Haliloğlu T, Gönen M. Protein dynamics analysis reveals that missense mutations in cancer-related genes appear frequently on hinge-neighboring residues. Proteins. 87: 512-519. PMID 30785643 DOI: 10.1002/Prot.25673 |
0.307 |
|
| 2018 |
Yang M, Livnat Levanon N, Acar B, Aykac Fas B, Masrati G, Rose J, Ben-Tal N, Haliloglu T, Zhao Y, Lewinson O. Single-molecule probing of the conformational homogeneity of the ABC transporter BtuCD. Nature Chemical Biology. 14: 715-722. PMID 29915236 DOI: 10.1038/S41589-018-0088-2 |
0.746 |
|
| 2017 |
Onel M, Sumbul F, Liu J, Nussinov R, Haliloglu T. Cullin Neddylation May Allosterically Tune Polyubiquitin Chain Length and Topology. The Biochemical Journal. PMID 28082425 DOI: 10.1042/Bcj20160748 |
0.411 |
|
| 2016 |
Acuner-Ozbabacan SE, Sumbul F, Torun H, Haliloglu T. Allosteric Regulation of Rac1-PAK1 Binding Affinity by Mutant Residues through Molecular Simulations and AFM Biophysical Journal. 110. DOI: 10.1016/J.Bpj.2015.11.2070 |
0.375 |
|
| 2015 |
Soner S, Ozbek P, Garzon JI, Ben-Tal N, Haliloglu T. DynaFace: Discrimination between Obligatory and Non-obligatory Protein-Protein Interactions Based on the Complex's Dynamics. Plos Computational Biology. 11: e1004461. PMID 26506003 DOI: 10.1371/Journal.Pcbi.1004461 |
0.365 |
|
| 2015 |
Sumbul F, Acuner-Ozbabacan SE, Haliloglu T. Allosteric Dynamic Control of Binding. Biophysical Journal. 109: 1190-201. PMID 26338442 DOI: 10.1016/J.Bpj.2015.08.011 |
0.43 |
|
| 2015 |
Haliloglu T, Bahar I. Adaptability of protein structures to enable functional interactions and evolutionary implications. Current Opinion in Structural Biology. 35: 17-23. PMID 26254902 DOI: 10.1016/J.Sbi.2015.07.007 |
0.566 |
|
| 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 |
0.384 |
|
| 2014 |
Gofman Y, Schärfe C, Marks DS, Haliloglu T, Ben-Tal N. Structure, dynamics and implied gating mechanism of a human cyclic nucleotide-gated channel. Plos Computational Biology. 10: e1003976. PMID 25474149 DOI: 10.1371/Journal.Pcbi.1003976 |
0.304 |
|
| 2014 |
Sahillioglu AC, Sumbul F, Ozoren N, Haliloglu T. Structural and dynamics aspects of ASC speck assembly. Structure (London, England : 1993). 22: 1722-34. PMID 25458835 DOI: 10.1016/J.Str.2014.09.011 |
0.356 |
|
| 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 |
0.366 |
|
| 2013 |
Ozbek P, Soner S, Haliloglu T. Hot spots in a network of functional sites. Plos One. 8: e74320. PMID 24023934 DOI: 10.1371/Journal.Pone.0074320 |
0.414 |
|
| 2013 |
Aykaç Fas B, Tutar Y, Haliloğlu T. Dynamic fluctuations provide the basis of a conformational switch mechanism in apo cyclic AMP receptor protein. Plos Computational Biology. 9: e1003141. PMID 23874183 DOI: 10.1371/Journal.Pcbi.1003141 |
0.752 |
|
| 2013 |
Kaya C, Armutlulu A, Ekesan S, Haliloglu T. MCPath: Monte Carlo path generation approach to predict likely allosteric pathways and functional residues. Nucleic Acids Research. 41: W249-55. PMID 23742907 DOI: 10.1093/Nar/Gkt284 |
0.367 |
|
| 2012 |
Gofman Y, Haliloglu T, Ben-Tal N. The Transmembrane Helix Tilt May Be Determined by the Balance between Precession Entropy and Lipid Perturbation. Journal of Chemical Theory and Computation. 8: 2896-2904. PMID 24932138 DOI: 10.1021/Ct300128X |
0.362 |
|
| 2012 |
Korkmaz EN, Nussinov R, Haliloğlu T. Conformational control of the binding of the transactivation domain of the MLL protein and c-Myb to the KIX domain of CREB. Plos Computational Biology. 8: e1002420. PMID 22438798 DOI: 10.1371/Journal.Pcbi.1002420 |
0.39 |
|
| 2012 |
Schushan M, Rimon A, Haliloglu T, Forrest LR, Padan E, Ben-Tal N. A model-structure of a periplasm-facing state of the NhaA antiporter suggests the molecular underpinnings of pH-induced conformational changes. The Journal of Biological Chemistry. 287: 18249-61. PMID 22431724 DOI: 10.1074/Jbc.M111.336446 |
0.376 |
|
| 2011 |
Fleishman SJ, Whitehead TA, Strauch EM, Corn JE, Qin S, Zhou HX, Mitchell JC, Demerdash ON, Takeda-Shitaka M, Terashi G, Moal IH, Li X, Bates PA, Zacharias M, Park H, ... ... Haliloglu T, et al. Community-wide assessment of protein-interface modeling suggests improvements to design methodology. Journal of Molecular Biology. 414: 289-302. PMID 22001016 DOI: 10.1016/J.Jmb.2011.09.031 |
0.306 |
|
| 2011 |
Ma B, Tsai CJ, Haliloğlu T, Nussinov R. Dynamic allostery: linkers are not merely flexible. Structure (London, England : 1993). 19: 907-17. PMID 21742258 DOI: 10.1016/J.Str.2011.06.002 |
0.394 |
|
| 2010 |
Ozer N, Schiffer CA, Haliloglu T. Rationale for more diverse inhibitors in competition with substrates in HIV-1 protease. Biophysical Journal. 99: 1650-9. PMID 20816079 DOI: 10.1016/J.Bpj.2010.06.064 |
0.337 |
|
| 2010 |
Haliloglu T, Gul A, Erman B. Predicting important residues and interaction pathways in proteins using Gaussian Network Model: binding and stability of HLA proteins. Plos Computational Biology. 6: e1000845. PMID 20628622 DOI: 10.1371/Journal.Pcbi.1000845 |
0.585 |
|
| 2010 |
Wainreb G, Ashkenazy H, Bromberg Y, Starovolsky-Shitrit A, Haliloglu T, Ruppin E, Avraham KB, Rost B, Ben-Tal N. MuD: an interactive web server for the prediction of non-neutral substitutions using protein structural data. Nucleic Acids Research. 38: W523-8. PMID 20542913 DOI: 10.1093/Nar/Gkq1208 |
0.305 |
|
| 2010 |
Schushan M, Barkan Y, Haliloglu T, Ben-Tal N. C(alpha)-trace model of the transmembrane domain of human copper transporter 1, motion and functional implications. Proceedings of the National Academy of Sciences of the United States of America. 107: 10908-13. PMID 20534491 DOI: 10.1073/Pnas.0914717107 |
0.369 |
|
| 2010 |
Yeheskel A, Haliloglu T, Ben-Tal N. Independent and cooperative motions of the Kv1.2 channel: voltage sensing and gating. Biophysical Journal. 98: 2179-88. PMID 20483326 DOI: 10.1016/J.Bpj.2010.01.049 |
0.311 |
|
| 2010 |
Ozbek P, Soner S, Erman B, Haliloglu T. DNABINDPROT: fluctuation-based predictor of DNA-binding residues within a network of interacting residues. Nucleic Acids Research. 38: W417-23. PMID 20478828 DOI: 10.1093/Nar/Gkq396 |
0.582 |
|
| 2010 |
Schushan M, Barkan Y, Haliloglu T, Ben-Tal N. Human Copper Transporter 1: Model-Structure, Function and Motion Biophysical Journal. 98: 6-6. DOI: 10.1016/J.Bpj.2009.12.3539 |
0.387 |
|
| 2009 |
Ulutaş B, Haliloglu T, Bozma I. Folding pathways explored with artificial potential functions Physical Biology. 6: 36008. PMID 19443950 DOI: 10.1088/1478-3975/6/3/036008 |
0.355 |
|
| 2009 |
Haliloglu T, Erman B. Analysis of correlations between energy and residue fluctuations in native proteins and determination of specific sites for binding. Physical Review Letters. 102: 088103. PMID 19257794 DOI: 10.1103/Physrevlett.102.088103 |
0.586 |
|
| 2009 |
Ozen A, Haliloglu T, Schiffer CA. Using Molecular Dynamics to Investigate Substrate Recognition and Co-evolution in HIV-1 Protease Biophysical Journal. 96: 598a. DOI: 10.1016/J.Bpj.2008.12.3129 |
0.358 |
|
| 2008 |
Haliloglu T, Ben-Tal N. Cooperative transition between open and closed conformations in potassium channels. Plos Computational Biology. 4: e1000164. PMID 18769593 DOI: 10.1371/Journal.Pcbi.1000164 |
0.35 |
|
| 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 |
0.375 |
|
| 2008 |
Haliloglu T, Seyrek E, Erman B. Prediction of binding sites in receptor-ligand complexes with the Gaussian Network Model. Physical Review Letters. 100: 228102. PMID 18643462 DOI: 10.1103/Physrevlett.100.228102 |
0.543 |
|
| 2008 |
Emekli U, Schneidman-Duhovny D, Wolfson HJ, Nussinov R, Haliloglu T. HingeProt: automated prediction of hinges in protein structures. Proteins. 70: 1219-27. PMID 17847101 DOI: 10.1002/Prot.21613 |
0.344 |
|
| 2006 |
Ertekin A, Nussinov R, Haliloglu T. Association of putative concave protein-binding sites with the fluctuation behavior of residues. Protein Science : a Publication of the Protein Society. 15: 2265-77. PMID 17008715 DOI: 10.1110/Ps.051815006 |
0.364 |
|
| 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 |
0.337 |
|
| 2005 |
Konuklar FAS, Aviyente V, Haliloğlu T. Coupling of structural fluctuations to deamidation reaction in triosephosphate isomerase by Gaussian network model. Proteins. 62: 715-727. PMID 16323206 DOI: 10.1002/Prot.20668 |
0.376 |
|
| 2005 |
Shental-Bechor D, Kirca S, Ben-Tal N, Haliloglu T. Monte Carlo studies of folding, dynamics, and stability in alpha-helices. Biophysical Journal. 88: 2391-402. PMID 15653741 DOI: 10.1529/Biophysj.104.050708 |
0.359 |
|
| 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 |
0.358 |
|
| 2004 |
Haliloglu T, Keskin O, Ma B, Nussinov R. How similar are protein folding and protein binding nuclei? Examination of vibrational motions of energy hot spots and conserved residues. Biophysical Journal. 88: 1552-9. PMID 15596504 DOI: 10.1529/Biophysj.104.051342 |
0.384 |
|
| 2004 |
Ozkan SB, Dalgýn GS, Haliloglu T. Unfolding events of Chymotrypsin Inhibitor 2 (CI2) revealed by Monte Carlo (MC) simulations and their consistency from structure-based analysis of conformations Polymer. 45: 581-595. DOI: 10.1016/J.Polymer.2003.10.092 |
0.39 |
|
| 2003 |
Haliloglu T, Kolinski A, Skolnick J. Use of Residual Dipolar Couplings as Restraints in Ab Initio Protein Structure Prediction Biopolymers. 70: 548-562. PMID 14648765 DOI: 10.1002/Bip.10511 |
0.361 |
|
| 2003 |
Kessel A, Haliloglu T, Ben-Tal N. Interactions of the M2delta segment of the acetylcholine receptor with lipid bilayers: a continuum-solvent model study. Biophysical Journal. 85: 3687-95. PMID 14645060 DOI: 10.1016/S0006-3495(03)74785-7 |
0.314 |
|
| 2003 |
Kessel A, Shental-Bechor D, Haliloglu T, Ben-Tal N. Interactions of hydrophobic peptides with lipid bilayers: Monte Carlo simulations with M2delta. Biophysical Journal. 85: 3431-44. PMID 14645040 DOI: 10.1016/S0006-3495(03)74765-1 |
0.306 |
|
| 2003 |
Kurt N, Haliloglu T, Schiffer CA. Structure-based prediction of potential binding and nonbinding peptides to HIV-1 protease. Biophysical Journal. 85: 853-63. PMID 12885633 DOI: 10.1016/S0006-3495(03)74525-1 |
0.349 |
|
| 2003 |
Kurt N, Scott WR, Schiffer CA, Haliloglu T. Cooperative fluctuations of unliganded and substrate-bound HIV-1 protease: a structure-based analysis on a variety of conformations from crystallography and molecular dynamics simulations. Proteins. 51: 409-22. PMID 12696052 DOI: 10.1002/Prot.10350 |
0.395 |
|
| 2002 |
Kurt N, Haliloglu T. Distribution of cooperative interactions in barnase at different time windows by coarse-grained simulations Polymer. 43: 403-408. DOI: 10.1016/S0032-3861(01)00431-1 |
0.395 |
|
| 2001 |
Kurt N, Haliloğlu T. Conformational Dynamics of Subtilisin-Chymotrypsin Inhibitor 2 Complex by Coarse-Grained Simulations Journal of Biomolecular Structure & Dynamics. 18: 713-731. PMID 11334109 DOI: 10.1080/07391102.2001.10506702 |
0.386 |
|
| 2000 |
Haliloglu T, Bahar I. Structure-based analysis of protein dynamics: comparison of theoretical results for hen lysozyme with X-ray diffraction and NMR relaxation data. Proteins. 37: 654-67. PMID 10651280 DOI: 10.1002/(Sici)1097-0134(19991201)37:4<654::Aid-Prot15>3.0.Co;2-J |
0.57 |
|
| 1999 |
Kurt N, Haliloğlu T. Conformational dynamics of chymotrypsin inhibitor 2 by coarse-grained simulations. Proteins. 37: 454-464. PMID 10591104 DOI: 10.1002/(Sici)1097-0134(19991115)37:3<454::Aid-Prot12>3.0.Co;2-V |
0.419 |
|
| 1999 |
Haliloglu T, Mattice WL. Simulation of rotational isomeric state models for polypropylene melts on a high coordination lattice Reviews in Chemical Engineering. 15: 293-305. DOI: 10.1515/Revce.1999.15.4.293 |
0.386 |
|
| 1999 |
Haliloglu T, Mattice WL. Detection of the onset of demixing in simulations of polypropylene melts in which the chains differ only in stereochemical composition Journal of Chemical Physics. 111: 4327-4333. DOI: 10.1063/1.479731 |
0.355 |
|
| 1999 |
Haliloğlu T. Coarse-grained simulations of the conformational dynamics of proteins Computational and Theoretical Polymer Science. 9: 255-260. DOI: 10.1016/S1089-3156(99)00012-4 |
0.401 |
|
| 1998 |
Haliloglu T, Bahar I. Coarse-grained simulations of conformational dynamics of proteins: application to apomyoglobin. Proteins. 31: 271-81. PMID 9593198 DOI: 10.1002/(Sici)1097-0134(19980515)31:3<271::Aid-Prot4>3.0.Co;2-M |
0.581 |
|
| 1998 |
Atilgan A, Haliloglu T, Bahar I, Erman B. Correlated fluctuations in polymer networks Computational and Theoretical Polymer Science. 8: 55-59. DOI: 10.1016/S1089-3156(98)00014-2 |
0.623 |
|
| 1998 |
Haliloglu T, Cho J, Mattice WL. Simulations of rotational isomeric state models for poly(propylene) melts on a high coordination lattice Macromolecular Theory and Simulations. 7: 613-617. DOI: 10.1002/(Sici)1521-3919(19981101)7:6<613::Aid-Mats613>3.0.Co;2-I |
0.353 |
|
| 1997 |
Bahar I, Erman B, Haliloglu T, Jernigan RL. Efficient characterization of collective motions and interresidue correlations in proteins by low-resolution simulations. Biochemistry. 36: 13512-23. PMID 9354619 DOI: 10.1021/Bi971611F |
0.654 |
|
| 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 |
0.642 |
|
| 1997 |
Haliloglu T, Bahar I, Erman B. Gaussian Dynamics of Folded Proteins Physical Review Letters. 79: 3090-3093. DOI: 10.1103/Physrevlett.79.3090 |
0.658 |
|
| 1997 |
Haliloglu T, Mattice WL. Conformational transitions of end-adsorbed triblock copolymers in a nonselective solvent Macromolecular Theory and Simulations. 6: 667-677. DOI: 10.1002/Mats.1997.040060306 |
0.34 |
|
| 1996 |
Haliloglu T, Bahar I, Erman B. Response of a single grafted polyethylene chain to simple shear flow: A Brownian dynamics simulation study The Journal of Chemical Physics. 105: 2919-2926. DOI: 10.1063/1.472154 |
0.651 |
|
| 1996 |
Haliloǧlu T, Bahar I, Erman B, Kim E, Mattice WL. A dynamic rotational isomeric state approach for extension of the time scale of the local dynamics observed in fully atomistic molecular dynamics simulations: Application to polybutadiene The Journal of Chemical Physics. 104: 4828-4834. DOI: 10.1063/1.471177 |
0.649 |
|
| 1996 |
Haliloglu T, Bahar I, Erman B, Mattice WL. Relative Contributions of Coupled Rotations and Small-Amplitude Torsions to Conformational Relaxation in Polymers Macromolecules. 29: 8942-8947. DOI: 10.1021/Ma961021+ |
0.652 |
|
| 1996 |
Haliloǧlu T, Bahar I, Erman B, Mattice WL. Mechanisms of the exchange of diblock copolymers between micelles at dynamic equilibrium Macromolecules. 29: 4764-4771. DOI: 10.1021/Ma951301+ |
0.552 |
|
| 1995 |
Haliloglu T, Erman B, Bahar I. Dependence of segmental orientation on polymer conformational characteristics Polymer. 36: 4131-4134. DOI: 10.1016/0032-3861(95)90995-E |
0.638 |
|
| 1994 |
Bahar I, Erman B, Haliloglu T. Role of Structural Heterogeneities on Segmental Orientation in Deformed Chains: Application to Alternating Copolymers Macromolecules. 27: 1703-1709. DOI: 10.1021/Ma00085A007 |
0.664 |
|
| 1994 |
Haliloglu T, Balaji R, Mattice WL. Mobility of Free Ends and Junction Points as a Lamellar Block Copolymer Macromolecules. 27: 1473-1476. DOI: 10.1021/Ma00084A030 |
0.333 |
|
| 1993 |
Haliloglu T, Erman B, Bahar I. Orientational mobility in uniaxially deformed polymer chains: a Brownian dynamics simulation study Polymer. 34: 440-442. DOI: 10.1016/0032-3861(93)90105-J |
0.666 |
|
| 1992 |
Haliloglu T, Erman B, Bahar I. Time‐dependent probability distribution functions for orientational motions of segments in polymer chains The Journal of Chemical Physics. 97: 4438-4444. DOI: 10.1063/1.463886 |
0.653 |
|
| 1992 |
Haliloglu T, Bahar I, Erman B. Orientational and conformational correlations in deformed polymer chains with fixed end‐to‐end separation: A Brownian dynamics simulation study The Journal of Chemical Physics. 97: 4428-4437. DOI: 10.1063/1.463885 |
0.672 |
|
| 1991 |
Erman B, Haliloglu T, Bahar I, Mark JE. Segmental orientation in uniaxially deformed networks: a higher order approximation for finite chains and large deformations Macromolecules. 24: 901-907. DOI: 10.1021/Ma00004A015 |
0.624 |
|
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