Pemra Doruker
Pemra Doruker
University of Pittsburgh, Bogazici University
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Cited by
Cited by
Bridging the gap between atomistic and coarse-grained models of polymers: Status and perspectives
J Baschnagel, K Binder, P Doruker, AA Gusev, O Hahn, K Kremer, ...
Viscoelasticity, atomistic models, statistical chemistry, 41-156, 2000
Dynamics of proteins predicted by molecular dynamics simulations and analytical approaches: Application to α‐amylase inhibitor
P Doruker, AR Atilgan, I Bahar
Proteins: Structure, Function, and Bioinformatics 40 (3), 512-524, 2000
Dynamics of large proteins through hierarchical levels of coarse‐grained structures
P Doruker, RL Jernigan, I Bahar
Journal of computational chemistry 23 (1), 119-127, 2002
Reverse mapping of coarse-grained polyethylene chains from the second nearest neighbor diamond lattice to an atomistic model in continuous space
P Doruker, WL Mattice
Macromolecules 30 (18), 5520-5526, 1997
Mathematical description of ethanol fermentation by immobilised Saccharomyces cerevisiae
G Birol, P Doruker, B Kirdar, Zİ Önsan, K Ülgen
Process Biochemistry 33 (7), 763-771, 1998
Functional motions of influenza virus hemagglutinin: a structure-based analytical approach
B Isin, P Doruker, I Bahar
Biophysical journal 82 (2), 569-581, 2002
Simulation of polyethylene thin films on a high coordination lattice
P Doruker, WL Mattice
Macromolecules 31 (4), 1418-1426, 1998
Molecular simulations of small gas diffusion and solubility in copolymers of styrene
E Kucukpinar, P Doruker
Polymer 44 (12), 3607-3620, 2003
Mobility of the surface and interior of thin films composed of amorphous polyethylene
P Doruker, WL Mattice
Macromolecules 32 (1), 194-198, 1999
Effect of cooperative hydrogen bonding in azo− hydrazone tautomerism of azo dyes
AS Özen, P Doruker, V Aviyente
The Journal of Physical Chemistry A 111 (51), 13506-13514, 2007
ProDy 2.0: increased scale and scope after 10 years of protein dynamics modelling with Python
S Zhang, JM Krieger, Y Zhang, C Kaya, B Kaynak, K Mikulska-Ruminska, ...
Bioinformatics 37 (20), 3657-3659, 2021
Intrinsic dynamics is evolutionarily optimized to enable allosteric behavior
Y Zhang, P Doruker, B Kaynak, S Zhang, J Krieger, H Li, I Bahar
Current opinion in structural biology 62, 14-21, 2020
Mixed levels of coarse-graining of large proteins using elastic network model succeeds in extracting the slowest motions
O Kurkcuoglu, RL Jernigan, P Doruker
Polymer 45 (2), 649-657, 2004
The ribosome structure controls and directs mRNA entry, translocation and exit dynamics
O Kurkcuoglu, P Doruker, TZ Sen, A Kloczkowski, RL Jernigan
Physical biology 5 (4), 046005, 2008
Molecular dynamics simulations on constraint metal binding peptides
N Kantarci, C Tamerler, M Sarikaya, T Haliloglu, P Doruker
Polymer 46 (12), 4307-4313, 2005
Loop motions of triosephosphate isomerase observed with elastic networks
O Kurkcuoglu, RL Jernigan, P Doruker
Biochemistry 45 (4), 1173-1182, 2006
Conformational transition pathways explored by Monte Carlo simulation integrated with collective modes
N Kantarci-Carsibasi, T Haliloglu, P Doruker
Biophysical journal 95 (12), 5862-5873, 2008
Functional motions can be extracted from on‐lattice construction of protein structures
P Doruker, RL Jernigan
Proteins: Structure, Function, and Bioinformatics 53 (2), 174-181, 2003
Coupling between catalytic loop motions and enzyme global dynamics
Z Kurkcuoglu, A Bakan, D Kocaman, I Bahar, P Doruker
Public Library of Science 8 (9), e1002705, 2012
Focused functional dynamics of supramolecules by use of a mixed-resolution elastic network model
O Kurkcuoglu, OT Turgut, S Cansu, RL Jernigan, P Doruker
Biophysical journal 97 (4), 1178-1187, 2009
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