"Dissecting Allosteric Mutations for Antibiotic Resistance by Time-Dependent Linear Response Theory," P Campitelli, T Modi, SB Ozkan, Journal of Chemical Theory and Computation
"Evidence that the cold-and menthol-sensing functions of the human TRPM8 channel evolved separately," Dustin D Luu, Nikhil Ramesh, I Can Kazan, Karan H Shah, Gourab Lahiri, Miyeko D Mana, S Banu Ozkan, Wade D Van Horn, Science Advances
"RNA-induced Allosteric Coupling Drives Viral Capsid Assembly," S Hamilton, T Modi, P Šulc, SB Ozkan, PRX Life 2 (1), 013012
"Some mechanistic underpinnings of molecular adaptations of SARS-COV-2 spike protein by integrating candidate adaptive polymorphisms with protein dynamics," NJ Ose, P Campitelli, T Modi, IC Kazan, S Kumar, SB Ozkan, Elife
"Enhancing deep learning model design through protein dynamics information integration," J Lu, ICJ Kazan, BK Kartchner, N Huynh, JH Mills, SB Ozkan, Biophysical Journal 123 (3), 207a-208a
"Engineering gain-of-function mutants of a WW domain by dynamics and structural analysis," ICJ Kazan, J Lu, MI Rahman, N Halloran, AA Bobkov, SB Ozkan, Biophysical Journal 123 (3), 64a
"Probing impact of allosteric (or distal) mutations on protein function through time-dependent linear response theory," P Campitelli, T Modi, SB Ozkan, Biophysical Journal 123 (3), 65a
"Engineering gain‐of‐function mutants of a WW domain by dynamics and structural analysis," J Lu, MI Rahman, IC Kazan, NR Halloran, AA Bobkov, SB Ozkan, Protein Science 32 (9), e4759
"Allosteric regulatory control in dihydrofolate reductase is revealed by dynamic asymmetry," IC Kazan, JH Mills, SB Ozkan, Protein Science 32 (8), e4700
"Protein dynamics provide mechanistic insights about epistasis among common missense polymorphisms," NJ Ose, P Campitelli, R Patel, S Kumar, SB Ozkan, Biophysical journal 122 (14), 2938-2947
"Understanding the evolution of cold sensing and menthol activation in TRPM8," N Ramesh, D Luu, KH Shah, ICJ Kazan, SB Ozkan, WD Van Horn, Biophysical journal 122 (3), 197a
"RNA-induced allosteric coupling drives viral capsid assembly in the single-stranded RNA virus bacteriophage MS2," S Hamilton, T Modi, P Sulc, SB Ozkan, Biophysical Journal 122 (3), 48a-49a
"Dynamics-based network analysis identifies laci rheostats with high accuracy," P Campitelli, SB Ozkan, L Swint-Kruse, D Ross, Biophysical journal 122 (3), 189a-190a
Allosteric regulatory control in dihydrofolate reductase (DHFR) revealed with dynamic asymmetry in unliganded ensemble, ICJ Kazan, JH Mills, SB Ozkan, Biophysical Journal 122 (3), 48a
"Correlated Evolution of Low-Frequency Vibrations and Function in Enzymes," T Modi, P Campitelli, M Heyden, SB Ozkan, The Journal of Physical Chemistry B 127 (3), 616-622
"RNA-induced allosteric coupling drives viral capsid assembly in bacteriophage MS2," S Hamilton, T Modi, P Sulc, SB Ozkan, bioRxiv, 2023.06. 05.543665
"Design of novel cyanovirin-N variants by modulation of binding dynamics through distal mutations," IC Kazan, P Sharma, MI Rahman, A Bobkov, R Fromme, G Ghirlanda, Elife 11, e67474
"Investigating the allosteric response of the PICK1 PDZ domain to different ligands with all‐atom simulations," AO Stevens, IC Kazan, B Ozkan, Y He, Protein Science 31 (12), e4474
Dynamic allostery highlights the evolutionary differences between the CoV-1 and CoV-2 main proteases, P Campitelli, J Lu, SB Ozkan, Biophysical journal 121 (8), 1483-1492
"Dynamic coupling of residues within proteins as a mechanistic foundation of many enigmatic pathogenic missense variants," NJ Ose, BM Butler, A Kumar, IC Kazan, M Sanderford, S Kumar, PLoS computational biology 18 (4), e1010006
"Understanding ligand specificity through protein network dynamics," P Campitelli, SB Ozkan, L Swint-Kruse, Biophysical Journal 121 (3), 51a
"Protein dynamics provide mechanistic insights about the epistatic relationships among highly observed potentially adaptive missense variants," NJ Ose, P Campitelli, RP Patel, SB Ozkan, S Kumar, Biophysical Journal 121 (3), 456a
"Vibrational density of states capture the role of dynamic allostery in protein evolution," T Modi, M Heyden, SB Ozkan, Biophysical Journal 121 (3), 456a
"Can sequence-specific and dynamics-based metrics allow us to decipher the function in IDP sequences?" SB Ozkan, Biophysical Journal 120 (10), 1857-1859
"Hinge-shift mechanism as a protein design principle for the evolution of β-lactamases from substrate promiscuity to specificity," T Modi, VA Risso, S Martinez-Rodriguez, JA Gavira, MD Mebrat, SB Ozkan, Nature Communications 12 (1), 1852
"The role of rigid residues in modulating TEM-1 β-lactamase function and thermostability," B Kolbaba-Kartchner, IC Kazan, JH Mills, SB Ozkan, International Journal of Molecular Sciences 22 (6), 2895
"Local interactions that contribute minimal frustration determine foldability," T Zou, BW Woodrum, N Halloran, P Campitelli, AA Bobkov, G Ghirlanda, SB Ozkan, The Journal of Physical Chemistry B 125 (10), 2617-2626
"Information Propagation in Time through Allosteric Signaling," T Modi, SB Ozkan, S Pressé, Biophysical Journal 120 (3), 300a
"Adaptive Evolution of SARS-CoV-2: A Perspective from Dynamics," IC Kazan, SB Ozkan, Biophysical Journal 120 (3), 300a-301a
"Allostery and Epistasis as Inherent Properties of Anisotropic Networks," P Campitelli, SB Ozkan, Biophysical Journal 120 (3), 300a
"Emerging Features of Rheostat Positions," L Swint-Kruse, AW Fenton, SB Ozkan, B Hagenbuch, P Campitelli, Biophysical Journal 120 (3), 277a-278a
"Protein folding stability and binding interactions through the lens of evolution: a dynamical perspective," T Modi, P Campitelli, IC Kazan, SB Ozkan, Current Opinion in Structural Biology 66, 207-215
"Dynamic Allostery Highlights the Evolutionary Differences between the CoV-1 and CoV-2 Main Proteases (preprint)," P Campitelli, J Lu, SB Ozkan, 2021
"Substitutions at nonconserved rheostat positions modulate function by rewiring long-range, dynamic interactions," P Campitelli, L Swint-Kruse, SB Ozkan, Molecular Biology and Evolution 38 (1), 201-214
"Design of novel CV-N variants: Modulation of binding dynamics through distal mutations," IC Kazan, P Sharma, A Bobkov, R Fromme, G Ghirlanda, SB Ozkan, bioRxiv, 2020.12. 21.423842
"Information propagation in time through allosteric signaling," T Modi, SB Ozkan, S Pressé, Physical Review Research 2 (2), 023367
"Allostery and epistasis: emergent properties of anisotropic networks," P Campitelli, SB Ozkan, Entropy 22 (6), 667
"The role of conformational dynamics and allostery in modulating protein evolution," P Campitelli, T Modi, S Kumar, SB Ozkan, Annual Review of Biophysics 49, 267-288
"Plant-expressed cocaine hydrolase variants of butyrylcholinesterase and methods of reducing cocaine-primed reinstatement," T Mor, K Larrimore, IJ Kazan, S Ozkan, J Neisewander, US Patent App. 16/560,993
"Dynamic allosteric residue coupling reveals disease mechanism for Gaucher disease and nSNVs across the proteome," N Ose, BM Butler, A Kumar, SB Ozkan, S Kumar, Biophysical Journal 118 (3), 53a
"Large Scale Disease Susceptibility Prediction of nSNVs by Dynamics Information Based Neural Networks," IC Kazan, SB Ozkan, Biophysical Journal 118 (3), 205a
"Asymmetry in dynamic allosteric residue coupling (DARC) interactions captures evolutionary landscape," P Campitelli, SB Ozkan, L Swint-Kruse, Biophysical Journal 118 (3), 52a
"What are the Design Principles for Evolution from Promiscuous to Substrate Specificity?" T Modi, VA Risso, S Martinez-Rodriguez, JA Gavira, SB Ozkan, Biophysical Journal 118 (3), 205a
"A method for the incorporation of protein dynamics into computational enzyme design using the Rosetta software suite," BK Kartchner, IC Kazan, SB Ozkan, JH Mills, Biophysical Journal 118 (3), 320a-321a
"DESIGN OF NOVEL LECTINS BY COMPUTER-AIDED DIRECTED EVOLUTION," P Sharma, IC Kazan, SB Ozkan, G Ghirlanda, Protein Science 28, 81-81
"Conformational dynamics play critical role in protein evolution," SB Ozkan, Abstracts of Papers of the American Chemical Society 258
"Allostery and structural dynamics in protein evolution," P Campitelli, SB Ozkan, Evolution, Origin of Life, Concepts and Methods, 179-194
"Coevolving residues inform protein dynamics profiles and disease susceptibility of nSNVs," BM Butler, IC Kazan, A Kumar, SB Ozkan, PLoS Computational Biology 14 (11), e1006626
"Mutations utilize dynamic allostery to confer resistance in TEM-1 β-lactamase," T Modi, SB Ozkan, International Journal of Molecular Sciences 19 (12), 3808
"Plant-expressed cocaine hydrolase variants of butyrylcholinesterase exhibit altered allosteric effects of cholinesterase activity and increased inhibitor sensitivity," KE Larrimore, I Kazan, L Kannan, R Kendle, T Jamal, M Barcus, A Bolia, SB Ozkan, Scientific Reports 8
"Biotechnological and protein-engineering implications of ancestral protein resurrection," VA Risso, JM Sanchez-Ruiz, SB Ozkan, Current Opinion in Structural Biology 51, 106-115
"Design of Novel Lectins by Computer‐Guided Directed Evolution," P Sharma, IC Kazan, SB Ozkan, G Ghirlanda, The FASEB Journal 32, 673.24-673.24
"A novel modelling mechanism of PAEL receptor and GABARAPL2 interaction involved in Parkinson's disease," P Dutta, L Dargahi, KE O'Connell, A Bolia, B Ozkan, AW Saile, KK Dev, Neuroscience Letter 673, 12-18
"Allostery and Conformational Dynamics in Protein Evolution," SB Ozkan, Biophysical Journal 114 (3), 400a-401a
"Hinge-shift mechanism modulates allosteric regulations in human Pin1," P Campitelli, J Guo, HX Zhou, SB Ozkan, The Journal of Physical Chemistry B 122 (21), 5623-5629
"Author Correction: Plant-expressed cocaine hydrolase variants of butyrylcholinesterase exhibit altered allosteric effects of cholinesterase activity and increased inhibitor sensitivity," KE Larrimore, IC Kazan, L Kannan, RP Kendle, T Jamal, M Barcus, SB Ozkan, Scientific Reports 8
"Ancient thioredoxins evolved to modern-day stability–function requirement by altering native state ensemble," T Modi, J Huihui, K Ghosh, SB Ozkan, Philosophical Transactions of the Royal Society B
"Plant-expressed cocaine hydrolase variants of butyrylcholinesterase exhibit altered allosteric effects of cholinesterase activity and increased inhibitor sensitivity," KE Larrimore, IC Kazan, L Kannan, RP Kendle, T Jamal, M Barcus, Scientific Reports 7 (1), 10419
"Dynamic Flexibility Index Sheds Light on Pin1 Allostery," P Campitelli, HX Zhou, G Ghirlanda, SB Ozkan, Biophysical Journal 112 (3), 317a
"Intrinsically Disordered Protein Dynamics Uncovered through Dynamic Flexibility Index (DFI) Analysis," T Modi, GH Zerze, J Mittal, SM Vaiana, SB Ozkan, Biophysical Journal 112 (3), 208a-209a
"Adaptive BP-dock: an induced fit docking approach for full receptor flexibility," A Bolia, SB Ozkan, Journal of Chemical Information and Modeling 56 (4), 734-746
"Integration of structural dynamics and molecular evolution via protein interaction networks: a new era in genomic medicine," A Kumar, BM Butler, S Kumar, SB Ozkan, Current Opinion in Structural Biology 35, 135-142
"Partial unfolding and refolding for structure refinement: A unified approach of geometric simulations and molecular dynamics," A Kumar, P Campitelli, MF Thorpe, SB Ozkan, Proteins: Structure, Function, and Bioinformatics 83 (12), 2279-2292
"A rigid hinge region is necessary for high-affinity binding of dimannose to cyanovirin and associated constructs," Z Li, A Bolia, JD Maxwell, AA Bobkov, G Ghirlanda, SB Ozkan, Biochemistry 54 (46), 6951-6960
"Evolutionary hinge migration sheds light on the mechanism of green-to-red photoconversion in GFP-like proteins," RM Wachter, SB Ozkan, H Kim, T Zhou, Protein Science 24, 168-168
"Dynamics and Allostery in Ferritin," A Kumar, T Glembo, S Ozkan, Dynamics
"The role of conformational dynamics and allostery in the disease development of human ferritin," A Kumar, TJ Glembo, SB Ozkan, Biophysical Journal 109 (6), 1273-1281
"Mechanism of protein evolution: conformational dynamics and allostery," T Zou, A Kumar, BM Butler, SB Ozkan, Journal of Biomolecular Structure and Dynamics 33 (sup1), 114-114
"Conformational dynamics of nonsynonymous variants at protein interfaces reveals disease association," BM Butler, ZN Gerek, S Kumar, SB Ozkan, Proteins: Structure, Function, and Bioinformatics 83 (3), 428-435
"Physics Based Structure Refinement in Casp11 using Geometric Unfolding and Hierarchically Restrained Replica Exchange Molecular Dynamics," A Kumar, P Campitelli, SB Ozkan, MF Thorpe, Biophysical Journal 108 (2), 519a
"A Hinge Migration Mechanism Unlocks the Evolution of Green-To-Red Photoconversion in GFP-Like Proteins," RM Wachter, H Kim, T Zou, SB Ozkan, Biophysical Journal 108 (2), 380a-381a
"A hinge migration mechanism unlocks the evolution of green-to-red photoconversion in GFP-like proteins," H Kim, T Zou, C Modi, K Dörner, TJ Grunkemeyer, L Chen, R Fromme, SB Ozkan, Structure 23 (1), 34-43
"Partial unfolding and refolding for structure refinement," A Kumar, P Campitelli, MF Thorpe, SB Ozkan, Proteins: Structure, Function and Bioinformatics
"Evolution of conformational dynamics determines the conversion of a promiscuous generalist into a specialist enzyme," T Zou, VA Risso, JA Gavira, JM Sanchez-Ruiz, SB Ozkan, Molecular Biology and Evolution 32 (1), 132-143
"Proteome folding kinetics is limited by protein halflife," T Zou, N Williams, SB Ozkan, K Ghosh, PLoS One 9 (11), e112701
"Antiviral lectin cyanovirin-N: Probing multivalency and glycan recognition through experimental and computational approaches," G Ghirlanda, B Woodrum, J Maxwell, A Bolia, SB Ozkan, Abstracts of Papers of the American Chemical Society 248
"The protein interacting with C‐kinase (PICK 1) interacts with and attenuates parkin‐associated endothelial‐like (PAEL) receptor‐mediated cell death," P Dutta, KE O'Connell, SB Ozkan, AW Sailer, KK Dev, Journal of Neurochemistry 130 (3), 360-373
"Adenine Nucleotide Translocase Is Acetylated in Vivo in Human Muscle: Modeling Predicts a Decreased ADP Affinity and Altered Control of Oxidative …," C Mielke, N Lefort, CG McLean, JM Cordova, PR Langlais, AJ Bordner, SB Ozkan, Biochemistry 53 (23), 3817-3829
"BP-Dock: a flexible docking scheme for exploring protein–ligand interactions based on unbound structures," A Bolia, ZN Gerek, SB Ozkan, Journal of Chemical Information and Modeling 54 (3), 913-925
"A flexible docking scheme efficiently captures the energetics of glycan-cyanovirin binding," A Bolia, BW Woodrum, A Cereda, MA Ruben, X Wang, SB Ozkan, Biophysical Journal 106 (5), 1142-1151
"Mechanistic Insights of β-Lactmases Evolution," T Zou, VA Risso, JA Gavira, JM Sanchez-Ruiz, SB Ozkan, Biophysical Journal 106 (2), 663a
"Biophysical Insights of Neutral and Non-Neutral Sequence Variants in the Human Proteome," BM Butler, S Kumar, SB Ozkan, Biophysical Journal 106 (2), 462a
Designing Foldable Protein Sequence Through Zipping Contacts, S Ozkan, Bulletin of the American Physical Society 58
The antiviral lectin cyanovirin-N: probing multivalency and glycan recognition through experimental and computational approaches, BW Woodrum, JD Maxwell, A Bolia, SB Ozkan, G Ghirlanda, Biochemical Society Transactions 41 (5), 1170-1176
Electrostatic effect of the ribosomal surface on nascent polypeptide dynamics, AM Knight, PH Culviner, N Kurt-Yilmaz, T Zou, SB Ozkan, S Cavagnero, ACS chemical biology 8 (6), 1195-1204
Novel Physics-Based Protein Structure Refinement Method, A Kumar, MF Thorpe, SB Ozkan, Biophysical Journal 104 (2), 229a
Structural dynamics flexibility informs function and evolution at a proteome scale, ZN Gerek, S Kumar, SB Ozkan, Biophysical Journal 104 (2), 228a
Dissecting the Determinants for Dimmanose Binding in Cyanovirin-N, B Woodrum, A Bolia, A Cereda, X Wang, SB Ozkan, G Ghirlanda, PROTEIN SCIENCE 21, 132-133
Dissipative electro-elastic network model of protein electrostatics, DR Martin, SB Ozkan, DV Matyushov, Physical biology 9 (3), 036004
The binding affinities of proteins interacting with the PDZ domain of PICK1, A Bolia, ZN Gerek, O Keskin, S Banu Ozkan, KK Dev, Proteins: Structure, Function, and Bioinformatics 80 (5), 1393-1408
Collective dynamics differentiates functional divergence in protein evolution, TJ Glembo, DW Farrell, ZN Gerek, MF Thorpe, SB Ozkan, PLoS computational biology 8 (3), e1002428
Protein evolution and foldability by conformational dynamics, SB Ozkan, ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY 243
Local and non-local native topologies reveal the underlying folding landscape of proteins, T Zou, SB Ozkan, Physical biology 8 (6), 066011
Change in allosteric network affects binding affinities of PDZ domains: analysis through perturbation response scanning, ZN Gerek, SB Ozkan, PLoS computational biology 7 (10), e1002154
Perturbation Response Scanning Method for Identifying Allosteric Transitions and Utilizing in Flexible Docking, ZN Gerek, A Bolia, SB Ozkan, Biophysical Journal 100 (3), 372a-373a
Manipulation of conformational change in proteins by single-residue perturbations, C Atilgan, ZN Gerek, SB Ozkan, AR Atilgan, Biophysical journal 99 (3), 933-943
A flexible docking scheme to explore the binding selectivity of PDZ domains, ZN Gerek, SB Ozkan, Protein Science 19 (5), 914-928
Union of geometric constraint-based simulations with molecular dynamics for protein structure prediction, TJ Glembo, SB Ozkan, Biophysical journal 98 (6), 1046-1054
Recreating the Structure and Dynamics of Ancestral Proteins, T Glembo, M Thorpe, SB Ozkan, Biophysical Journal 98 (3), 460a
Application of Linear Response Theory on Protein Networks For Identifying Allosteric Transitions, ZN Gerek, SB Ozkan, Biophysical Journal 98 (3), 26a
A Physics-Based Approach for Understanding Foldability, T Zou, SB Ozkan, Biophysical Journal 98 (3), 637a-638a
Identification of specificity and promiscuity of PDZ domain interactions through their dynamic behavior, ZN Gerek, O Keskin, SB Ozkan, Proteins: Structure, Function, and Bioinformatics 77 (4), 796-811
Essential sub-networks based on contact strength reveal folding kinetics, T Zou, C Atilgan, AR Atilgan, SB Ozkan, arXiv preprint arXiv:0907.3750
Blind test of physics-based prediction of protein structures, MS Shell, SB Ozkan, V Voelz, GA Wu, KA Dill, Biophysical journal 96 (3), 917-924
Pressure Induced Denaturation in Proteins: Stability and Kinetics, K Ghosh, SB Ozkan, Biophysical Journal 96 (3), 569a
Protein Structure Refinement Using Physics-Based Models And Sampling, SB Ozkan, X Ni, J Gee, MS Shell, Biophysical Journal 96 (3), 653a-654a
Flexible Docking in PDZ domains using Elastic Network Model and Replica Exchange Molecular Dynamics, ZN Gerek, SB Ozkan, Biophysical Journal 96 (3), 598a-599a
Structure and dynamic regulation of Src-family kinases, JR Engen, TE Wales, JM Hochrein, MA Meyn, S Banu Ozkan, I Bahar, Cellular and Molecular Life Sciences 65, 3058-3073
The protein folding problem, KA Dill, SB Ozkan, MS Shell, TR Weikl, Annu. Rev. Biophys. 37, 289-316
Robust Design Of Carbon Catabolite Repression, ZN Gerek, B Sariyar-Akbulut, SB Ozkan, The 2007 Annual Meeting
The ultimate speed limit to protein folding is conformational searching, K Ghosh, SB Ozkan, KA Dill, Journal of the American Chemical Society 129 (39), 11920-11927
Protein folding by zipping and assembly, SB Ozkan, GA Wu, JD Chodera, KA Dill, Proceedings of the National Academy of Sciences 104 (29), 11987-11992
The protein folding problem: when will it be solved?, KA Dill, SB Ozkan, TR Weikl, JD Chodera, VA Voelz, Current opinion in structural biology 17 (3), 342-346
Protein structure prediction by zipping and assembly, SB Ozkan, MS Shell, AG Wu, VA Voelz, KA Dill, BIOPHYSICAL JOURNAL, 535A-535A
Mining energy landscape parameters from two-state protein folding experiments, SB Ozkan, K Ghosh, KA Dill, BIOPHYSICAL JOURNAL 88 (1), 40A-40A
Conformational search of peptides and proteins: Monte Carlo minimization with an adaptive bias method applied to the heptapeptide deltorphin, SB Ozkan, H Meirovitch, Journal of computational chemistry 25 (4), 565-572
Efficient conformational search method for peptides and proteins: Monte Carlo minimization with an adaptive bias, SB Ozkan, H Meirovitch, The Journal of Physical Chemistry B 107 (34), 9128-9131
Computing the transition state populations in simple protein models, SB Ozkan, KA Dill, I Bahar, Biopolymers: Original Research on Biomolecules 68 (1), 35-46
Fast‐folding protein kinetics, hidden intermediates, and the sequential stabilization model, SB Ozkan, KA Dill, I Bahar, Protein Science 11 (8), 1958-1970
Unfolding events of chymotrypsin inhibitor 2 (CI2) revealed by Monte Carlo simulations, SG Kirca, SB Ozkan, T Haliloglu, BIOPHYSICAL JOURNAL 82 (1), 134A-134A, 2002
Transition states and the meaning of Φ-values in protein folding kinetics, SB Ozkan, I Bahar, KA Dill, nature structural biology 8 (9), 765-769
Identification of native conformations of proteins using a low resolution model, ŞB Özkan, Fen Bilimleri Enstitüsü
Recognition of native structure from complete enumeration of low-resolution models with constraints., B Ozkan, I Bahar, Proteins 32 (2), 211-222