Items where Author is "Atılgan, Ali Rana"

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Number of items: 60.

Article

Çetin, Ebru and Güçlü, Tandaç Fürkan and Kantarcıoğlu, Işık and Gaszek, Ilona K. and Toprak, Erdal and Atılgan, Ali Rana and Dedeoglu, Burcu and Atılgan, Canan (2023) Kinetic barrier to enzyme inhibition is manipulated by dynamical local interactions in E. coli DHFR. Journal of Chemical Information and Modeling, 63 (15). pp. 4839-4849. ISSN 1549-9596 (Print) 1549-960X (Online)

Liu, Gökşin and Ekmen, Erhan and Jalalypour, Farzaneh and Mertens, Haydyn D. T. and Jeffries, Cy M. and Svergun, Dmitri and Atılgan, Ali Rana and Atılgan, Canan and Sayers, Zehra (2023) Conformational multiplicity of bacterial ferric binding protein revealed by small angle x-ray scattering and molecular dynamics calculations. Journal of Chemical Physics, 158 (8). ISSN 0021-9606 (Print) 1089-7690 (Online)

Arlı, Cihan and Atılgan, Ali Rana and Mısırlıoğlu, Burç (2023) Volumetric effects in electrocaloric response of ferroelectric thin films. Journal of Materials Chemistry C, 11 (3). pp. 1134-1143. ISSN 2050-7526 (Print) 2050-7534 (Online)

Çetin, Ebru and Atılgan, Ali Rana and Atılgan, Canan (2022) DHFR mutants modulate their synchronized dynamics with the substrate by shifting hydrogen bond occupancies. Journal of Chemical Information and Modeling, 62 (24). pp. 6715-6726. ISSN 1549-9596 (Print) 1549-960X (Online)

Papila, Melih and Atılgan, Ali Rana (2022) All-composite honeycomb core sandwich structures: master curves for stiffness-based design. Forces in Mechanics, 6 . ISSN 2666-3597

Atılgan, Ali Rana and Atılgan, Canan (2022) Computational strategies for protein conformational ensemble detection. Current Opinion in Structural Biology, 72 . pp. 79-87. ISSN 0959-440X (Print) 1879-033X (Online)

Burak Okan, Osman and Turgut, Deniz and Atılgan, Canan and Atılgan, Ali Rana and Ozisik, Rahmi (2022) Could network structures generated with simple rules imposed on a cubic lattice reproduce the structural descriptors of globular proteins? Journal of Complex Networks, 10 (1). ISSN 2051-1310 (Print) 2051-1329 (Online)

Manna, Madhu Sudan and Tamer, Yusuf Talha and Gaszek, Ilona and Poulides, Nicole and Ahmed, Ayesha and Wang, Xiaoyu and Toprak, Furkan C.R. and Woodard, Da Nae R. and Koh, Andrew Y. and Williams, Noelle S. and Borek, Dominika and Atılgan, Ali Rana and Hulleman, John D. and Atılgan, Canan and Tambar, Uttam and Toprak, Erdal (2021) A trimethoprim derivative impedes antibiotic resistance evolution. Nature Communications, 12 (1). ISSN 2041-1723

Güçlü, Tandaç Fürkan and Atılgan, Ali Rana and Atılgan, Canan (2021) Dynamic community composition unravels allosteric communication in pdz3. Journal of Physical Chemistry B, 125 (9). pp. 2266-2276. ISSN 1520-6106 (Print) 1520-5207 (Online)

Güçlü, Tandaç Fürkan and Kocatuğ, Nazlı and Atılgan, Ali Rana and Atılgan, Canan (2021) N-terminus of the third PDZ domain of PSD-95 orchestrates allosteric communication for selective ligand binding. Journal of Chemical Information and Modeling, 61 (1). pp. 347-357. ISSN 1549-9596 (Print) 1549-960X (Online)

Abdizadeh, Haleh and Jalalypour, Farzaneh and Atılgan, Ali Rana and Atılgan, Canan (2020) A coarse-grained methodology identifies intrinsic mechanisms that dissociate interacting protein pairs. Frontiers in Molecular Biosciences, 7 . ISSN 2296-889X

Tamer, Yusuf Talha and Gazsek, Ilona K. and Abdizadeh, Haleh and Batur, Tuğçe and Reynolds, Kimberly and Atılgan, Ali Rana and Atılgan, Canan and Toprak, Erdal (2019) High-order epistasis in catalytic power of dihydrofolate reductase gives rise to a rugged fitness landscape in the presence of trimethoprim selection. Molecular Biology and Evolution, 36 (7). pp. 1533-1550. ISSN 0737-4038 (Print) 1537-1719 (Online)

Ross, Caroline and Nizami, Bilal and Glenister, Michael and Amamuddy, Olivier Sheik and Atılgan, Ali Rana and Atılgan, Canan and Bishop, Özlem Tastan (2018) MODE-TASK: large-scale protein motion tools. Bioinformatics, 34 (21). pp. 3759-3763. ISSN 1367-4803 (Print) 1460-2059 (Online)

Ross, Caroline Jane and Atılgan, Ali Rana and Taştan Bishop, Özlem and Atılgan, Canan (2018) Unraveling the motions behind Enterovirus 71 uncoating. Biophysical Journal, 114 (4). pp. 822-838. ISSN 0006-3495 (Print) 1542-0086 (Online)

Abdizadeh, Haleh and Atılgan, Ali Rana and Atılgan, Canan and Dedeoğlu, Burcu (2017) Computational approaches for deciphering the equilibrium and kinetic properties of iron transport proteins. Metallomics, 9 (11). pp. 1513-1533. ISSN 1756-5901 (Print) 1756-591X (Online)

Brown, David K. and Penkler, David L. and Amamuddy, Olivier Sheik and Ross, Caroline and Atılgan, Ali Rana and Atılgan, Canan and Bishop, Özlem Taştan (2017) MD-TASK: a software suite for analyzing molecular dynamics trajectories. Bioinformatics, 33 (17). pp. 2768-2771. ISSN 1367-4803 (Print) 1460-2059 (Online)

Abdizadeh, Haleh and Tamer, Yusuf Talha and Acar, Ömer and Toprak, Erdal and Atılgan, Ali Rana and Atılgan, Canan (2017) Increased substrate affinity in the escherichia coli L28R dihydrofolate reductase mutant causes trimethoprim resistance. Physical Chemistry Chemical Physics, 19 (18). pp. 11416-11428. ISSN 1463-9076 (Print) 1463-9084 (Online)

Abdizadeh, Haleh and Atılgan, Ali Rana and Atılgan, Canan (2017) Mechanisms by which salt concentration moderates the dynamics of human serum transferrin. Journal of Physical Chemistry B, 121 (18). pp. 4778-4789. ISSN 1520-6106 (Print) 1520-5207 (Online)

Şensoy, Özge and Atılgan, Ali Rana and Atılgan, Canan (2017) FbpA iron storage and release are governed by periplasmic microenvironments. Physical Chemistry Chemical Physics, 19 (8). pp. 6064-6075. ISSN 1463-9076 (Print) 1463-9084 (Online)

Abdizadeh, Haleh and Güven, Gökçe and Atılgan, Ali Rana and Atılgan, Canan (2015) Perturbation response scanning specifies key regions in subtilisin serine protease for both function and stability. Journal of Enzyme Inhibition and Medicinal Chemistry, 30 (6). pp. 867-873. ISSN 1475-6366 (Print) 1475-6374 (Online)

Özbaykal, Gizem and Atılgan, Ali Rana and Atılgan, Canan (2015) In silico mutational studies of Hsp70 disclose sites with distinct functional attributes. Proteins: Structure, Function and Bioinformatics, 83 (11). pp. 2077-2090. ISSN 0887-3585 (Print) 1097-0134 (Online)

Abdizadeh, Haleh and Atılgan, Ali Rana and Atılgan, Canan (2015) Detailed molecular dynamics simulations of human transferrin provide insights into iron release dynamics at serum and endosomal pH. Journal of Biological Inorganic Chemistry, 20 (4). pp. 705-718. ISSN 0949-8257 (Print) 1432-1327 (Online)

Güven, Gökçe and Atılgan, Ali Rana and Atılgan, Canan (2014) Protonation states of remote residues affect binding-release dynamics of the ligand but not the conformation of apo ferric binding protein. Journal of Physical Chemistry B, 118 (40). pp. 11677-11687. ISSN 1520-6106 (Print) 1520-5207 (Online)

Aykut, Ayşe Özlem and Atılgan, Ali Rana and Atılgan, Canan (2013) Designing molecular dynamics simulations to shift populations of the conformational states of calmodulin. PLoS Computational Biology, 9 (12). ISSN 1553-734X

Atılgan, Canan and İnanç, İbrahim and Atılgan, Ali Rana (2012) On modifying properties of polymeric melts by nanoscopic particles. Journal of Polymer Science Part B: Polymer Physics, 50 (23). pp. 1653-1662. ISSN 0887-6266 (Print) 1099-0488 (Online)

Atılgan, Ali Rana and Atılgan, Canan (2012) Local motifs in proteins combine to generate global functional moves. Briefings in Functional Genomics (Sl), 11 (6). pp. 479-488. ISSN 2041-2649 (Print) 2041-2657 (Online)

Negi, Sunita and Aykut, Ayşe Özlem and Atılgan, Ali Rana and Atılgan, Canan (2012) Calmodulin readily switches conformation upon protonating high pK(a) acidic residues. Journal of Physical Chemistry B, 116 (24). pp. 7145-7153. ISSN 1520-6106

Atılgan, Canan and Okan, Osman Burak and Atılgan, Ali Rana (2012) Network-based models as tools hinting at nonevident protein functionality. Annual Review of Biophysics, 41 . pp. 205-225. ISSN 1936-122X (Print) 1936-1238 (Online)

Atılgan, Ali Rana and Aykut, Ayşe Özlem and Atılgan, Canan (2011) Subtle pH differences trigger single residue motions for moderating conformations of calmodulin. Journal of Chemical Physics, 135 (15). ISSN 0021-9606

Turgut, Deniz and Atılgan, Ali Rana and Atılgan, Canan (2010) Assortative mixing in close-packed spatial networks. PLoS One, 5 (12). ISSN 1932-6203

Atılgan, Canan and Okan, Osman Burak and Atılgan, Ali Rana (2010) How orientational order governs collectivity of folded proteins. Proteins: Structure, Function, Bioinformatics, 78 (16). pp. 3363-3375. ISSN 1097-0134

Servantie, James and Atılgan, Canan and Atılgan, Ali Rana (2010) Depth dependent dynamics in the hydration shell of a protein. Journal of Chemical Physics, 133 (8). ISSN 0021-9606

Atılgan, Canan and Gerek, Z. N. and Özkan, S. B. and Atılgan, Ali Rana (2010) Manipulation of conformational change in proteins by single-residue perturbations. Biophysical Journal, 99 (3). pp. 933-943. ISSN 0006-3495

Atılgan, Canan and Atılgan, Ali Rana (2009) Perturbation-response scanning reveals ligand entry-exit mechanisms of ferric binding protein. PLoS Computational Biology, 5 (10). pp. 1-14. ISSN 1553-734X

Okan, Osman Burak and Atılgan, Ali Rana and Atılgan, Canan (2009) Nanosecond motions in proteins impose bounds on the timescale distributions of local dynamics. Biophysical Journal, 97 (7). pp. 2080-2088. ISSN 0006-3495

Atılgan, Canan and Demirel, Güven and Atılgan, Ali Rana (2008) Collective behavior of El Farol attendees. Advances in Complex Systems, 11 (4). pp. 629-639. ISSN 0219-5259

Atılgan, Canan and Aykut, Ayşe Özlem and Atılgan, Ali Rana (2008) How a vicinal layer of solvent modulates the dynamics of proteins. Biophysical Journal, 94 . pp. 79-89. ISSN 0006-3495

Atılgan, Ali Rana and Turgut, Deniz and Atılgan, Canan (2007) Screened nonbonded interactions in native proteins manipulate optimal paths for robust residue communication. Biophysical Journal, 92 (9). pp. 3052-3062. ISSN 0006-3495

Atılgan, Ali Rana and Turgut, Deniz and Atılgan, Canan (2007) A Few designed-in interactions imposed on chain connectivity are sufficient for robust residue communications. Biophysical Journal, Suppl (Abstra). 217A-218A. ISSN 0006-3495

Atılgan, Canan and Sezerman, Ayşe Özlem and Baloğlu, Çetin and Sirer, Irmak and Okan, Osman Burak and Atılgan, Ali Rana (2007) Solvent mobility and surface group flexibility at the dynamical transition. Biophysical Journal, Suppl (Abstra). 405A-406A. ISSN 0006-3495

Baysal, Canan and Atılgan, Ali Rana (2005) Relaxation kinetics and the glassiness of native proteins: coupling of timescales. Biophysical Journal, 88 (3). pp. 1570-1576. ISSN 0006-3495 (Print) 1542-0086 (Online)

Okan, Osman Burak and Atılgan, Ali Rana and Baysal, Canan (2005) Distribution of relaxation times on the pico-nano time scales for a functional protein (ABSTRACT). Biophysical Journal, 88 (1). 16A-16A. ISSN 0006-3495

Atılgan, Ali Rana and Atılgan, Canan (2004) Thermodynamics of residue networks in folded proteins. WSEAS Transactions in Biology and Biomedicine, 1 (2). pp. 205-209. ISSN 1109-9518

Atılgan, Ali Rana and Akan, Pelin and Baysal, Canan (2004) Small-world communication of residues and significance for protein dynamics. Biophysical Journal, 86 (Issue:). pp. 85-91. ISSN 0006-3495 (Print) 1542-0086 (Online)

Baysal, Canan and Atılgan, Ali Rana (2002) Relaxation kinetics and the glassiness of proteins: the case of bovine pancreatic trypsin inhibitor. Biophysical Journal, 83 (2). pp. 699-705. ISSN 0006-3495 (Print) 1542-0086 (Online)

Baysal, Canan and Atılgan, Ali Rana (2001) Coordination topology and stability for the native and binding conformers of chymotrypsin inhibitor 2. Proteins: Structure, Function, and Bioinformatics, 45 (1). pp. 62-70. ISSN 0887-3585

Baysal, Canan and Atılgan, Ali Rana (2001) Elucidating the structural mechanisms for biological activity of the chemokine family. Proteins: Structure, Function, and Bioinformatics, 43 (2). pp. 150-160. ISSN 0887-3585

Bahar, Ivet and Erman, Burak and Jernigan, Robert L. and Atılgan, Ali Rana and Covell, David G. (1999) Collective motions in HIV-1 reverse transcriptase: examination of flexibility and enzyme function. Journal of Molecular Biology, 285 (3). pp. 1023-1037. ISSN 0022-2836

Demirel, Melik C. and Atılgan, Ali Rana and Jernigan, Robert L. and Erman, Burak and Bahar, Ivet (1998) Identification of kinetically hot residues in proteins. Protein Science, 7 (12). pp. 2522-2532. ISSN 0961-8368 (Print) 1469-896X (Online)

Papers in Conference Proceedings

Atılgan, Canan and Liu, Gökşin and Jalalpour, Farzaneh and Ekmen, Erhan and Berksöz, Melike and Atılgan, Ali Rana and Sayers, Zehra (2023) Increased ionic strength triggers multiple conformations in both apo and holo forms of bacterial ferric binding protein. In: Biophysical Society Annual Meeting, San Diego, CA, USA

Abdizadeh, Haleh and Atılgan, Ali Rana and Atılgan, Canan (2016) Computational modeling of iron binding and release in human serum transferrin. In: 41st FEBS Congress on Molecular and Systems Biology for a Better Life, Kusadasi, Turkey

Abdizadeh, Haleh and Acar, Ömer and Güçlü, Tandaç Fürkan and Tamer, Yusuf Talha and Altınuşak, Tuğçe and Toprak, Erdal and Atılgan, Ali Rana and Atılgan, Canan (2016) Computational assessment of trimethoprim resistance in dihydrofolate reductase. In: 60th Annual Meeting of the Biophysical Society, Los Angeles, CA

Atılgan, Ali Rana and Aykut, Ayşe Özlem and Atılgan, Canan (2013) Non-equilibrium fluctuation theorems, redundant paths in proteins, and elucidating conformational changes by single-residue perturbations. In: 57th Annual Meeting of the Biophysical-Society, Philadelphia, PA

Atılgan, Canan and Güven, Gökçe and Atılgan, Ali Rana (2013) Structural basis of how ferric binding proteins utilize pH differences for controlled release of iron. In: 57th Annual Meeting of the Biophysical-Society, Philadelphia, PA

Negi, Sunita and Atılgan, Ali Rana and Atılgan, Canan (2012) Driving calmodulin protein towards conformational shift by changing ionization states of select residues. In: 23rd IUPAP C20 Conference on Computational Physics (CCP 2011), Gatlinburg, Tennessee

Atılgan, Canan and İnanç, İbrahim and Atılgan, Ali Rana (2012) Effect of van der Waals interaction strength and nanocluster size on the dynamical and mechanical properties of 1,4-cis-polybutadiene melts. In: Materials Research Society Fall Meeting 2011, Boston

Özden Yenigün, Elif and Atılgan, Ali Rana and Bilge, Kaan and Menceloğlu, Yusuf Z. and Atılgan, Canan and Papila, Melih (2011) Designed-in molecular interactions lead to superior thermo-mechanical properties in nanocomposites. In: 2010 MRS Fall Meeting, Boston, Massachusetts

Aykut, Ayşe Özlem and Atılgan, Ali Rana and Atılgan, Canan (2011) Molecular recognition mechanisms of calmodulin examined by perturbation-response scanning. In: 2010 MRS Fall Meeting, Boston, Massachusetts

Atılgan, Canan and İnanç, İbrahim and Atılgan, Ali Rana (2010) Long-range structural regularities and collectivity of folded proteins. In: 2009 MRS Fall Meeting, Boston, MA

Atılgan, Canan and Demirel, Güven and Atılgan, Ali Rana (2007) Landscape Dynamics of El Farol Attendees. In: The 2007 International Conference of the System Dynamics Society, Boston

This list was generated on Thu Mar 28 22:32:57 2024 +03.