Pemra Doruker: search on Z-Library

The world's largest scientific articles store. 70,000,000+ articles for free.

1

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

Year:

2006

Language:

english

File:

PDF, 4.25 MB

english, 2006

2

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

Year:

2002

Language:

english

File:

PDF, 1.08 MB

english, 2002

3

How an Inhibitor Bound to Subunit Interface Alters Triosephosphate Isomerase Dynamics

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

Journal:

Biophysical Journal

Year:

2015

Language:

english

File:

PDF, 1.90 MB

english, 2015

4

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

Year:

2014

Language:

english

File:

PDF, 1.74 MB

english, 2014

5

Correction: Ligand Docking to Intermediate and Close-To-Bound Conformers Generated by an Elastic Network Model Based Algorithm for Highly Flexible Proteins

Kurkcuoglu, Zeynep, Doruker, Pemra

Journal:

Year:

2016

Language:

english

File:

PDF, 89 KB

english, 2016

6

Modulation of toroidal proteins dynamics in favor of functional mechanisms upon ligand binding

Li, Hongchun, Doruker, Pemra, Hu, Guang, Bahar, Ivet

Journal:

Biophysical Journal

Year:

2020

File:

PDF, 1.07 MB

2020

7

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

Esra Kucukpinar, Pemra Doruker

Journal:

Year:

2006

Language:

english

File:

PDF, 648 KB

english, 2006

8

Protein-ligand complexes as constrained dynamical systems

Kaynak, Burak T., Doruker, Pemra

Journal:

Journal of Chemical Information and Modeling

Year:

2019

File:

PDF, 794 KB

2019

9

Towards gaining sight of multiscale events: utilizing network models and normal modes in hybrid methods

Krieger, James M, Doruker, Pemra, Scott, Ana Ligia, Perahia, David, Bahar, Ivet

Journal:

Current Opinion in Structural Biology

Year:

2020

File:

PDF, 1.85 MB

2020

10

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

Year:

2009

Language:

english

File:

PDF, 494 KB

english, 2009

11

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:

Year:

2004

Language:

english

File:

PDF, 808 KB

english, 2004

12

Simulation of Polyethylene Thin Films on a High Coordination Lattice

Doruker, Pemra, Mattice, Wayne L.

Journal:

Year:

1998

Language:

english

File:

PDF, 148 KB

english, 1998

13

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

Year:

2009

Language:

english

File:

PDF, 829 KB

english, 2009

14

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

Year:

1999

Language:

english

File:

PDF, 225 KB

english, 1999

15

Loop Motions of Triosephosphate Isomerase Observed with Elastic Networks †

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

Journal:

Year:

2006

Language:

english

File:

PDF, 912 KB

english, 2006

16

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

Doruker, Pemra, Mattice, Wayne L.

Journal:

Year:

1999

Language:

english

File:

PDF, 208 KB

english, 1999

17

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

Year:

1993

Language:

english

File:

PDF, 1.26 MB

english, 1993

18

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

Year:

2012

Language:

english

File:

PDF, 2.49 MB

english, 2012

19

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

Pemra Doruker, Robert L. Jernigan, Ivet Bahar

Journal:

Journal of Computational Chemistry

Year:

2002

Language:

english

File:

PDF, 329 KB

english, 2002

20

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

Pemra Doruker, Robert L. Jernigan

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2003

Language:

english

File:

PDF, 472 KB

english, 2003

21

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

Ozge Kurkcuoglu, Robert L. Jernigan, Pemra Doruker

Journal:

Molecular Informatics

Year:

2005

Language:

english

File:

PDF, 468 KB

english, 2005

22

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

Isin, Basak, Doruker, Pemra, Bahar, Ivet

Journal:

Biophysical Journal

Year:

2002

Language:

english

File:

PDF, 795 KB

english, 2002

23

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

Year:

1999

Language:

english

File:

PDF, 100 KB

english, 1999

24

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

Year:

2007

Language:

english

File:

PDF, 151 KB

english, 2007

25

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

Year:

2014

Language:

english

File:

PDF, 75 KB

english, 2014

26

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

Year:

2005

Language:

english

File:

PDF, 360 KB

english, 2005

27

Substrate Effect on Catalytic Loop and Global Dynamics of Triosephosphate Isomerase

Kurkcuoglu, Zeynep, Doruker, Pemra

Journal:

Year:

2013

Language:

english

File:

PDF, 2.37 MB

english, 2013

28

Intrinsic dynamics is evolutionarily optimized to enable allosteric behavior

Zhang, Yan, Doruker, Pemra, Kaynak, Burak, Zhang, She, Krieger, James, Li, Hongchun, Bahar, Ivet

Journal:

Current Opinion in Structural Biology

Year:

2020

Language:

english

File:

PDF, 1.67 MB

english, 2020

29

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

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

Journal:

Biophysical Journal

Year:

2008

Language:

english

File:

PDF, 593 KB

english, 2008

30

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

Year:

2011

Language:

english

File:

PDF, 1.71 MB

english, 2011

31

Allosteric interactions in the parathyroid hormone GPCRâarrestin complex formation

Clark, Lisa J., Krieger, James, White, Alex D., Bondarenko, Vasyl, Lei, Saifei, Fang, Fei, Lee, Ji Young, Doruker, Pemra, BÃ¶ttke, Thore, Jean-Alphonse, Frederic, Tang, Pei, Gardella, Thomas J., Xiao,

Journal:

Nature Chemical Biology

Year:

2020

File:

PDF, 12.49 MB

2020

32

Mathematical description of ethanol fermentation by immobilised Saccharomyces cerevisiae

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

Journal:

Process Biochemistry

Year:

1998

Language:

english

File:

PDF, 683 KB

english, 1998

33

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

Year:

2013

Language:

english

File:

PDF, 2.18 MB

english, 2013

34

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

Year:

1996

Language:

english

File:

PDF, 402 KB

english, 1996

35

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

Year:

2016

Language:

english

File:

PDF, 3.56 MB

english, 2016

36

Intrinsic dynamics is evolutionarily optimized to enable allosteric behavior

Zhang, Yan, Doruker, Pemra, Kaynak, Burak, Zhang, She, Krieger, James, Li, Hongchun, Bahar, Ivet

Journal:

Current Opinion in Structural Biology

Year:

2020

File:

PDF, 1.67 MB

2020

37

Essential Site Scanning Analysis: a new approach for detecting sites that modulate the dispersion of protein global motions

Kaynak, Burak T., Bahar, Ivet, Doruker, Pemra

Journal:

Computational and Structural Biotechnology Journal

Year:

2020

File:

PDF, 12.88 MB

2020

38

Effect of Surface Roughness on Structure and Dynamics in Thin Films

Pemra Doruker, Wayne L. Mattice

Journal:

Macromolecular Theory and Simulations

Year:

2001

Language:

english

File:

PDF, 143 KB

english, 2001

39

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

Pemra Doruker, Ivet Bahar, Canan Baysal, Burak Erman

Journal:

Year:

2002

Language:

english

File:

PDF, 260 KB

english, 2002

40

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

Year:

2000

Language:

english

File:

PDF, 400 KB

english, 2000

41

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

Esra Kucukpinar, Pemra Doruker

Journal:

Year:

2004

Language:

english

File:

PDF, 495 KB

english, 2004

42

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

Year:

2009

Language:

english

File:

PDF, 4.04 MB

english, 2009

43

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

Year:

2014

Language:

english

File:

PDF, 47 KB

english, 2014

44

Time series analysis of collective motions in proteins

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

Journal:

The Journal of Chemical Physics

Year:

2004

Language:

english

File:

PDF, 481 KB

english, 2004

45

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

Year:

2004

Language:

english

File:

PDF, 388 KB

english, 2004

46

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

Year:

2005

Language:

english

File:

PDF, 388 KB

english, 2005

47

Dynamics of bulk polyethylene on a high coordination lattice

Doruker, Pemra, Mattice, Wayne L.

Journal:

Macromolecular Symposia

Year:

1998

Language:

english

File:

PDF, 654 KB

english, 1998

48

RESPEC Incorporates Residue Specificity and Ligand Effect into Elastic Network Model

Kaynak, Burak T, Findik, Doga, Doruker, Pemra

Journal:

Journal of Physical Chemistry B

Year:

2017

Language:

english

File:

PDF, 1.30 MB

english, 2017

49

Effect of ligand binding on the intraminimum dynamics of proteins

Burak Alakent, Sena Baskan, Pemra Doruker

Journal:

Journal of Computational Chemistry

Year:

2011

Language:

english

File:

PDF, 876 KB

english, 2011

50

Simulation of polyethylene thin films composed of various chain lengths

Journal:

Year:

2002

Language:

english

File:

PDF, 142 KB

english, 2002

To build up a library is to create a life. It’s never just a random collection of books.

— Carlos María Domínguez

Official channel

Z-Library Desktop Launcher

Z-Library Since 2009 support@1delivery.pm

EnglishРусскийEspañolItalianoελληνικάاللغة العربيةBahasa IndonesiaBahasa Malaysiaहिन्दीDeutschFrançaisPortuguêsУкраїнськаPolski中文繁體中文日本語Tiếng ViệtAzərbaycan DiliՀայոց լեզուภาษาไทยTürk Diliქართველიবাংলাپښتوతెలుగుاردو한국어SrpskiБългарски