Pemra Doruker

发表

Coupling between Catalytic Loop Motions and Enzyme Global Dynamics

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

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

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

Protein-Ligand Complexes as Constrained Dynamical Systems

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

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.

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..

Substrate Effect on Catalytic Loop and Global Dynamics of Triosephosphate Isomerase

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

Effect of ligand binding on the intraminimum dynamics of proteins

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

ClustENMD: efficient sampling of biomolecular conformational space at atomic resolution

Ivet Bahar, Pemra Doruker, She Zhang, 2021, Bioinform..

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

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

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 .

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

Pemra Doruker, Wayne L. Mattice, 1999 .

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

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

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.

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.

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

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

Reverse Mapping of Coarse-Grained Polyethylene Chains from the Second Nearest Neighbor Diamond Lattice to an Atomistic Model in Continuous Space

Pemra Doruker, Wayne L. Mattice, 1997 .

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

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

Loop motions of triosephosphate isomerase observed with elastic networks.

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

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

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

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 .

Time series analysis of collective motions in proteins.

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

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

Kurt Kremer, Kurt Binder, Pemra Doruker, 2000 .

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

Robert L. Jernigan, Pemra Doruker, Ozge Kurkcuoglu, 2005 .

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.

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

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

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

Ivet Bahar, Burak Erman, Pemra Doruker, 2002 .

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

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

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.

Simulation of polyethylene thin films composed of various chain lengths

Pemra Doruker, P. Doruker, 2002 .

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

Robert L Jernigan, Pemra Doruker, 2003, Proteins.

Important Fluctuation Dynamics of Large Protein Structures Are Preserved upon Coarse-Grained Renormalization ∗

Robert L. Jernigan, Rigoberto Hernandez, Pemra Doruker, 2002 .