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List of works by Pemra Doruker

A docking study using atomistic conformers generated via elastic network model for cyclosporin A/cyclophilin A complex.

scientific article published in August 2009

Allosteric interactions in the parathyroid hormone GPCR-arrestin complex formation

scientific article published on 06 July 2020

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

scientific article published in September 2004

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

scientific article published on 30 November 2011

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

scientific article

Collective dynamics of EcoRI-DNA complex by elastic network model and molecular dynamics simulations

scientific article

Collective dynamics of the ribosomal tunnel revealed by elastic network modeling

scientific article published on June 2009

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

scientific article

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

scientific article published on August 2008

Cooperative fluctuations point to the dimerization interface of p53 core domain

scientific article published on July 2006

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

scientific article published on 21 July 2016

Coupling between catalytic loop motions and enzyme global dynamics

scientific article

Dimerization affects collective dynamics of triosephosphate isomerase

scientific article published on 12 January 2008

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

scientific article

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

scientific article published on 5 December 2007

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

scientific article

Effect of ligand binding on the intraminimum dynamics of proteins

scientific article published on 20 August 2010

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

scientific article published on 18 June 2020

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

scientific article published on June 2014

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

scientific article published on August 2009

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

scientific article published on November 1, 2003

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

scientific article published on February 2002

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

scientific article published in October 2005

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

scientific article published on October 2005

How an Inhibitor Bound to Subunit Interface Alters Triosephosphate Isomerase Dynamics

scientific article

Intrinsic dynamics is evolutionarily optimized to enable allosteric behavior

scientific article published on 27 November 2019

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

scientific article

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

scientific article

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

scientific article published on 12 February 2019

Loop motions of triosephosphate isomerase observed with elastic networks.

scientific article published in January 2006

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

scientific article published on 18 February 2020

Molecular dynamics simulations on constraint metal binding peptides

article

Protein-Ligand Complexes as Constrained Dynamical Systems

scientific article published on 04 April 2019

RESPEC Incorporates Residue Specificity and Ligand Effect into Elastic Network Model

scientific article published on 22 December 2017

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

scientific article published on 24 November 2008

Time series analysis of collective motions in proteins

scientific article published in January 2004

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

scientific article published on 01 July 2020

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