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1.
Kurkcuoglu, O., Doruker, P. &
Jernigan, R. L., “Loop Motions of Triosephosphate Isomerase Observed with
Elastic Networks”, Biochemistry 45: 1173-1182, 2. Doruker, P., Nilsson, L. & Kurkcuoglu, O., “Collective Dynamics of EcoRI-DNA Complex by Elastic Network Model and Molecular Dynamics Simulations”, Journal of Biomolecular Structure & Dynamics 24(1): 1-15, 2006.
3. Ozer N., T. Haliloglu and C.A. Schiffer, "Substrate specificity in HIV-1 protease by a biased seqeunce search method", Proteins 64: 444-456, 2006.
4. Kantarci N, Doruker P, Haliloglu T, “Cooperative fluctuations point to the dimerization interface of p53 core domain”, Biophysical Journal 91 (2): 421-432, 2006.
5. Ertekin A, Nussinov R, Haliloglu T, “Association of putative protein binding sites with the fluctuation behavior of residues”, Protein Science 15(10): 2265-77, 2006.
6. Konuklar, FAS, Aviyente, V, Haliloglu T, "Influence of Structural Fluctuations on Relationship between the Catalytic Activity and Deamidation Reaction in Triosephosphate Isomerase by Gaussian Network Model (GNM)", Proteins: Structure, Function and Bioinformatics, 62(3): 715-727, 2006.
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1. Kantarci N., Tamerler C., Sarikaya M., Haliloglu T., and Doruker P. “Molecular dynamics simulations on constraint metal binding peptides” Polymer 46: 4307-4313, 2005.
2. Shental-Bechor, D, Kirca, S, Ben-Tal, N, Haliloglu, T, "Monte Carlo Studies of Folding, Dynamic and Stability in a-Helices", Biophysical Journal, 88 (4): 2391-2402, 2005.
3. Haliloglu, T, Keskin, O, Ma, B, Nussinov, R, "How similar are protein folding and protein binding nuclei? Examination of fluctuations of energy hot spots and conserved residues", Biophysical Journal 88 (3): 1552-1559, 2005.
4. Kurkcuoglu, O., Jernigan, R.L., Doruker, P. “Collective dynamics of large proteins from mixed coarse-grained elastic network model” QSAR & Combinatorial Science 24: 443-448, 2005.
5. Alakent B., Camurdan M.C., Doruker P. “Hierarchical structure of the energy landscape of proteins revisited by time series analysis. I. Mimicking protein dynamics in different time scales” Journal of Chemical Physics 123, 144910, 2005.
6. Alakent B., Camurdan M.C., Doruker P. “Hierarchical structure of the energy landscape of proteins revisited by time series analysis. II. Investigation of explicit solvent effects” Journal of Chemical Physics 123, 144911, 2005.
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1.
Z.T. Hamaudi, N. Nugay N, T. Nugay ,
“Anionic Polymerization of Methyl
Methacrylate as Promoted by a N-butyl Lithium-pyridazine-polyether Alkoxide Based
Complex Initiator System”, TURKISH
JOURNAL OF CHEMISTRY, Vol. 28, 387-394, 2004.
2.
E. Kucukpinar,
P. Doruker, “Effect of Absorbed Water on Oxygen
Transport in EVOH Matrices. A Molecular Dynamics Study”, POLYMER, Vol. 45, 3555-3564, 2004.
3. O.G. Ersoy, N. Nugay,
“A New Approach to Increase Weld
Line Strength of Incompatible Polymer Blend Composites: Selective Filler
Addition”, POLYMER, Vol. 45, 1243-1252, 2004.
4.
T. Eren, S.H. Kusefoglu,
“Hydroxymethylation and Polymerization of Plant Oil Triglycerides”, JOURNAL OF APPLIED POLYMER SCIENCE, Vol. 91, 4037-4046, 2004.
5.
T. Eren, S.H. Kusefoglu,
“One Step Hydroxybromination of
Fatty Acid Derivatives”, EUROPEAN JOURNAL OF
LIPID SCIENCE AND TECHNOLOGY, Vol. 106, 27-34, 2004.
6. S.
Kirca, S.B.
Ozkan, T. Haliloglu,
“Unfolding Events of Chymotrypsin
Inhibitor 2 (CI2) Revealed by Monte Carlo (MC) Simulations and Their
Consistency from Structure-based Analysis of Conformations”, POLYMER, Vol. 45, 581-595, 2004.
7.
O. Kurkcuoglu, R.L. Jernigan, P. Doruker,
“Mixed Levels of Coarse-graining of
Large Proteins Using Elastic Network Model Succeeds in Extracting the
Slowest Motions”, POLYMER, Vol. 45,
649-657, 2004.
8.
T. Eren, S.H. Kusefoglu,
“Synthesis and Polymerization of the
Bromoacrylated Plant Oil Triglycerides to Rigid, Flame-retardant Polymers”, JOURNAL OF APPLIED POLYMER SCIENCE,
Vol. 91, 2700-2710, 2004. 9. B. Alakent, P. Doruker, M.C. Camurdan, “Time series analysis of collective motions in proteins”, JOURNAL OF CHEMICAL PHYSICS, Vol. 120, 1072-1088, 2004.
10. Yildirim Y., Doruker P. “Collective motions of RNA polymerases. Analysis of core enzyme, elongation complex and holoenzyme” Journal of Biomolecular structure & dynamics, 22: 267-280, 2004.
11. Alakent B., Doruker, P., Camurdan, M.C. “Application of time series analysis on molecular dynamics simulations of proteins. A study on different conformational spaces by principal component analysis” Journal of Chemical Physics 121: 4759-4769, 2004.
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1.
S.B. Ozkan, K.A. Dill,
2.
O.G. Ersoy, N. Nugay, “Effect of Inorganic Filler Phase
on Mechanical and Morphological Properties of Binary Immiscible Polymer
Blends”, POLYMER BULLETIN, Vol. 49, 465-472,
2003.
3.
N. Kurt, W.R.P. Scott, C.A. Schiffer, T. Haliloglu,
“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-STRUCTURE FUNCTION AND GENETICS 2003, Vol. 51, 409-422, 2003.
4.
E. Kucukpinar, P.
Doruker, “Molecular Simulations of Small Gas Diffusion and Solubility in
Copolymers of Styrene”, POLYMER, Vol. 44, 3607-3620, 2003.
5.
N. Kurt, T. Haliloglu, C.A. Schiffer,
“Structure-based prediction of potential binding and nonbinding peptides to
HIV-1 protease”, BIOPHYSICAL JOURNAL, Vol. 85, 853-863, 2003.
6.
T. Eren, S.H. Kusefoglu, R. Wool,
“Polymerization of Maleic
Anhydride-modified Plant Oils with Polyols”, JOURNAL OF APPLIED POLYMER SCIENCE, Vol. 90, 197-202, 2003.
7.
H. Esen, S.H. Kusefoglu, “Photolytic and Free-radical
Polymerization of Cinnamate Esters of Epoxidized Plant Oil Triglycerides”, JOURNAL OF APPLIED POLYMER
SCIENCE, Vol. 89, 3882-3888, 2003.
8.
S. Sen, N.
Nugay, T. Nugay, “Synthesis and Properties of
Poly(4-vinylpyridine)/Montmorillonite Nanocomposites”, E-POLYMERS, art. No. 049, 2003.
9. A. Kessel, T. Haliloglu, N. Ben-Tal,
“Interactions of the M2 Delta
Segment of the Acetylcholine Receptor with Lipid Bilayers: A Continuum-solvent
Model Study”, BIOPHYSICAL JOURNAL, Vol. 85, 3687-3695, 2003.
10.
A. Kessel, D. Shental-Bechor, T. Haliloglu,
N. Ben-Tal,
“Interactions of Hydrophobic
Peptides with Lipid Bilayers:
11. T. Haliloglu,
A. Kolinski, J. Skolnick, “Use of Residual Dipolar Couplings
as Restraints in ab initio Protein Structure Prediction”, BIOPOLYMERS, Vol. 70, 548-562, 2003. 12. P. Doruker, R.L. Jernigan, “Functional Motions can be Extracted From on-lattice Construction of Protein Structures”, PROTEINS-STRUCTURE FUNCTION AND GENETICS, Vol. 53, 174-181, 2003.
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1.
C. Baysal , A.R. Atilgan,
"Relaxation
Kinetics and the Glassiness of Proteins: The Case of Bovine Pancreatic
Trypsin Inhibitor", Biophysics Journal, Vol 83,
699-705, 2002.
2.
T. Nugay, N. Nugay, R. Jerome, "Anionic polymerisation of methyl
methacrylate with complex initiator system", Polymer Bulletin, Vol 48, 457-462, 2002.
3.
T. Kayhan, N. Nugay, T. Nugay,
"Metallation of Metistylene by
Organolithium Compounds in the Presence of Lithium Polyether Alkoxides", Turk J Chem , Vol 26, 965-971, 2002.
4.
P. Doruker, R. L. Jernigan,Isabelle Navizet, Rigoberto
Hernandez,
"Important Fluctuation Dynamics of
Large Protein Structures Are Preserved Upon Coarse-Grained Renormalization", International J. of Quantum Chemistry, Vol 90, 822-837, 2002.
5.
N. Kurt, T. Haliloglu,
"Distribution of cooperative
interactions in barnase at different time windows by coarse-grained
simulations", Polymer, Vol 43, 403-408, 2002.
6.
P. Doruker, "Simulation of polyethlene
thin films composed of various chain lengths", Polymer, Vol 43,
425-430, 2002.
7.
P. Doruker, I. Bahar, C. Baysal, B. Erman,
"Collective deformations in proteins determined by a mode analysis of
molecular dynamics trajectories" Polymer, Vol 43, 431-439, 2002.
8.
P. Doruker, R.
Jernigan, I. Bahar,
"Dynamics of Large Proteins through Hierarchical Levels of Coarse- Grained
Structures" J Comput Chem, Vol 23, 119-127, 2002.
9.
N. Nugay, S. Sen, "Swelling, Viscosity and Static-Mechanical
Behaviour of Polyester Composites Based on Hybrid Filler System" Makromol Symp, Vol 175, 421-428, 2002.
10.
B. Isin, P. Doruker,
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1.
A.R.
Atilgan, S.R. Durell, R.L. Jernigan, M.C. Demirel, O. Keskin, I. Bahar,
"Anisotropy
of Flutuation Dynamics of Proteins with an Elastic Network Model" Biophysical Journal, Vol 80, 505-515, 2001.
2.
C. Baysal, A.R. Atilgan,
"Elucidating
the Structural Mechanisms for Biological Activity of the Chemokine
Family" Proteins, Vol 43, 150-160, 2001.
3.
P. Doruker, Y. Wang, W.L. Mattice,
"Simulation of random scission of C-C bonds in the initial stage of the
thermal degradation of polyethylene" Computational and Theoretical Polymer Science , Vol 11, 155-166, 2001.
4.
N. Kurt, T. Haliloglu, "Conformational
Dynamics of Subtilisin-Chymotrypsin Inhibitor 2 Complex by Coarse-Grained
Simulations" Journal of Biomolecular Structure & Dynamics, Vol 18, 713-731, 2001.
5.
M. Kahraman, N. Nugay,
"Polydimethylsiloxane
Composites Reinforced by Fumed Silica/Mica Hybrid Reinfocers" Intern J.
Polymeric Mater, Vol 00, 1-15, 2001.
6.
N. Nugay, B. Erman,
"Hybrid
Reinforcement in Nitrile Rubber Composites,Macromol Symp, Vol 169, 269-274, 2001.
7.
C. Baysal, A.R. Atilgan,
"Coordination
Topology and Stability for the Native and Binding Conformers of Chymotrypsin
Inhibitor 2" Proteins, Vol 45, 62-70, 2001.
8.
S. Banu Ozkan, I. Bahar, Ken A. Dill,
"Transition states and the meaning of Phi values in protein folding
kinetics" Nature Structural Biology, Vol 8, 765-769,
2001.
9.
P. Doruker, Wayne L. Mattice, "Effect of
Surface Rougheness on Structure and Dynamics in Thin Films", Macromol
Theory Simul, Vol 10, 363-367, 2001.
10.
N. Nugay, B. Erman, "Propperty
Optimization in Nitrile Rubber Composites via Hybrid Filler System" J. Applied
Polymer Science, Vol 79, 366-374, 2001.
11.
L. Bokobza, N. Nugay, "Orientational Effect of Mica in Fumed Silica
Reinforced Composites" J. Applied Polymer Science, Vol 80, 1-8, 2001.
12.
S. Sen,
13.
M. Sahin,
14.
T. Nugay, Zahi Tim Hamoudi, "Anionic
Polymerization of methyl Methacrylate By Using Self Ligated Initiators"
Polymer Preprints, Vol 42, 421, 2001.
15.
Osman Ersoy, N. Nugay, "Weld Line
Strength of Polypropylene/Polyarmide Blends" Polymeric Materials Science
& Engrineering, Vol 85, 354, 2001.
16.
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1.
O. Keskin, R. L. Jernigan
& I. Bahar,
"Proteins with similar architecture exhibit similar large-scale
dynamic behavior. Specificity resides in local differences" Biophysical Journal 78, 2093-2106, 2000. Full paper(Acrobat)
2.
T. Haliloglu, I. Bahar & R.L. Jernigan,
"Collective
dynamics of class I MHC/peptide complexes and binding to T cell receptors" Biophys. J. 78,
34A, 2000.
3.
G. Duman, O. Keskin, I. Bahar & J. R. Robinson, "Stabilization
of the molten globule state of hen egg white lysozyme with solutions
containing polyvinyl pyrrolidone" J. Controlled Release 64, 331-333, 2000.
4.
O. Keskin, I. Bahar, R.L.Jernigan,
T.G.Myers, J.A.Beutler, R.H.Shoemaker, E.A.Sausville, D.G.Covell,
"Characterization of anticancer agents by their growth inhibitory activity
and relationships to mechanism of action and structure" Anticancer
Drug Design,15, 79-98, 2000.
5.
R.L.Jernigan, I. Bahar, D.G.Covell, A.R.Atilgan, B. Erman & D. Flatow, "Relating
the structure of HIV-1 reverse transcriptase to its processing step"
J. Biomol. Structure & Dynamics, 1, 49-55, 2000.
6.
N. Kurt, T. Haliloglu,
"Conformational
Dynamics of Chymotrypsin Inhibitor 2 in Free and Complex Forms" ACS
Polymeric Materials Science and Engineering, Vol 83,
397-398, 2000.
7.
N. Nugay, T. Nugay,
"Inter polymer
complexes of poly(methyl methacrylate) block-poly(4- vinlypyridine)with
polyacrylate)" Eurapean Polymer Journal, 36,
1027-1033, 2000.
8.
I. Bahar, "Dynamics
of proteins and biomolecular complexes: Inferring functional motions from
structure" Reviews in Chemical Engineering, Vol 15, 319-347,
2000.
9.
T. Haliloglu, W.L. Mattice, "Simulation of rotational isomeric state models
for polypropylene melts on a high coordination lattice" Reviews in Chemical
Engineering, Vol 15, 293-305, 2000.
10.
J.H. Jang, T.
Haliloglu, E.D. vonMeerwall, W.L. Mattice,
"Effect of
vinyl content on self-diffusion in polybutadiene melts" Macromolecules, Vol 33, 4271-4277,
2000.
11.
P. Doriker, A.R.
Atilgan, I. Bahar,
"Dynamics of proteins predicted by molecular dynamics simulations and
analytical approaches: Application to alpha-Amylase Inhibitor" Proteins, Vol 40, 512-524, 2000.
12. L.S. Yilmaz, A.R. Atilgan, "Identifying the adaptive mechanism in globular proteins: Fluctuations in densely packed regions manipulate flexible parts" J of Chemical Physics, Vol 113, 4454-4464, 2000. |
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1. I. Bahar, B. Erman, R. L.
Jernigan, A. R. Atilgan, & D. Covell,
"Collective dynamics of HIV-1 reverse transcriptase" J. Mol. Biol. 285, 1023-1037, 1999.
2.
I. Bahar
& R.L. Jernigan
"Cooperative
fluctuations and subunit communication in tryptophan synthase" Biochemistry 38, 3478-3490, 1999. Full paper(Acrobat)
3.
T. Haliloglu,
"Characterization
of Internal Motions of Escherichia coli Ribonuclease H by
4.
T. Z. Sen, I.
Bahar, B. Erman, F. Laupretre & L. Monnerie
"Local
dynamics of cis-polybutadiene and cis-polyisoprene. A comparative study based
on cooperative kinematics theory and NMR experiments" Macromolecules 32, 3017-3024,
1999.
5.
O. Keskin, I. Bahar, R. L.
Jernigan & D. G. Covell,
"Characterization of anticancer agents and their growth inhibitory potency.
Relationship between potency and chemical structure" Biophys. J. 76, A386, 1999.
6.
R.L. Jernigan, M. C. Demirel &
7.
I.Bahar & R. L. Jernigan,
“Subunit communication, processing and fluctuations
in tryptophan synthase" Biophys. J. 76,
A115, 1999.
8.
Haliloglu,
T.,
"Coarse-grained
simulations of conformational dynamics of proteins" Theoretical and Computational Polymer Science, 9/3-4, 255-260, 1999.
9.
R. L. Jernigan & I. Bahar. "Geometric
Regularities among bonded and nonbonded residues in proteins" In Perspectives in Structural Biology (GN
Ramachandran Volume) M. Vijayan, N. Yathindra and A.S. Kolaskar Eds., Indian
Academy of Sciences, Universities Press, Hyderabad, 209-225, 1999.
10.
T. Haliloglu
& I. Bahar,
"Structure-based
analysis of protein dynamics. Comparison of theoretical results for hen
lysozyme with X-ray diffraction and NMR relaxation data" Proteins: Structure, Function, & Genetics 37, 654-667,
1999.
11.
T. Haliloglu, W. L. Mattice, "Simulation of Rotational Isomeric State Models
for Polypropylene Melts in a High Coordination Lattice", Reviews in Chemical
Engineering, 15, No:4, 1999.
12.
N. Kurt, T. Haliloglu, "Conformational
Dynamics of Chymotrypsin Inhibitor 2 by Coarse-Grained Simulations", Proteins: Structure, Function and Genetics, 37, 454-464,
1999.
13.
T. Haliloglu,
"Conformational
Dynamics of Cytochrome c by Coarse-Grained Simulations", Polymer Preprints Am. Chem. S., 81, 155, 1999.
14.
T. Haliloglu,
W. L. Mattice, "Detection
of the onset of demixing in simulations of polypropylene melts in which the
chains differ only in stereochemical composition", J. Chem. Phys., 111(9), 4327-4333, 1999.
15.
P. Doruker,
W. L. Mattice,
"The effect of chain segregation on the mobility of thin films", Polymer Preprints Am. Chem. S., 81, 555-556, 1999.
16.
M. Kahraman,
17. M.C. Demirel, I. Bahar, A. R. Atilgan, "Predicting the Unsemble of Unfolding Pathways for Proteins: An Updated Incremental Lagrangian Model", Biophysical Journal., Vol. 76, |