• 1939 Citations
  • 20 h-Index
19982022
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Research Output 1998 2018

  • 1939 Citations
  • 20 h-Index
  • 45 Article
  • 1 Conference contribution
  • 1 Comment/debate
  • 1 Review article
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Article
2018
7 Citations (Scopus)

Ancient thioredoxins evolved to modern-day stability–function requirement by altering native state ensemble

Modi, T., Huihui, J., Ghosh, K. & Ozkan, S., Jun 19 2018, In : Philosophical Transactions of the Royal Society B: Biological Sciences. 373, 1749, 20170184.

Research output: Contribution to journalArticle

Thioredoxins
protein
Proteins
proteins
Catalytic Domain
2 Citations (Scopus)

A novel modelling mechanism of PAEL receptor and GABARAPL2 interaction involved in Parkinson's disease

Dutta, P., Dargahi, L., O'Connell, K. E., Bolia, A., Ozkan, S., Sailer, A. W. & Dev, K. K., Apr 23 2018, In : Neuroscience Letters. 673, p. 12-18 7 p.

Research output: Contribution to journalArticle

Endothelin Receptors
Parkinson Disease
Autophagy
Receptor Aggregation
Aminobutyrates

Coevolving residues inform protein dynamics profiles and disease susceptibility of nSNVs

Butler, B. M., Kazan, I. C., Kumar, A. & Ozkan, S., Nov 1 2018, In : PLoS Computational Biology. 14, 11, e1006626.

Research output: Contribution to journalArticle

Disease Susceptibility
Susceptibility
disease resistance
Proteins
Protein
8 Citations (Scopus)

Hinge-Shift Mechanism Modulates Allosteric Regulations in Human Pin1

Campitelli, P., Guo, J., Zhou, H. X. & Ozkan, S., May 31 2018, In : Journal of Physical Chemistry B. 122, 21, p. 5623-5629 7 p.

Research output: Contribution to journalArticle

Allosteric Regulation
Peptidylprolyl Isomerase
hinges
Hinges
shift
3 Citations (Scopus)

Mutations utilize dynamic allostery to confer resistance in TEM-1 β-lactamase

Modi, T. & Ozkan, S., Dec 1 2018, In : International Journal of Molecular Sciences. 19, 12, 3808.

Research output: Contribution to journalArticle

mutations
Catalytic Domain
Antibiotics
antibiotics
Transmission electron microscopy
2017
6 Citations (Scopus)

Plant-expressed cocaine hydrolase variants of butyrylcholinesterase exhibit altered allosteric effects of cholinesterase activity and increased inhibitor sensitivity

Larrimore, K. E., Kazan, I. C., Kannan, L., Kendle, R. P., Jamal, T., Barcus, M., Bolia, A., Brimijoin, S., Zhan, C. G., Ozkan, S. & Leket-Mor, T., Dec 1 2017, In : Scientific Reports. 7, 1, 10419.

Research output: Contribution to journalArticle

Butyrylcholinesterase
Cholinesterases
Hydrolases
Cocaine
Enzymes
2016
8 Citations (Scopus)

Adaptive BP-Dock: An Induced Fit Docking Approach for Full Receptor Flexibility

Bolia, A. & Ozkan, S., Apr 25 2016, In : Journal of Chemical Information and Modeling. 56, 4, p. 734-746 13 p.

Research output: Contribution to journalArticle

Docks
flexibility
Conformations
fluctuation
drug
2015
21 Citations (Scopus)

A hinge migration mechanism unlocks the evolution of green-to-red photoconversion in GFP-like proteins

Kim, H., Zou, T., Modi, C., Dörner, K., Grunkemeyer, T. J., Chen, L., Fromme, R., Matz, M. V., Ozkan, S. & Wachter, R., Jan 6 2015, In : Structure. 23, 1, p. 34-43 10 p.

Research output: Contribution to journalArticle

Catalytic Domain
Molecular Dynamics Simulation
Articular Range of Motion
Microscopy
Proteins
4 Citations (Scopus)

A Rigid Hinge Region Is Necessary for High-Affinity Binding of Dimannose to Cyanovirin and Associated Constructs

Li, Z., Bolia, A., Maxwell, J. D., Bobkov, A. A., Ghirlanda, G., Ozkan, S. & Margulis, C. J., Oct 28 2015, In : Biochemistry. 54, 46, p. 6951-6960 10 p.

Research output: Contribution to journalArticle

Hinges
Mutation
Binding Sites
Oligomerization
Calorimetry
14 Citations (Scopus)

Conformational dynamics of nonsynonymous variants at protein interfaces reveals disease association

Butler, B. M., Gerek, Z. N., Kumar, S. & Ozkan, S., Mar 1 2015, In : Proteins: Structure, Function and Bioinformatics. 83, 3, p. 428-435 8 p.

Research output: Contribution to journalArticle

Nucleotides
Proteins
Structural dynamics
Proteome
Amino Acids
43 Citations (Scopus)

Evolution of Conformational Dynamics Determines the Conversion of a Promiscuous Generalist into a Specialist Enzyme

Zou, T., Risso, V. A., Gavira, J. A., Sanchez-Ruiz, J. M. & Ozkan, S., Jan 1 2015, In : Molecular Biology and Evolution. 32, 1, p. 132-143 12 p.

Research output: Contribution to journalArticle

generalist
antibiotics
enzyme
Anti-Bacterial Agents
Catalytic Domain
15 Citations (Scopus)

Integration of structural dynamics and molecular evolution via protein interaction networks: A new era in genomic medicine

Kumar, A., Butler, B. M., Kumar, S. & Ozkan, S. B., 2015, (Accepted/In press) In : Current Opinion in Structural Biology.

Research output: Contribution to journalArticle

Protein Interaction Maps
Molecular Evolution
Medicine
Nucleotides
Exome
4 Citations (Scopus)

Partial unfolding and refolding for structure refinement: A unified approach of geometric simulations and molecular dynamics

Kumar, A., Campitelli, P., Thorpe, M. & Ozkan, S., Dec 1 2015, In : Proteins: Structure, Function and Bioinformatics. 83, 12, p. 2279-2292 14 p.

Research output: Contribution to journalArticle

Molecular Dynamics Simulation
Molecular dynamics
Proteins
Sampling
Drug Design
25 Citations (Scopus)

The Role of Conformational Dynamics and Allostery in the Disease Development of Human Ferritin

Kumar, A., Glembo, T. J. & Ozkan, S., Apr 9 2015, In : Biophysical Journal. 109, 6, p. 1273-1281 9 p.

Research output: Contribution to journalArticle

Human Development
Ferritins
Allosteric Regulation
Proteins
Mutation
2014
20 Citations (Scopus)

Adenine nucleotide translocase is acetylated in vivo in human muscle: Modeling predicts a decreased ADP affinity and altered control of oxidative phosphorylation

Mielke, C., Lefort, N., McLean, C. G., Cordova, J. M., Langlais, P. R., Bordner, A. J., Te, J. A., Ozkan, S., Willis, W. T. & Mandarino, L. J., Jun 17 2014, In : Biochemistry. 53, 23, p. 3817-3829 13 p.

Research output: Contribution to journalArticle

ATP Translocases Mitochondrial ADP
Acetylation
Oxidative Phosphorylation
Adenosine Diphosphate
Muscle
6 Citations (Scopus)

A flexible docking scheme efficiently captures the energetics of glycan-cyanovirin binding

Bolia, A., Woodrum, B. W., Cereda, A., Ruben, M. A., Wang, X., Ozkan, S. & Ghirlanda, G., Mar 4 2014, In : Biophysical Journal. 106, 5, p. 1142-1151 10 p.

Research output: Contribution to journalArticle

Polysaccharides
Mutation
cyanovirin N
Lectins
Computer Simulation
25 Citations (Scopus)

BP-dock: A flexible docking scheme for exploring protein-ligand interactions based on unbound structures

Bolia, A., Gerek, Z. N. & Ozkan, S., Mar 24 2014, In : Journal of Chemical Information and Modeling. 54, 3, p. 913-925 13 p.

Research output: Contribution to journalArticle

Docks
flexibility
Ligands
Proteins
interaction
6 Citations (Scopus)

Proteome folding kinetics is limited by protein halflife

Zou, T., Williams, N., Ozkan, S. & Ghosh, K., Nov 13 2014, In : PLoS One. 9, 11, e112701.

Research output: Contribution to journalArticle

Proteome
proteome
half life
Half-Life
kinetics
7 Citations (Scopus)

The protein interacting with C-kinase (PICK1) interacts with and attenuates parkin-associated endothelial-like (PAEL) receptor-mediated cell death

Dutta, P., O'Connell, K. E., Ozkan, S., Sailer, A. W. & Dev, K. K., 2014, In : Journal of Neurochemistry. 130, 3, p. 360-373 14 p.

Research output: Contribution to journalArticle

Cell death
Cell Death
Phosphotransferases
Rotenone
Proteasome Endopeptidase Complex
2013
33 Citations (Scopus)

Electrostatic effect of the ribosomal surface on nascent polypeptide dynamics

Knight, A. M., Culviner, P. H., Kurt-Yilmaz, N., Zou, T., Ozkan, S. & Cavagnero, S., Jun 21 2013, In : ACS Chemical Biology. 8, 6, p. 1195-1204 10 p.

Research output: Contribution to journalArticle

Static Electricity
Electrostatics
Ribosomes
Peptides
Proteins
45 Citations (Scopus)

Structural dynamics flexibility informs function and evolution at a proteome scale

Nevin Gerek, Z., Kumar, S. & Ozkan, S., Apr 2013, In : Evolutionary Applications. 6, 3, p. 423-433 11 p.

Research output: Contribution to journalArticle

Proteome
proteome
protein
Proteins
proteins
8 Citations (Scopus)

The antiviral lectin cyanovirin-N: Probing multivalency and glycan recognition through experimental and computational approaches

Woodrum, B. W., Maxwell, J. D., Bolia, A., Ozkan, S. & Ghirlanda, G., Oct 2013, In : Biochemical Society Transactions. 41, 5, p. 1170-1176 7 p.

Research output: Contribution to journalArticle

Lectins
Antiviral Agents
Polysaccharides
Anti-HIV Agents
Mutagenesis
2012
20 Citations (Scopus)

Collective dynamics differentiates functional divergence in protein evolution

Glembo, T. J., Farrell, D. W., Gerek, Z. N., Thorpe, M. & Ozkan, S., Mar 2012, In : PLoS Computational Biology. 8, 3, e1002428.

Research output: Contribution to journalArticle

Differentiate
Divergence
divergence
Proteins
Protein
7 Citations (Scopus)

Dissipative electro-elastic network model of protein electrostatics

Martin, D. R., Ozkan, S. & Matyushov, D., Jun 2012, In : Physical Biology. 9, 3, 036004.

Research output: Contribution to journalArticle

Static Electricity
Proteins
Catalytic Domain
Friction
Molecular Dynamics Simulation
17 Citations (Scopus)

The binding affinities of proteins interacting with the PDZ domain of PICK1

Bolia, A., Gerek, Z. N., Keskin, O., Ozkan, S. & Dev, K. K., May 2012, In : Proteins: Structure, Function and Bioinformatics. 80, 5, p. 1393-1408 16 p.

Research output: Contribution to journalArticle

Carrier Proteins
Substance-Related Disorders
Proteins
Substance-Induced Psychoses
Pharmaceutical Preparations
2011
82 Citations (Scopus)
PDZ Domains
Domain Analysis
Allosteric Regulation
Affine transformation
Scanning
16 Citations (Scopus)

Local and non-local native topologies reveal the underlying folding landscape of proteins

Zou, T. & Ozkan, S., Dec 2011, In : Physical Biology. 8, 6, 066011.

Research output: Contribution to journalArticle

Protein Folding
Proteins
Carbon Monoxide
2010
41 Citations (Scopus)

A flexible docking scheme to explore the binding selectivity of PDZ domains

Nevin Gerek, Z. & Ozkan, S., May 2010, In : Protein Science. 19, 5, p. 914-928 15 p.

Research output: Contribution to journalArticle

Post-Synaptic Density
Molecular Dynamics Simulation
Conformations
Molecular dynamics
Binding Sites
68 Citations (Scopus)

Manipulation of conformational change in proteins by single-residue perturbations

Atilgan, C., Gerek, Z. N., Ozkan, S. & Atilgan, A. R., Aug 4 2010, In : Biophysical Journal. 99, 3, p. 933-943 11 p.

Research output: Contribution to journalArticle

Proteins
Adenylate Kinase
Kinesin
Myosins
Protein Binding
6 Citations (Scopus)

Union of geometric constraint-based simulations with molecular dynamics for protein structure prediction

Glembo, T. J. & Ozkan, S., Mar 17 2010, In : Biophysical Journal. 98, 6, p. 1046-1054 9 p.

Research output: Contribution to journalArticle

Molecular Dynamics Simulation
Amino Acid Sequence
Proteins
2009
34 Citations (Scopus)

Blind test of physics-based prediction of protein structures

Scott Shell, M., Ozkan, S., Voelz, V., Wu, G. A. & Dill, K. A., Feb 4 2009, In : Biophysical Journal. 96, 3, p. 917-924 8 p.

Research output: Contribution to journalArticle

Physics
Protein Folding
Proteins
Molecular Dynamics Simulation
Computational Biology
42 Citations (Scopus)

Identification of specificity and promiscuity of PDZ domain interactions through their dynamic behavior

Gerek, Z. N., Keskin, O. & Ozkan, S., 2009, In : Proteins: Structure, Function and Bioinformatics. 77, 4, p. 796-811 16 p.

Research output: Contribution to journalArticle

Protein Interaction Domains and Motifs
PDZ Domains
Point Mutation
Cluster Analysis
Carrier Proteins
2008
117 Citations (Scopus)

Structure and dynamic regulation of Src-family kinases

Engen, J. R., Wales, T. E., Hochrein, J. M., Meyn, M. A., Ozkan, S., Bahar, I. & Smithgall, T. E., Oct 2008, In : Cellular and Molecular Life Sciences. 65, 19, p. 3058-3073 16 p.

Research output: Contribution to journalArticle

src Homology Domains
src-Family Kinases
Phosphotransferases
regulation
family member
577 Citations (Scopus)

The protein folding problem

Dill, K. A., Ozkan, S., Shell, M. S. & Weikl, T. R., 2008, In : Annual Review of Biophysics. 37, p. 289-316 28 p.

Research output: Contribution to journalArticle

Protein folding
Protein Folding
Proteins
Peptide Fragments
Global optimization
2007
105 Citations (Scopus)

Protein folding by zipping and assembly

Ozkan, S., Wu, G. A., Chodera, J. D. & Dill, K. A., Jul 17 2007, In : Proceedings of the National Academy of Sciences of the United States of America. 104, 29, p. 11987-11992 6 p.

Research output: Contribution to journalArticle

Protein Folding
Proteins
Physics
Molecular Dynamics Simulation
Databases
171 Citations (Scopus)

The protein folding problem: when will it be solved?

Dill, K. A., Ozkan, S., Weikl, T. R., Chodera, J. D. & Voelz, V. A., Jun 2007, In : Current Opinion in Structural Biology. 17, 3, p. 342-346 5 p.

Research output: Contribution to journalArticle

Protein Folding
Proteins
Thermodynamics
Polymers
53 Citations (Scopus)

The ultimate speed limit to protein folding is conformational searching

Ghosh, K., Ozkan, S. & Dill, K. A., Oct 3 2007, In : Journal of the American Chemical Society. 129, 39, p. 11920-11927 8 p.

Research output: Contribution to journalArticle

Protein folding
Protein Folding
Temperature
Highway systems
Chemical activation
2004
7 Citations (Scopus)
Peptides
Proteins
Protein
Leucine Enkephalin
Energy
8 Citations (Scopus)

Unfolding events of Chymotrypsin Inhibitor 2 (CI2) revealed by Monte Carlo (MC) simulations and their consistency from structure-based analysis of conformations

Ozkan, S., Dalgýn, G. S. & Haliloglu, T., Jan 15 2004, In : Polymer. 45, 2, p. 581-595 15 p.

Research output: Contribution to journalArticle

Conformations
Hinges
Chymotrypsin
chymotrypsin inhibitor 2
Monte Carlo simulation
2003
42 Citations (Scopus)

Computing the transition state populations in simple protein models

Ozkan, S., Dill, K. A. & Bahar, I., Jan 2003, In : Biopolymers. 68, 1, p. 35-46 12 p.

Research output: Contribution to journalArticle

Protein folding
Protein Folding
Proteins
Population
Kinetics
10 Citations (Scopus)

Efficient conformational search method for peptides and proteins: Monte Carlo minimization with an adaptive bias

Ozkan, S. & Meirovitch, H., Aug 28 2003, In : Journal of Physical Chemistry B. 107, 34, p. 9128-9131 4 p.

Research output: Contribution to journalArticle

Peptides
peptides
proteins
Proteins
Leucine Enkephalin
2002
61 Citations (Scopus)

Fast-folding protein kinetics, hidden intermediates, and the sequential stabilization model

Ozkan, S., Dill, K. A. & Bahar, I., 2002, In : Protein Science. 11, 8, p. 1958-1970 13 p.

Research output: Contribution to journalArticle

Protein folding
Protein Folding
Hydrogen
Stabilization
Kinetics
2001
125 Citations (Scopus)

Transition states and the meaning of Φ-values in protein folding kinetics

Ozkan, S., Bahar, I. & Dill, K. A., 2001, In : Nature Structural Biology. 8, 9, p. 765-769 5 p.

Research output: Contribution to journalArticle

Protein folding
Protein Folding
Free energy
Mutation
Kinetics
1999

Identification of native conformations of proteins using a low resolution model

Ozkan, S. & Bahar, I., 1999, In : Turkish Journal of Physics. 23, 1, p. 257-258 2 p.

Research output: Contribution to journalArticle

proteins
1998
13 Citations (Scopus)

Recognition of native structure from complete enumeration of low- resolution models with constraints

Ozkan, S. & Bahar, I., Aug 1 1998, In : Proteins: Structure, Function and Genetics. 32, 2, p. 211-222 12 p.

Research output: Contribution to journalArticle

Conformations
Protein C
Proteins
X-Rays
Dihedral angle