P. Doruker

发表

Cooperative fluctuations point to the dimerization interface of p53 core domain.

Pemra Doruker, Turkan Haliloglu, T. Haliloglu, 2006, Biophysical journal.

Intrinsic dynamics is evolutionarily optimized to enable allosteric behavior.

Hongchun Li, I. Bahar, P. Doruker, 2019, Current opinion in structural biology.

Functional motions of influenza virus hemagglutinin: a structure-based analytical approach.

Ivet Bahar, Pemra Doruker, I. Bahar, 2002, Biophysical journal.

Collective dynamics of the ribosomal tunnel revealed by elastic network modeling

R. Jernigan, P. Doruker, O. Kurkcuoglu, 2009, Proteins.

Modulation of Toroidal Proteins Dynamics in Favor of Functional Mechanisms upon Ligand Binding.

Hongchun Li, I. Bahar, P. Doruker, 2020, Biophysical journal.

Focused functional dynamics of supramolecules by use of a mixed-resolution elastic network model.

Robert L Jernigan, Pemra Doruker, R. Jernigan, 2009, Biophysical journal.

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

Ivet Bahar, Pemra Doruker, A. Atilgan, 2000, Proteins.

9.3 In Silico Coarse-Grained Approaches to Structural Dynamics and Function of Proteins and their Assemblies

I. Bahar, P. Doruker, Y. Liu, 2012 .

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

Robert L. Jernigan, Pemra Doruker, R. Jernigan, 2004 .

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

R. Jernigan, A. Kloczkowski, P. Doruker, 2008, Physical biology.

ClustENM: ENM-Based Sampling of Essential Conformational Space at Full Atomic Resolution.

I. Bahar, P. Doruker, Z. Kurkcuoglu, 2016, Journal of chemical theory and computation.

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

P. Doruker, Z. Kurkcuoglu, 2016, PloS one.

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

P. Doruker, Z. Kurkcuoglu, 2016, PloS one.

How an Inhibitor Bound to Subunit Interface Alters Triosephosphate Isomerase Dynamics.

P. Doruker, Z. Kurkcuoglu, Doga Findik, 2015, Biophysical journal.

RESPEC Incorporates Residue Specificity and the Ligand Effect into the Elastic Network Model.

P. Doruker, B. Kaynak, Doga Findik, 2018, The journal of physical chemistry. B.

Mathematical description of ethanol fermentation by immobilised Saccharomyces cerevisiae

K. Ulgen, B. Kirdar, G. Birol, 1998 .

Essential site scanning analysis: A new approach for detecting sites that modulate the dispersion of protein global motions

I. Bahar, P. Doruker, B. Kaynak, 2020, Computational and structural biotechnology journal.

Activation and Speciation Mechanisms in Class A GPCRs

I. Bahar, P. Doruker, B. Wingert, 2022, Journal of molecular biology.

The elastic network model reveals a consistent picture on intrinsic functional dynamics of type II restriction endonucleases

L. Nilsson, P. Doruker, O. Kurkcuoglu, 2011, Physical biology.

GPCR kinases generate an APH1A phosphorylation barcode to regulate amyloid-β generation

I. Bahar, P. Doruker, James M. Krieger, 2022, Cell reports.

Bridging the Gap Between Atomistic and Coarse-Grained Models of Polymers: Status and Perspectives

Kurt Kremer, Kurt Binder, Pemra Doruker, 2000 .

Dynamics of bulk polyethylene on a high coordination lattice

W. Mattice, P. Doruker, 1998 .

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

W. Mattice, P. Doruker, R. Rapold, 1996 .

Effect of cooperative hydrogen bonding in azo-hydrazone tautomerism of azo dyes.

P. Doruker, V. Aviyente, A. S. Ozen, 2007, The journal of physical chemistry. A.

SEGREGATION OF CHAIN ENDS IS A WEAK CONTRIBUTOR TO INCREASED MOBILITY AT FREE POLYMER SURFACES

W. Mattice, P. Doruker, 1999 .

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

Robert L. Jernigan, Ivet Bahar, Pemra Doruker, 2002, J. Comput. Chem..

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

P. Doruker, Y. Yıldırım, Y Yildirim, 2004, Journal of biomolecular structure & dynamics.

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

E. Demet Akten, Pemra Doruker, P. Doruker, 2009, Journal of biomolecular structure & dynamics.

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

I. Bahar, P. Doruker, B. Badur, 1993 .

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

Pemra Doruker, Ivet Bahar, David Perahia, 2020, Current opinion in structural biology.

Precise druggability of the PTH type 1 receptor

Hongchun Li, I. Bahar, P. Doruker, 2021, Nature Chemical Biology.

ProDy 2.0: increased scale and scope after 10 years of protein dynamics modelling with Python

Ivet Bahar, Pemra Doruker, Hongchun Li, 2021, Bioinform..

Simulation of the random scission of C–C bonds in the initial stage of the thermal degradation of polyethylene

W. Mattice, P. Doruker, Yongmei Wang, 2001 .

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

W. Mattice, P. Doruker, 1999 .

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

P. Doruker, Esra Kucukpinar, 2006 .

Coupling between Catalytic Loop Motions and Enzyme Global Dynamics

Ivet Bahar, Zeynep Kurkcuoglu, Ahmet Bakan, 2012, PLoS Comput. Biol..

Features of large hinge-bending conformational transitions. Prediction of closed structure from open state.

Pemra Doruker, Turkan Haliloglu, T. Haliloglu, 2014, Biophysical journal.

Conformational dynamics of bacterial trigger factor in apo and ribosome-bound states

P. Doruker, O. Kurkcuoglu, A. Uyar, 2017, PloS one.

Allosteric interactions in the parathyroid hormone GPCR–arrestin complex formation

I. Bahar, P. Doruker, James M. Krieger, 2020, Nature Chemical Biology.

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

P. Doruker, Esra Kucukpinar, 2004 .

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

Burak Alakent, Pemra Doruker, P. Doruker, 2005, The Journal of chemical physics.

Time series analysis of collective motions in proteins.

Burak Alakent, Pemra Doruker, P. Doruker, 2004, The Journal of chemical physics.

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

P. Doruker, Zeynep Kurkcuoglu , Gulgun Ural , 2011, Molecular informatics.

Loop motions of triosephosphate isomerase observed with elastic networks.

Robert L Jernigan, Pemra Doruker, R. Jernigan, 2006, Biochemistry.

Mimicking Protein Dynamics by the Integration of Elastic Network Model with Time Series Analysis

Burak Alakent, Pemra Doruker, Mehmet C. Camurdan, 2007, Int. J. High Perform. Comput. Appl..

Conformational transition pathways explored by Monte Carlo simulation integrated with collective modes.

Pemra Doruker, Turkan Haliloglu, T. Haliloglu, 2008, Biophysical journal.

Cooperative mechanics of PR65 scaffold underlies the allosteric regulation of the phosphatase PP2A.

I. Bahar, L. Itzhaki, P. Doruker, 2023, Structure.

Sampling of Protein Conformational Space Using Hybrid Simulations: A Critical Assessment of Recent Methods

I. Bahar, D. Pérahia, P. Doruker, 2022, Frontiers in Molecular Biosciences.

ClustENMD: efficient sampling of biomolecular conformational space at atomic resolution

I. Bahar, P. Doruker, B. Kaynak, 2021, bioRxiv.

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

P. Doruker, A. Uyar, E. D. Akten, 2013, BMC Structural Biology.

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

P. Doruker, E. D. Akten, C. Ozgur, 2016, BMC Structural Biology.

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

Burak Alakent, Pemra Doruker, P. Doruker, 2004, The Journal of chemical physics.

Simulation of an amorphous polyethylene nanofiber on a high coordination lattice

W. Mattice, P. Doruker, Visit Vao‐soongnern, 2000 .

Simulations of Thin Films and Fibers of Amorphous Polymers

W. Mattice, P. Doruker, Visit Vao‐soongnern, 2002 .

Simulation of polyethylene thin films composed of various chain lengths

Pemra Doruker, P. Doruker, 2002 .

Role of water on unfolding kinetics of helical peptides studied by molecular dynamics simulations.

I. Bahar, P. Doruker, 1997, Biophysical journal.

Ligand‐binding affinity of alternative conformers of human β2‐adrenergic receptor in the presence of intracellular loop 3 (ICL3) and their potential use in virtual screening studies

P. Doruker, E. D. Akten, Gonca Dilcan, 2019, Chemical biology & drug design.

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

P. Doruker, Esra Kucukpinar, 2003 .

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

Lennart Nilsson, Pemra Doruker, L. Nilsson, 2006, Journal of biomolecular structure & dynamics.

Molecular dynamics simulations on constraint metal binding peptides

Candan Tamerler, Mehmet Sarikaya, Pemra Doruker, 2005 .

Dimerization affects collective dynamics of triosephosphate isomerase.

P. Doruker, Sertan Cansu, 2008, Biochemistry.

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

Burak Alakent, Pemra Doruker, P. Doruker, 2005, The Journal of chemical physics.

Protein-Ligand Complexes as Constrained Dynamical Systems

Pemra Doruker, Burak T Kaynak, P. Doruker, 2019, J. Chem. Inf. Model..

Predicting allosteric pockets in protein biological assemblages

R. Jernigan, K. Dorman, P. Doruker, 2023, Bioinformatics.

Effect of ligand binding on the intraminimum dynamics of proteins

Burak Alakent, Pemra Doruker, Sena Baskan, 2011, J. Comput. Chem..

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

Ivet Bahar, Burak Erman, Pemra Doruker, 2002 .

Conformational transition pathways explored by Monte Carlo simulation integrated with collective modes.

T. Haliloglu, P. Doruker, Nigar Kantarci-Carsibasi, 2008, Biophysical journal.

Elastic Network Models of Coarse-Grained Proteins Are Effective for Studying the Structural Control Exerted over Their Dynamics

Guang Song, R. Jernigan, Lei Yang, 2008 .

Influence of point mutations on PR65 conformational adaptability: Insights from molecular simulations and nanoaperture optical tweezers

L. Itzhaki, P. Doruker, Mohsin M. Naqvi, 2024, Science advances.

Influence of Point Mutations on PR65 Conformational Adaptability: Insights from Nanoaperture Optical Tweezer Experiments and Molecular Simulations

L. Itzhaki, P. Doruker, Mohsin M. Naqvi, 2023, Research square.

Substrate Effect on Catalytic Loop and Global Dynamics of Triosephosphate Isomerase

Zeynep Kurkcuoglu, Pemra Doruker, P. Doruker, 2013, Entropy.