2026
B. Tayhan, S. Horozoglu, A.R. Atilgan, C. Atilgan,
"Functional Calmodulin States are Selected from an Electrostatically Tuned Free Energy Landscape," Journal of Chemical Information and Theory, ASAP article (2026).
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K. Kazan, M. Berksoz, B. Kocuk, A.R. Atilgan, C. Atilgan,
"Multiply Perturbed Response: A Protocol to Identify Cooperative Allosteric Residue Combinations Driving Protein Conformational Transitions," Bio-protocol, in press (2026).
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T.F. Guclu, C. Atilgan, A.R. Atilgan,
"Temporal Hydrogen-Bond Network Analysis Reveals Substrate-Directed Connectivity in Dihydrofolate Reductase," bioRxiv (2026).
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2025
M. Berksoz, A.R. Atilgan, B. Kocuk, C. Atilgan,
"Multiply Perturbed Response to Disclose Allosteric Control of Conformational Change: Application to Fluorescent Biosensor Design," Journal of Molecular Biology, 437, 169234 (2025).
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E. Cetin, H. Abdizadeh, A.R. Atilgan, C. Atilgan,
"A Thermodynamic Cycle to Predict the Competitive Inhibition Outcomes of an Evolving Enzyme," Journal of Chemical Theory and Computation, 21, 4910-4920 (2025).
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T.F. Guclu, B. Tayhan, E. Cetin, A.R. Atilgan, C. Atilgan,
"High Throughput Mutational Scanning of a Protein via Alchemistry on a High-performance Computing Resource," Concurrency and Computation: Practice and Experience, 37, 38371 (2025).
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M. Berksoz, C. Atilgan,
"Ranking Single Fluorescent Protein Based Calcium Biosensor Performance by Molecular Dynamics Simulations," Journal of Chemical Information and Modeling; 65, 338-350 (2025).
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2024
T.F. Guclu, A.R. Atilgan, C. Atilgan,
"Deciphering GB1's Single Mutational Landscape: Insights from MuMi Analysis," Journal of Physical Chemistry B; 128, 7987-7996 (2024).
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I. Kantarcioglu, I. Gaszek, T.F. Guclu, M.S. Yildiz, A.R. Atilgan, E. Toprak, C. Atilgan,
"Structural Shifts in TolC Facilitate Efflux-Mediated β-lactam Resistance," Communications Biology; 7, 1051 (2024).
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M. Berksoz, C. Atilgan,
"Allosteric Modulation of Fluorescence Revealed by Hydrogen Bond Dynamics in a Genetically Encoded Maltose Biosensor," Proteins: Structure, Function, Bioinformatics, 92, 923 - 932 (2024).
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2023
E. Cetin, T.F. Guclu, I. Kantarcioglu, I.K. Gaszek, E. Toprak, A.R. Atilgan, B. Dedeoglu, C. Atilgan,
"Kinetic Barrier to Enzyme Inhibition Is Manipulated by Dynamical Local Interactions in E. coli DHFR," Journal of Chemical Information and Modeling, 63, 4839-4849 (2023).
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A.B. Alhamwi, C. Atilgan, O. Sensoy,
"Nonlocal Effects of Antibiotic-Resistance-Causing Mutations Reveal an Alternative Region for Targeting on FtsW–Penicillin-Binding Protein 3 Complex of Haemophilus influenzae," Journal of Chemical Information and Modeling, 63, 3094-3104 (2023).
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G. Liu, E. Ekmen, F. Jalalypour, H.D.T. Mertens, C.M. Jeffries, D.I. Svergun, A.R. Atilgan, C. Atilgan, Z. Sayers,
"Conformational Multiplicity of Bacterial Ferric Binding Protein Revealed by Small Angle X-Ray Scattering and Molecular Dynamics Calculations," Journal of Chemical Physics, 158, 085101 (2023).
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2022
E. Cetin, A.R. Atilgan, C. Atilgan,
"DHFR mutants modulate their synchronized dynamics with the substrate by shifting hydrogen bond occupancies," Journal of Chemical Information and Modeling, 62, 6715-6726 (2022).
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M. Ilter, R. Kasmer, F. Jalalypour, C. Atilgan, O. Topcu, N. Karakas, O. Sensoy,
"Inhibition of mutant RAS-RAF interaction by mimicking structural and dynamic properties of phosphorylated RAS," eLife, 11, e79747 (2022).
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B. Koca Findik, U. Çilesiz, S.K. Bali, C. Atılgan, V. Aviyente, B. Dedeoglu,
"Investigation of iron release from the N- and C-lobes of human serum transferrin by quantum chemical calculations," Organic and Biomolecular Chemistry, 20, 8766-8774 (2022).
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S. Piepoli, S. Barakat, L. Nogay, B. Simsek, U. Akkose, H. Taskiran, N. Tolay, M. Gezen, C. Yesilada, M. Tuncay, O. Adebali, C. Atilgan, B. Erman,
"Sibling rivalry among the ZBTB transcription factor family: homo vs. heterodimers," Life Science Alliance, 5, e202201474 (2022).
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O.B. Okan, D. Turgut, C. Atilgan, A.R. Atilgan, R. Ozisik,
"Could network structures generated with simple rules imposed on a cubic lattice reproduce the structural descriptors of globular proteins?" Journal of Complex Networks, 10, cnab048 (2022).
link
A.R. Atilgan, C. Atilgan,
"Computational strategies for protein conformational ensemble detection," Current Opinion in Structural Biology, 72, 79-87 (2022).
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2021
M.S. Manna, Y.T. Tamer, I. Gaszek, N. Poulides, A. Ahmed, X. Wang, F.C.R. Toprak, D.R. Woodard, A.Y. Koh, N.S. Williams, D. Borek, A.R. Atilgan, J.D. Hulleman, C. Atilgan, U. Tambar, E. Toprak,
"A trimethoprim derivative impedes antibiotic resistance evolution," Nature Communications, 12, 2949 (2021).
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T.F. Guclu, A.R. Atilgan, C. Atilgan,
"Dynamic Community Composition Unravels Allosteric Communication in PDZ3," Journal of Physical Chemistry B, 125, 2266-2276 (2021).
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T.F. Guclu, N. Kocatug, A.R. Atilgan, C. Atilgan,
"N-terminus of the Third PDZ Domain of PSD-95 Orchestrates Allosteric Communication for Selective Ligand Binding," Journal of Chemical Information and Modeling, 61, 347-357 (2021).
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2020
H. Abdizadeh, F. Jalalypour, A.R. Atilgan, C. Atilgan,
"A Coarse-Grained Methodology Identifies Intrinsic Mechanisms That Dissociate Interacting Protein Pairs," Frontiers in Molecular Biosciences, 7, 210 (2020).
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F. Jalalypour, O. Sensoy, C. Atilgan,
"Perturb-Scan-Pull: A Novel Method Facilitating Conformational Transitions in Proteins," Journal of Chemical Theory and Computation, 16, 3825-3841 (2020).
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S. Piepoli, A.O. Alt, C. Atilgan, E.Z. Mancini, B. Erman,
"Structural analysis of the PATZ1 BTB domain homodimer," Acta Crystallographica D, D76, 581-593 (2020).
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E.B. Sevinis Ozbulut, M.S. Seven, K. Bilge, T. Akkas, C.E. Tas, B. Yildiz, C. Atilgan, Y.Z. Menceloglu, S. Unal,
"Blends of highly branched and linear poly(arylene ether sulfone)s: The multiscale effect of degree of branching on the morphology and mechanical properties," Polymer, 188, 122114 (2020).
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2019
Y.T. Tamer, I.K. Gaszek, H. Abdizadeh, T. Altunbasak Batur, K. Reynolds, A.R. Atilgan, C. Atilgan, E. Toprak,
"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, 1533-1550 (2019).
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S.M. Avaz Seven, O. Oguz, Y.Z. Menceloglu, C. Atilgan,
"Tuning interaction parameters of thermoplastic polyurethanes in a binary solvent to achieve precise control over micro-phase separation," Journal of Chemical Information and Modeling, 59, 1946-1956 (2019).
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G. Bulbul, G. Liu, N. Rao Vithalapur, C. Atilgan, Z. Sayers, N. Pourmand,
"Employment of iron binding protein from Haemophilus influenza in functional nanopipettes for iron monitoring," ACS Chemical Neuroscience, 10, 1970-1977 (2019).
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2018
C. Ross, B. Nizami, M. Glenister, O.S. Amamuddy, A.R. Atilgan, C. Atilgan, O. Tastan Bishop,
"MODE-TASK: large-scale protein motion tools," Bioinformatics, 34, 3759-3763 (2018).
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C. Atilgan,
"Computational Methods for Efficient Sampling of Protein Landscapes and Disclosing Allosteric Regions," Advances in Protein Chemistry and Structural Biology, 113, 33-63 (2018).
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D.L. Penkler, C. Atilgan, O. Tastan Bishop,
"Allosteric Modulation of Human Hsp90α Conformational Dynamics," Journal of Chemical Information and Modeling, 58, 383-404 (2018).
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C. Ross, A.R. Atilgan, O. Tastan Bishop, C. Atilgan,
"Unravelling the motions behind Enterovirus 71 uncoating," Biophysical Journal, 114, 822-838 (2018).
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2017
H. Abdizadeh, A.R. Atilgan, C. Atilgan, B. Dedeoglu,
"Computational approaches for deciphering equilibrium and kinetic properties of iron transport proteins," Metallomics, 9, 1513-1533 (2017).
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D.K. Brown, D.L. Penkler, O.S. Amamuddy, C. Ross, A.R. Atilgan, C. Atilgan, O. Tastan Bishop,
"MD-TASK: a software suite for analyzing molecular dynamics trajectories," Bioinformatics, 33, 2768-2771 (2017).
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D.L. Penkler, O. Sensoy, C. Atilgan, O. Tastan Bishop,
"Perturbation Response Scanning Reveals Key Residues for Allosteric Control in Hsp70," Journal of Chemical Information and Modeling, 57, 1359-1374 (2017).
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S. Avaz, O. Oguz, H. Kurt, Y.Z. Menceloglu, C. Atilgan,
"Soft segment length controls morphology of poly(ethylene oxide) based segmented poly(urethane-urea) copolymers in a binary solvent," Computational Materials Science, 138, 58-69 (2017).
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H. Abdizadeh, A.R. Atilgan, C. Atilgan,
"Mechanisms by Which Salt Concentration Moderates the Dynamics of Human Serum Transferrin," Journal of Physical Chemistry B, 121, 4778-4789 (2017).
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H. Abdizadeh, Y.T. Tamer, O. Acar, E. Toprak, A.R. Atilgan, C. Atilgan,
"Increased Substrate Affinity in the Escherichia Coli L28R Dihydrofolate Reductase Mutant Causes Trimethoprim Resistance," Phys. Chem. Chem. Phys., 19, 11416-11428 (2017).
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O. Sensoy, A.R. Atilgan, C. Atilgan,
"FbpA Iron Storage and Release are Governed by Periplasmic Microenvironments," Phys. Chem. Chem. Phys., 19, 6064-6075 (2017).
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T. Ozaltin, V. Aviyente, A.L. Demirel, C. Atilgan,
"Multiscale Modeling of Poly(2-isopropyl-2-oxazoline) Chains in Aqueous Solutions," European Polymer Journal, 88, 594-604 (2017).
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E. Ozden-Yenigun, C. Atilgan J. Elliott,
"Multiscale Modeling of Nanostructured Crosslinked Interfaces," Computational Materials Science, 129, 279-289 (2017).
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2015
G. Ozbaykal, A.R. Atilgan, C. Atilgan,
"In Silico Mutational Studies of Hsp70 Disclose Sites with Distinct Functional Attributes," Proteins: Structure, Function, Bioinformatics, 83, 2077-2090 (2015).
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H. Abdizadeh, A.R. Atilgan, C. Atilgan,
"Detailed Molecular Dynamics Simulations of Human Transferrin Provide Insights on Iron Release Dynamics at Serum and Endosomal pH," Journal of Biological Inorganic Chemistry, 20, 705-718 (2015).
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H. Abdizadeh, G. Guven, A.R. Atilgan, C. Atilgan,
"Perturbation Response Scanning Specifies Key Regions in Subtilisin Serine Protease for both Function and Stability," Journal of Enzyme Inhibition and Medicinal Chemistry, 30, 867-873 (2015).
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2013
A. O. Aykut, A.R. Atilgan, C. Atilgan,
"Designing Molecular Dynamics Simulations to Shift Populations of the Conformational States of Calmodulin," PLoS Computational Biology, 9, e1003366 (2013) .
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E. Ozden-Yenigun, E. Simsek, Y.Z. Menceloglu, C. Atilgan,
"Molecular Basis for Solvent Dependent Morphologies Observed in Electro-Sprayed Surfaces," Phys. Chem. Chem. Phys., 15, 17862 (2013).
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2012
] A.R. Atilgan, C. Atilgan,
" Local Motifs in Proteins Combine to Generate Global Functional Moves, " Briefings in Functional Genomics, 11, 479-488 (2012).
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C. Atilgan, I. Inanc, A.R. Atilgan,
" On Modifying Properties of Polymeric Melts by Nanoscopic Particles, " Journal of Polymer Science Part B – Polymer Physics, 50, 1653-1662 (2012).
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S. Negi, A.O. Aykut, A.R. Atilgan, C. Atilgan,
"Calmodulin Readily Switches Conformation upon Protonating High pKa Acidic Residues," J. Phys. Chem. B, 116, 7145-7153 (2012).
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C. Atilgan, O.B. Okan, A.R. Atilgan,
"Network-based Models as Tools Hinting at Non-evident Protein Functionality," Annual Review of Biophysics, 41, 205-225 (2012).
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2011
A.R. Atilgan, A.O. Aykut, C. Atilgan,
"Subtle pH differences trigger single residue motions for moderating conformations of calmodulin," J. Chem. Phys., 135, 155102 (2011).
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T.F. Ozaltın, I. Degirmenci, V. Aviyente, C. Atilgan, B. De Sterck, V. Van Speybroeck, M. Waroquier,
"Controlling the tacticity in the polymerization of N-isopropylacrylamide: A computational study," Polymer, 52, 5503-5512 (2011).
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2010
D. Turgut, A.R. Atilgan, C. Atilgan,
"Assortative Mixing in Close-Packed Spatial Networks," PLoS ONE, 5, e15551 (2010).
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C. Atilgan, O.B. Okan, A.R. Atilgan,
"Orientational Order Governs Collectivity of Folded Proteins," Proteins: Structure, Function, Bioinformatics, 78, 3363-3375 (2010).
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F. Meersman, C. Atilgan, A. J. Miles, R. Bader, W. Shang, A. Matagne, B. A. Wallace, M. H. J. Koch,
"A consistent picture of the reversible thermal unfolding of hen egg-white lysozyme from experiment and molecular dynamics," Biophys. J., 99, 2255-2263 (2010).
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J. Servantie, C. Atilgan, A.R. Atilgan,
"Depth Dependent Dynamics in the Hydration Shell of a Protein," J. Chem. Phys., 133, 085101 (2010).
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C. Atilgan, Z.N. Gerek, S.B. Ozkan, A.R. Atilgan,
"Manipulation of conformational change in proteins by single residue perturbations," Biophys. J., 99, 933-943 (2010).
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G. Kacar, C. Atilgan, A. S. Ozen,
"Mapping and Reverse-mapping of the Morphologies for a Molecular Understanding of the Self-Assembly of Fluorinated Block Copolymers," J. Phys. Chem. C., 114, 370-382 (2010).
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K. G. Topal, C. Atilgan, A. S. Demir, V. Aviyente,
"Understanding the Mode of Action of ThDP in Benzoylformate Decarboxylase," Biopolymers, 93, 32-46 (2010).
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2008
H. Can, G. Kacar, C. Atilgan,
"Surfactant Formation Efficiency of Fluorocarbon-Hydrocarbon Oligomers in Supercritical CO2," J. Chem. Phys., 131, 124701 (2009). [ link ] C. Atilgan, A.O. Aykut, A.R. Atilgan, "How a Vicinal Layer of Solvent Molecules Modulates the Dynamics of Proteins," Biophysical Journal, 93, 79 – 89 (2008).
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C. Atilgan, G. Demirel, A. R. Atilgan,
"Collective Behavior of El Farol Attendees," Adv. Complex Syst., 11, 629-639 (2008).
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2007
A. S. Ozen, C. Atilgan, G. Sonmez,
"Non-Covalent Intramolecular Interactions in the Monomers and Oligomers of the Acceptor and Donor Type of Low Band Gap Conducting Polymers," J. Phys. Chem. C, 111, 16362-16371 (2007) .
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C. Atilgan, V. Aviyente,
"Hybrid Usage of Computational Tools in Drug Synthesis," Current Computer-Aided Drug Design, 3, 149-159 (2007).
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A. R. Atilgan, D. Turgut, C. Atilgan,
"Screened Non-bonded Interactions in Native Proteins Manipulate Optimal Paths for Robust Residue Communication," Biophys. J., 92, 3052-3062 (2007).
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2004
A. R. Atilgan, P. Akan, C. Baysal,
"Small-World Communication of Residues and Significance for Protein Dynamics," Biophys. J., 86, 85-91 (2004).
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D. Duran, V. Aviyente, C. Baysal,
"A Computational Approach to the Synthesis of Dirithromycin," J. Mol. Model., 10, 94-101 (2004).
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D. Duran, V. Aviyente, C. Baysal,
"Theoretical Study of Selective Methylation in the Synthesis of Azithromycin," J. Comput. Aid. Mol. Des., 18, 1-11 (2004).
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D. Duran, V. Aviyente, C. Baysal,
"Solvent Effect on the Synthesis of Clarithromycin: A Molecular Dynamics Study," J. Comput. Aid. Mol. Des., 18, 145-154 (2004).
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2002
P. Doruker, I. Bahar, C. Baysal, B. Erman,
"Collective Deformations in Proteins Determined by a Mode Analysis of Molecular Dynamics Trajectories," Polymer, 43, 431-439 (2002).
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C. Baysal, A. R. Atilgan,
"Relaxation Kinetics and the Glassiness of Proteins: The Case of Bovine Pancreatic Trypsin Inhibitor," Biophys. J., 83, 699-705 (2002).
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D. Duran, V. Aviyente, C. Baysal,
"Modeling the Selective Methylation in the Synthesis of Clarithromycin," J. Chem. Soc. Perkin Trans. II, 670-675 (2002).
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2001
C. Baysal, A. R. Atilgan,
"Elucidating the Structural Mechanisms for Biological Activity of the Chemokine Family," Proteins, 43, 150-160 (2001).
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C. Baysal, B. Erman, B. Chu,
"Conformational Features of Poly(1,1-dihydroperfluorooctyl acrylate) and Poly(vinyl acetate) Diblock Oligomers in Supercritical Carbon Dioxide," J. Chem. Phys., 114, 5444-5449 (2001).
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C. Baysal, A. R. Atilgan,
"Coordination Topology and Stability for the Native and Binding Conformers of Chymotrypsin Inhibitor 2," Proteins, 45, 62-70 (2001).
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1999
C. Baysal, H. Meirovitch, I. M. Navon,
"Performance of Efficient Minimization Algorithms as Applied to Models of Peptides and Proteins," J. Comput. Chem., 20, 354-364 (1999).
link
C. Baysal, H. Meirovitch,
"Free Energy Based Populations of Interconverting Microstates of a Cyclic Peptide Lead to the Experimental NMR Data," Biopolymers, 50, 329-344 (1999).
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C. Baysal, H. Meirovitch,
"Efficiency of Simulated Annealing for Peptides with Increasing Geometrical Restrictions," J. Comput. Chem., 20, 1659-1670 (1999).
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1997
C. Baysal, H. Meirovitch,
"Efficiency of the Local Torsional Deformations Method for Identifying the Stable Structures of Cyclic Molecules," J. Phys. Chem. A, 101, 2185-2191 (1997).
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C. Baysal, B. Erman, I. Bahar, F. Laupretre, L. Monnerie,
"Local Dynamics of Bulk Polybutadienes of Various Microstructures: Comparison of Theory with NMR Measurements," Macromolecules, 30, 2058-2066 (1997).
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C. Baysal, H. Meirovitch,
"Novel Procedure for Developing Implicit Solvation Models for Peptides and Proteins," J. Phys. Chem. B, 101, 7368-7370 (1997).
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1996
C. Baysal, A. R. Atilgan, B. Erman, I. Bahar,
"Molecular Dynamics Analysis of Coupling between Librational Motions and Isomeric Jumps in Chain Molecules," Macromolecules, 29, 2510-2514 (1996).
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C. Baysal, I. Bahar, B. Erman, L. Monnerie,
"Kinematics of Polymer Chains in Dense Medium. 4. Effect of Backbone Geometry and Application to Polybutadiene," Macromolecules, 29, 2980-2988 (1996).
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C. Baysal, H. Meirovitch,
"New Conformational Search Method Based on Local Torsional Deformations for Cyclic Molecules, Loops in Proteins, and Dense Polymer Systems," J. Chem. Phys., 105, 7868-7871 (1996).
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