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1

A second generation of mapping/reverse mapping of coarse-grained and fully atomistic models of polymer melts

Pemra Doruker, Wayne L. Mattice

Journal:

Macromolecular Theory and Simulations

Année:

1999

Langue:

english

Fichier:

PDF, 225 KB

english, 1999

2

Simulation of an amorphous polyethylene nanofiber on a high coordination lattice

Visit Vao-soongnern, Pemra Doruker, Wayne L. Mattice

Journal:

Macromolecular Theory and Simulations

Année:

2000

Langue:

english

Fichier:

PDF, 223 KB

english, 2000

3

Dynamics of proteins predicted by molecular dynamics simulations and analytical approaches: Application to α-amylase inhibitor

Pemra Doruker, Ali Rana Atilgan, Ivet Bahar

Journal:

Proteins: Structure, Function, and Bioinformatics

Année:

2000

Langue:

english

Fichier:

PDF, 400 KB

english, 2000

4

Effect of Surface Roughness on Structure and Dynamics in Thin Films

Pemra Doruker, Wayne L. Mattice

Journal:

Macromolecular Theory and Simulations

Année:

2001

Langue:

english

Fichier:

PDF, 143 KB

english, 2001

5

Dynamics of large proteins through hierarchical levels of coarse-grained structures

Pemra Doruker, Robert L. Jernigan, Ivet Bahar

Journal:

Journal of Computational Chemistry

Année:

2002

Langue:

english

Fichier:

PDF, 329 KB

english, 2002

6

Effect of ligand binding on the intraminimum dynamics of proteins

Burak Alakent, Sena Baskan, Pemra Doruker

Journal:

Journal of Computational Chemistry

Année:

2011

Langue:

english

Fichier:

PDF, 876 KB

english, 2011

7

Blind Dockings of Benzothiazoles to Multiple Receptor Conformations of Triosephosphate Isomerase from Trypanosoma cruzi and Human

Zeynep Kurkcuoglu , Gulgun Ural , E. Demet Akten, Pemra Doruker

Journal:

Molecular Informatics

Année:

2011

Langue:

english

Fichier:

PDF, 1.71 MB

english, 2011

8

Molecular dynamics simulations on constraint metal binding peptides

Nigar Kantarci, Candan Tamerler, Mehmet Sarikaya, Turkan Haliloglu, Pemra Doruker

Journal:

Année:

2005

Langue:

english

Fichier:

PDF, 265 KB

english, 2005

9

Molecular simulations of gas transport in nitrile rubber and styrene butadiene rubber

Esra Kucukpinar, Pemra Doruker

Journal:

Année:

2006

Langue:

english

Fichier:

PDF, 648 KB

english, 2006

10

Collective deformations in proteins determined by a mode analysis of molecular dynamics trajectories

Pemra Doruker, Ivet Bahar, Canan Baysal, Burak Erman

Journal:

Année:

2002

Langue:

english

Fichier:

PDF, 260 KB

english, 2002

11

Simulation of polyethylene thin films composed of various chain lengths

Journal:

Année:

2002

Langue:

english

Fichier:

PDF, 142 KB

english, 2002

12

Molecular simulations of small gas diffusion and solubility in copolymers of styrene

Esra Kucukpinar, Pemra Doruker

Journal:

Année:

2003

Langue:

english

Fichier:

PDF, 493 KB

english, 2003

13

Functional motions can be extracted from on-lattice construction of protein structures

Pemra Doruker, Robert L. Jernigan

Journal:

Proteins: Structure, Function, and Bioinformatics

Année:

2003

Langue:

english

Fichier:

PDF, 472 KB

english, 2003

14

Collective dynamics of the ribosomal tunnel revealed by elastic network modeling

Ozge Kurkcuoglu, Zeynep Kurkcuoglu, Pemra Doruker, Robert L. Jernigan

Journal:

Proteins: Structure, Function, and Bioinformatics

Année:

2009

Langue:

english

Fichier:

PDF, 494 KB

english, 2009

15

Collective Dynamics of Large Proteins from Mixed Coarse-Grained Elastic Network Model

Ozge Kurkcuoglu, Robert L. Jernigan, Pemra Doruker

Journal:

Molecular Informatics

Année:

2005

Langue:

english

Fichier:

PDF, 468 KB

english, 2005

16

Important fluctuation dynamics of large protein structures are preserved upon coarse-grained renormalization

Pemra Doruker, Robert L. Jernigan, Isabelle Navizet, Rigoberto Hernandez

Journal:

International Journal of Quantum Chemistry

Année:

2002

Langue:

english

Fichier:

PDF, 1.08 MB

english, 2002

17

Mixed levels of coarse-graining of large proteins using elastic network model succeeds in extracting the slowest motions

Ozge Kurkcuoglu, Robert L. Jernigan, Pemra Doruker

Journal:

Année:

2004

Langue:

english

Fichier:

PDF, 808 KB

english, 2004

18

Effect of absorbed water on oxygen transport in EVOH matrices. A molecular dynamics study

Esra Kucukpinar, Pemra Doruker

Journal:

Année:

2004

Langue:

english

Fichier:

PDF, 495 KB

english, 2004

19

Mathematical description of ethanol fermentation by immobilised Saccharomyces cerevisiae

Gülnur Birol, Pemra Doruker, Betül Kirdar, Z. İlsen Önsan, Kutlu Ülgen

Journal:

Process Biochemistry

Année:

1998

Langue:

english

Fichier:

PDF, 683 KB

english, 1998

20

Effect of Cooperative Hydrogen Bonding in Azo−Hydrazone Tautomerism of Azo Dyes

Özen, Alimet Sema, Doruker, Pemra, Aviyente, Viktorya

Journal:

Journal of Physical Chemistry A

Année:

2007

Langue:

english

Fichier:

PDF, 151 KB

english, 2007

21

Functional Motions of Influenza Virus Hemagglutinin: A Structure-Based Analytical Approach

Isin, Basak, Doruker, Pemra, Bahar, Ivet

Journal:

Biophysical Journal

Année:

2002

Langue:

english

Fichier:

PDF, 795 KB

english, 2002

22

Focused Functional Dynamics of Supramolecules by Use of a Mixed-Resolution Elastic Network Model

Kurkcuoglu, Ozge, Turgut, Osman Teoman, Cansu, Sertan, Jernigan, Robert L., Doruker, Pemra

Journal:

Biophysical Journal

Année:

2009

Langue:

english

Fichier:

PDF, 829 KB

english, 2009

23

Cooperative Fluctuations Point to the Dimerization Interface of P53 Core Domain

Kantarci, Nigar, Doruker, Pemra, Haliloglu, Turkan

Journal:

Biophysical Journal

Année:

2006

Langue:

english

Fichier:

PDF, 484 KB

english, 2006

24

Conformational Transition Pathways Explored by Monte Carlo Simulation Integrated with Collective Modes

Kantarci-Carsibasi, Nigar, Haliloglu, Turkan, Doruker, Pemra

Journal:

Biophysical Journal

Année:

2008

Langue:

english

Fichier:

PDF, 593 KB

english, 2008

25

A Docking Study Using Atomistic Conformers Generated via Elastic Network Model for Cyclosporin A/Cyclophilin A Complex

Akten, E. Demet, Cansu, Sertan, Doruker, Pemra

Journal:

Journal of Biomolecular Structure and Dynamics

Année:

2009

Langue:

english

Fichier:

PDF, 4.04 MB

english, 2009

26

Effect of intracellular loop 3 on intrinsic dynamics of human β2-adrenergic receptor

Ozcan, Ozer, Uyar, Arzu, Doruker, Pemra, Akten, Ebru

Journal:

BMC Structural Biology

Année:

2013

Langue:

english

Fichier:

PDF, 2.18 MB

english, 2013

27

Assessing Dynamic Features of NF-κB via Molecular Dynamics Simulations and Elastic Network Model

Uyar, Arzu, Pande, Vineet, Mura, Cameron, McCammon, J. Andrew, Doruker, Pemra, Nilsson, Lennart

Journal:

Biophysical Journal

Année:

2014

Langue:

english

Fichier:

PDF, 47 KB

english, 2014

28

Effect of Intracellular Loop 3 on Intrinsic Dynamics of Human β2-Adrenergic Receptor

Ozcan, Ozer, Uyar, Arzu, Doruker, Pemra, Akten, Ebru Demet

Journal:

Biophysical Journal

Année:

2014

Langue:

english

Fichier:

PDF, 75 KB

english, 2014

29

Features of Large Hinge-Bending Conformational Transitions. Prediction of Closed Structure from Open State

Uyar, Arzu, Kantarci-Carsibasi, Nigar, Haliloglu, Turkan, Doruker, Pemra

Journal:

Biophysical Journal

Année:

2014

Langue:

english

Fichier:

PDF, 1.74 MB

english, 2014

30

Loop Motions of Triosephosphate Isomerase Observed with Elastic Networks †

Kurkcuoglu, Ozge, Jernigan, Robert L., Doruker, Pemra

Journal:

Année:

2006

Langue:

english

Fichier:

PDF, 912 KB

english, 2006

31

Mobility of the Surface and Interior of Thin Films Composed of Amorphous Polyethylene

Doruker, Pemra, Mattice, Wayne L.

Journal:

Année:

1999

Langue:

english

Fichier:

PDF, 208 KB

english, 1999

32

Dimerization Affects Collective Dynamics of Triosephosphate Isomerase †

Cansu, Sertan, Doruker, Pemra

Journal:

Année:

2008

Langue:

english

Fichier:

PDF, 1.89 MB

english, 2008

33

Segregation of Chain Ends Is a Weak Contributor to Increased Mobility at Free Polymer Surfaces

Doruker, Pemra, Mattice, Wayne L.

Journal:

Journal of Physical Chemistry B

Année:

1999

Langue:

english

Fichier:

PDF, 100 KB

english, 1999

34

Simulation of Polyethylene Thin Films on a High Coordination Lattice

Doruker, Pemra, Mattice, Wayne L.

Journal:

Année:

1998

Langue:

english

Fichier:

PDF, 148 KB

english, 1998

35

Collective Dynamics of Eco RI-DNA Complex by Elastic Network Model and Molecular Dynamics Simulations

Doruker, Pemra, Nilsson, Lennart, Kurkcuoglu, Ozge

Journal:

Journal of Biomolecular Structure and Dynamics

Année:

2006

Langue:

english

Fichier:

PDF, 4.25 MB

english, 2006

36

Collective Motions of RNA Polymerases. Analysis of Core Enzyme, Elongation Complex and Holoenzyme

Yildirim, Yesim, Doruker, Pemra

Journal:

Journal of Biomolecular Structure and Dynamics

Année:

2004

Langue:

english

Fichier:

PDF, 2.40 MB

english, 2004

37

Hierarchical structure of the energy landscape of proteins revisited by time series analysis. II. Investigation of explicit solvent effects

Alakent, Burak, Camurdan, Mehmet C., Doruker, Pemra

Journal:

The Journal of Chemical Physics

Année:

2005

Langue:

english

Fichier:

PDF, 360 KB

english, 2005

38

Application of time series analysis on molecular dynamics simulations of proteins: A study of different conformational spaces by principal component analysis

Alakent, Burak, Doruker, Pemra, Camurdan, Mehmet C.

Journal:

The Journal of Chemical Physics

Année:

2004

Langue:

english

Fichier:

PDF, 388 KB

english, 2004

39

Hierarchical structure of the energy landscape of proteins revisited by time series analysis. I. Mimicking protein dynamics in different time scales

Alakent, Burak, Camurdan, Mehmet C., Doruker, Pemra

Journal:

The Journal of Chemical Physics

Année:

2005

Langue:

english

Fichier:

PDF, 388 KB

english, 2005

40

Rotational isomeric state models for polyoxyethylene and polythiaethylene on a high coordination lattice

Doruker, Pemra, Rapold, Roland F., Mattice, Wayne L.

Journal:

The Journal of Chemical Physics

Année:

1996

Langue:

english

Fichier:

PDF, 402 KB

english, 1996

41

Solvent effect on translational diffusivity and orientational mobility of polymers in solution: A molecular dynamics study

Bahar, Ivet, Badur, Bertan, Doruker, Pemra

Journal:

The Journal of Chemical Physics

Année:

1993

Langue:

english

Fichier:

PDF, 1.26 MB

english, 1993

42

Time series analysis of collective motions in proteins

Alakent, Burak, Doruker, Pemra, Çamurdan, Mehmet C.

Journal:

The Journal of Chemical Physics

Année:

2004

Langue:

english

Fichier:

PDF, 481 KB

english, 2004

43

The ribosome structure controls and directs mRNA entry, translocation and exit dynamics

Kurkcuoglu, Ozge, Doruker, Pemra, Sen, Taner Z, Kloczkowski, Andrzej, Jernigan, Robert L

Journal:

Physical Biology

Année:

2008

Langue:

english

Fichier:

PDF, 1.47 MB

english, 2008

44

Substrate Effect on Catalytic Loop and Global Dynamics of Triosephosphate Isomerase

Kurkcuoglu, Zeynep, Doruker, Pemra

Journal:

Année:

2013

Langue:

english

Fichier:

PDF, 2.37 MB

english, 2013

45

Coupling between Catalytic Loop Motions and Enzyme Global Dynamics

Kurkcuoglu, Zeynep, Bakan, Ahmet, Kocaman, Duygu, Bahar, Ivet, Doruker, Pemra, Livesay, Dennis R.

Journal:

PLoS Computational Biology

Année:

2012

Langue:

english

Fichier:

PDF, 2.49 MB

english, 2012

46

How an Inhibitor Bound to Subunit Interface Alters Triosephosphate Isomerase Dynamics

Kurkcuoglu, Zeynep, Findik, Doga, Akten, Ebru Demet, Doruker, Pemra

Journal:

Biophysical Journal

Année:

2015

Langue:

english

Fichier:

PDF, 1.90 MB

english, 2015

47

Dynamics of bulk polyethylene on a high coordination lattice

Doruker, Pemra, Mattice, Wayne L.

Journal:

Macromolecular Symposia

Année:

1998

Langue:

english

Fichier:

PDF, 654 KB

english, 1998

48

Targeted Conformational Transitions of Multimeric Proteins by Monte Carlo Simulations Combined with Collective Anisotropic Network Model Modes

Yesiltepe, Yasemin, Uyar, Arzu, Turgut, Deniz, Haliloglu, Turkan, Doruker, Pemra, Ozisik, Rahmi

Journal:

Biophysical Journal

Année:

2015

Langue:

english

Fichier:

PDF, 39 KB

english, 2015

49

ClustENM: ENM-based sampling of essential conformational space at full atomic resolution

Kurkcuoglu, Zeynep, Bahar, Ivet, Doruker, Pemra

Journal:

Journal of Chemical Theory and Computation

Année:

2016

Langue:

english

Fichier:

PDF, 4.41 MB

english, 2016

50

Investigation of allosteric coupling in human β2-adrenergic receptor in the presence of intracellular loop 3

Ozgur, Canan, Doruker, Pemra, Akten, E. Demet

Journal:

BMC Structural Biology

Année:

2016

Langue:

english

Fichier:

PDF, 3.56 MB

english, 2016