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1

El Farol revisited

Hilmi Luş, Cevat Onur Aydın, Sinan Keten, Hakan İsmail Ünsal, Ali Rana Atılgan

Journal:

Physica A: Statistical Mechanics and its Applications

Année:

2005

Langue:

english

Fichier:

PDF, 203 KB

english, 2005

2

Network-Based Models as Tools Hinting at Nonevident Protein Functionality

Atilgan, Canan, Okan, Osman Burak, Atilgan, Ali Rana

Journal:

Annual Review of Biophysics

Année:

2012

Langue:

english

Fichier:

PDF, 1.89 MB

english, 2012

3

Unraveling the Motions behind Enterovirus 71 Uncoating

Ross, Caroline J., Atilgan, Ali Rana, Tastan Bishop, Özlem, Atilgan, Canan

Journal:

Biophysical Journal

Année:

2018

Langue:

english

Fichier:

PDF, 5.48 MB

english, 2018

4

Understanding the recognition of protein structural classes by amino acid composition

Ivet Bahar, Ali Rana Atilgan, Robert L. Jernigan, Burak Erman

Journal:

Proteins: Structure, Function, and Bioinformatics

Année:

1997

Langue:

english

Fichier:

PDF, 181 KB

english, 1997

5

A Nonlinear Model for the Kinking Behavior of Unidirectional Polymer Matrix Composites

Ali Rana Atilgan

Journal:

ZAMM - Journal of Applied Mathematics and Mechanics / Zeitschrift für Angewandte Mathematik und Mechanik

Année:

1998

Langue:

english

Fichier:

PDF, 198 KB

english, 1998

6

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

7

Elucidating the structural mechanisms for biological activity of the chemokine family

Canan Baysal, Ali Rana Atilgan

Journal:

Proteins: Structure, Function, and Bioinformatics

Année:

2001

Langue:

english

Fichier:

PDF, 267 KB

english, 2001

8

Identification of kinetically hot residues in proteins

Melik C. Demirel, Ali Rana Atilgan, Ivet Bahar, Robert L. Jernigan, Burak Erman

Journal:

Protein Science

Année:

1998

Langue:

english

Fichier:

PDF, 3.79 MB

english, 1998

9

Coordination topology and stability for the native and binding conformers of chymotrypsin inhibitor 2

Canan Baysal, Ali Rana Atilgan

Journal:

Proteins: Structure, Function, and Bioinformatics

Année:

2001

Langue:

english

Fichier:

PDF, 273 KB

english, 2001

10

How orientational order governs collectivity of folded proteins

Canan Atilgan, Osman Burak Okan, Ali Rana Atilgan

Journal:

Proteins: Structure, Function, and Bioinformatics

Année:

2010

Langue:

english

Fichier:

PDF, 574 KB

english, 2010

11

Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential

Ivet Bahar, Ali Rana Atilgan, Burak Erman

Journal:

Folding and Design

Année:

1997

Langue:

english

Fichier:

PDF, 142 KB

english, 1997

12

Collective Motions in HIV-1 Reverse Transcriptase: Examination of Flexibility and Enzyme Function

Ivet Bahar, Burak Erman, Robert L. Jernigan, Ali Rana Atilgan, David G. Covell

Journal:

Journal of Molecular Biology

Année:

1999

Langue:

english

Fichier:

PDF, 497 KB

english, 1999

13

Relaxation Kinetics and the Glassiness of Proteins: The Case of Bovine Pancreatic Trypsin Inhibitor

Baysal, Canan, Atilgan, Ali Rana

Journal:

Biophysical Journal

Année:

2002

Langue:

english

Fichier:

PDF, 135 KB

english, 2002

14

Small-World Communication of Residues and Significance for Protein Dynamics

Atilgan, Ali Rana, Akan, Pelin, Baysal, Canan

Journal:

Biophysical Journal

Année:

2004

Langue:

english

Fichier:

PDF, 206 KB

english, 2004

15

On modifying properties of polymeric melts by nanoscopic particles

Atilgan, Canan, Inanc, Ibrahim, Rana Atilgan, Ali

Journal:

Journal of Polymer Science Part B: Polymer Physics

Année:

2012

Langue:

english

Fichier:

PDF, 1.96 MB

english, 2012

16

Multiple Channels of Structural Relaxations in Functional Proteins

Atilgan, Canan, Okan, Osman B., Atilgan, Ali Rana

Journal:

Biophysical Journal

Année:

2009

Langue:

english

Fichier:

PDF, 35 KB

english, 2009

17

A Coarsened Network Model Reveals Allosteric Machinery

Atilgan, Ali Rana, Atilgan, Canan

Journal:

Biophysical Journal

Année:

2009

Langue:

english

Fichier:

PDF, 94 KB

english, 2009

18

Nanosecond Motions in Proteins Impose Bounds on the Timescale Distributions of Local Dynamics

Okan, Osman Burak, Atilgan, Ali Rana, Atilgan, Canan

Journal:

Biophysical Journal

Année:

2009

Langue:

english

Fichier:

PDF, 418 KB

english, 2009

19

Functional Pathways in Proteins Are Uncovered By Strong Disorder

Atilgan, Canan, Ermez, Sema, Keskin, Ozlem, Atilgan, Ali Rana

Journal:

Biophysical Journal

Année:

2010

Langue:

english

Fichier:

PDF, 31 KB

english, 2010

20

Relaxation Kinetics and the Glassiness of Native Proteins: Coupling of Timescales

Baysal, Canan, Atilgan, Ali Rana

Journal:

Biophysical Journal

Année:

2005

Langue:

english

Fichier:

PDF, 134 KB

english, 2005

21

Screened Nonbonded Interactions in Native Proteins Manipulate Optimal Paths for Robust Residue Communication

Atilgan, Ali Rana, Turgut, Deniz, Atilgan, Canan

Journal:

Biophysical Journal

Année:

2007

Langue:

english

Fichier:

PDF, 500 KB

english, 2007

22

How a Vicinal Layer of Solvent Modulates the Dynamics of Proteins

Atilgan, Canan, Aykut, Ayse Ozlem, Atilgan, Ali Rana

Journal:

Biophysical Journal

Année:

2008

Langue:

english

Fichier:

PDF, 372 KB

english, 2008

23

Changes in Bond-Orientational Order of Residues are Associated with Shifts in Energy Landscapes

Rana Atilgan, Ali, Burak Okan, Osman, Atilgan, Canan

Journal:

Biophysical Journal

Année:

2012

Langue:

english

Fichier:

PDF, 37 KB

english, 2012

24

Where do Proteins Fit in the Structural Classification of Condensed Matter?

Okan, Osman B., Ozisik, Rahmi, Atilgan, Canan, Rana Atilgan, Ali

Journal:

Biophysical Journal

Année:

2012

Langue:

english

Fichier:

PDF, 98 KB

english, 2012

25

Molecular Recognition Mechanism of Calmodulin Examined by Perturbation-Response Scanning

Atilgan, Canan, Aykut, A. Ozlem, Atilgan, Ali Rana

Journal:

Biophysical Journal

Année:

2011

Langue:

english

Fichier:

PDF, 36 KB

english, 2011

26

Structural Basis of How Ferric Binding Proteins Utilize pH Differences for Controlled Release of Iron

Atilgan, Canan, Guven, Gokce, Rana Atilgan, Ali

Journal:

Biophysical Journal

Année:

2013

Langue:

english

Fichier:

PDF, 36 KB

english, 2013

27

Non-Equilibrium Fluctuation Theorems, Redundant Paths in Proteins, and Elucidating Conformational Changes by Single-Residue Perturbations

Rana Atilgan, Ali, Aykut, Ayse Ozlem, Atilgan, Canan

Journal:

Biophysical Journal

Année:

2013

Langue:

english

Fichier:

PDF, 36 KB

english, 2013

28

Obituary.

Rana Atilgan, Ali, Aykut, Ayse Ozlem, Atilgan, Canan

Journal:

Année:

1926

Langue:

english

Fichier:

PDF, 219 KB

english, 1926

29

Exploring pH Dependent Landscape Shifts of Proteins

Atilgan, Canan, Ozlem Aykut, Ayse, Negi, Sunita, Rana Atilgan, Ali

Journal:

Biophysical Journal

Année:

2012

Langue:

english

Fichier:

PDF, 40 KB

english, 2012

30

Calmodulin Readily Switches Conformation upon Protonating High p K a Acidic Residues

Negi, Sunita, Aykut, Ayse Ozlem, Atilgan, Ali Rana, Atilgan, Canan

Journal:

Journal of Physical Chemistry B

Année:

2012

Langue:

english

Fichier:

PDF, 3.23 MB

english, 2012

31

Protonation States of Remote Residues Affect Binding–Release Dynamics of the Ligand but Not the Conformation of Apo Ferric Binding Protein

Guven, Gokce, Atilgan, Ali Rana, Atilgan, Canan

Journal:

Journal of Physical Chemistry B

Année:

2014

Langue:

english

Fichier:

PDF, 3.23 MB

english, 2014

32

Relating the Structure of HIV-1 Reverse Transcriptase to Its Processing Step

Jernigan, R. L., Bahar, Ivet, Covell, David G., Atilgan, Ali Rana, Erman, Burak, Flatow, Daniel T.

Journal:

Journal of Biomolecular Structure and Dynamics

Année:

2000

Langue:

english

Fichier:

PDF, 129 KB

english, 2000

33

Vibrational Dynamics of Folded Proteins: Significance of Slow and Fast Motions in Relation to Function and Stability

Bahar, Ivet, Atilgan, Ali Rana, Demirel, Melik C., Erman, Burak

Journal:

Physical Review Letters

Année:

1998

Langue:

english

Fichier:

PDF, 154 KB

english, 1998

34

Subtle pH differences trigger single residue motions for moderating conformations of calmodulin

Atilgan, Ali Rana, Aykut, Ayse Ozlem, Atilgan, Canan

Journal:

The Journal of Chemical Physics

Année:

2011

Langue:

english

Fichier:

PDF, 1.13 MB

english, 2011

35

Identifying the adaptive mechanism in globular proteins: Fluctuations in densely packed regions manipulate flexible parts

Yilmaz, Lutfu Safak, Atilgan, Ali Rana

Journal:

The Journal of Chemical Physics

Année:

2000

Langue:

english

Fichier:

PDF, 1.09 MB

english, 2000

36

COLLECTIVE BEHAVIOR OF EL FAROL ATTENDEES

ATILGAN, CANAN, ATILGAN, ALI RANA, DEMIREL, GÜVEN

Journal:

Advances in Complex Systems

Année:

2008

Langue:

english

Fichier:

PDF, 225 KB

english, 2008

37

Long-Range Structural Regularities and Collectivity of Folded Proteins

Atilgan, Canan, Inanc, Ibrahim, Atilgan, Ali Rana

Journal:

MRS Proceedings

Année:

2009

Langue:

english

Fichier:

PDF, 360 KB

english, 2009

38

Molecular Recognition Mechanisms of Calmodulin Examined by Perturbation-Response Scanning

Aykut, A. Ozlem, Atilgan, Ali Rana, Atilgan, Canan

Journal:

MRS Proceedings

Année:

2011

Fichier:

PDF, 977 KB

2011

39

Detailed molecular dynamics simulations of human transferrin provide insights into iron release dynamics at serum and endosomal pH

Abdizadeh, Haleh, Atilgan, Ali Rana, Atilgan, Canan

Journal:

JBIC Journal of Biological Inorganic Chemistry

Année:

2015

Langue:

english

Fichier:

PDF, 2.28 MB

english, 2015

40

Effect of van der Waals Interaction Strength and Nanocluster Size on the Dynamical and Mechanical Properties of 1,4-cis-polybutadiene Melts

Atilgan, Canan, Inanc, Ibrahim, Atilgan, Ali Rana

Journal:

MRS Proceedings

Année:

2012

Langue:

english

Fichier:

PDF, 222 KB

english, 2012

41

Perturbation response scanning specifies key regions in subtilisin serine protease for both function and stability

Abdizadeh, Haleh, Guven, Gokce, Atilgan, Ali Rana, Atilgan, Canan

Journal:

Journal of Enzyme Inhibition and Medicinal Chemistry

Année:

2015

Langue:

english

Fichier:

PDF, 331 KB

english, 2015

42

Designing Molecular Dynamics Simulations to Shift Populations of the Conformational States of Calmodulin

Aykut, Ayse Ozlem, Atilgan, Ali Rana, Atilgan, Canan, Livesay, Dennis R.

Journal:

PLoS Computational Biology

Année:

2013

Langue:

english

Fichier:

PDF, 1.06 MB

english, 2013

43

Perturbation-Response Scanning Reveals Ligand Entry-Exit Mechanisms of Ferric Binding Protein

Atilgan, Canan, Atilgan, Ali Rana, Nussinov, Ruth

Journal:

PLoS Computational Biology

Année:

2009

Langue:

english

Fichier:

PDF, 863 KB

english, 2009

44

Computational Assessment of Trimethoprim Resistance in Dihydrofolate Reductase

Abdizadeh, Haleh, Acar, Omer, Furkan Guclu, Tandac, Talha Tamer, Yusuf, Altinusak Batur, Tugce, Toprak, Erdal, Rana Atilgan, Ali, Atilgan, Canan

Journal:

Biophysical Journal

Année:

2016

Langue:

english

Fichier:

PDF, 69 KB

english, 2016

45

Driving Calmodulin Protein towards Conformational Shift by Changing Ionization States of Select Residues

Negi, Sunita, Atilgan, Ali Rana, Atilgan, Canan

Journal:

Journal of Physics Conference Series

Année:

2012

Langue:

english

Fichier:

PDF, 1.37 MB

english, 2012

46

In silico mutational studies of Hsp70 disclose sites with distinct functional attributes

Ozbaykal, Gizem, Rana Atilgan, Ali, Atilgan, Canan

Journal:

Proteins: Structure, Function, and Bioinformatics

Année:

2015

Langue:

english

Fichier:

PDF, 583 KB

english, 2015

47

FbpA iron storage and release are governed by periplasmic microenvironments

Sensoy, Ozge, Atilgan, Ali Rana, Atilgan, Canan

Journal:

Physical Chemistry Chemical Physics

Année:

2017

Langue:

english

Fichier:

PDF, 2.14 MB

english, 2017

48

Increased substrate affinity in the Escherichia coli L28R dihydrofolate reductase mutant causes trimethoprim resistance

Abdizadeh, Haleh, Tamer, Yusuf Talha, Acar, Omer, Toprak, Erdal, Atilgan, Ali Rana, Atilgan, Canan

Journal:

Physical Chemistry Chemical Physics

Année:

2017

Langue:

english

Fichier:

PDF, 1.31 MB

english, 2017

49

Mechanisms by Which Salt Concentration Moderates the Dynamics of Human Serum Transferrin

Abdizadeh, Haleh, Atilgan, Ali Rana, Atilgan, Canan

Journal:

Journal of Physical Chemistry B

Année:

2017

Langue:

english

Fichier:

PDF, 5.77 MB

english, 2017

50

Assortative Mixing in Close-Packed Spatial Networks

Turgut, Deniz, Atilgan, Ali Rana, Atilgan, Canan, Ben-Jacob, Eshel

Journal:

Année:

2010

Langue:

english

Fichier:

PDF, 743 KB

english, 2010