List of works - Türkan Haliloğlu

A mechanistic view of the role of E3 in sumoylation

scientific article

A model-structure of a periplasm-facing state of the NhaA antiporter suggests the molecular underpinnings of pH-induced conformational changes

scientific article

Adaptability of protein structures to enable functional interactions and evolutionary implications

scientific article published on 06 August 2015

Allosteric Dynamic Control of Binding.

scientific article published on 31 August 2015

Alternative allosteric mechanisms can regulate the substrate and E2 in SUMO conjugation

scientific article published on 7 January 2011

Analysis of correlations between energy and residue fluctuations in native proteins and determination of specific sites for binding

scientific article published on 27 February 2009

Association of putative concave protein-binding sites with the fluctuation behavior of residues

scientific article

C(alpha)-trace model of the transmembrane domain of human copper transporter 1, motion and functional implications

scientific article

Cataloging and organizing p73 interactions in cell cycle arrest and apoptosis

scientific article published on 26 July 2008

Changes to the dynamic nature of hemagglutinin and the emergence of the 2009 pandemic H1N1 influenza virus

scientific article

Community-wide assessment of protein-interface modeling suggests improvements to design methodology

scientific article

Conformational control of the binding of the transactivation domain of the MLL protein and c-Myb to the KIX domain of CREB

scientific article

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

scientific article published on August 2008

Cooperative fluctuations of unliganded and substrate-bound HIV-1 protease: a structure-based analysis on a variety of conformations from crystallography and molecular dynamics simulations

scientific article published on 01 May 2003

Cooperative fluctuations point to the dimerization interface of p53 core domain

scientific article published on July 2006

Cooperative transition between open and closed conformations in potassium channels

scientific article

Cullin neddylation may allosterically tune polyubiquitin chain length and topology

scientific article published on 12 January 2017

DNABINDPROT: fluctuation-based predictor of DNA-binding residues within a network of interacting residues.

scientific article

Detection of the onset of demixing in simulations of polypropylene melts in which the chains differ only in stereochemical composition

article

Distinct Allosteric Networks Underlie Mechanistic Speciation of ABC Transporters

scientific article published on 15 April 2020

Drug-resistant HIV-1 protease regains functional dynamics through cleavage site coevolution.

scientific article published on 11 January 2015

DynaFace: Discrimination between Obligatory and Non-obligatory Protein-Protein Interactions Based on the Complex's Dynamics

scientific article published on 27 October 2015

Dynamic allostery: linkers are not merely flexible

scientific article published on July 2011

Dynamic fluctuations provide the basis of a conformational switch mechanism in apo cyclic AMP receptor protein

scientific article

Dynamics of preferential substrate recognition in HIV-1 protease: redefining the substrate envelope

scientific article published on July 2011

Emergence and transmission of arbovirus evolutionary intermediates with epidemic potential

scientific article published on June 2014

Extreme Entropy–Enthalpy Compensation in a Drug-Resistant Variant of HIV-1 Protease ⬇️

scientific article published on July 2, 2012

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

scientific article published on June 2014

Gaussian Dynamics of Folded Proteins

scientific article published in Physical Review Letters

HIV-1 Protease and Substrate Coevolution Validates the Substrate Envelope As the Substrate Recognition Pattern.

scientific article published on February 2012

HingeProt: automated prediction of hinges in protein structures

scientific article

Hot spots in a network of functional sites

scientific article

How Does KCNE1 Regulate the Kv7.1 Potassium Channel? Model-Structure, Mutations, and Dynamics of the Kv7.1-KCNE1 Complex

article

How similar are protein folding and protein binding nuclei? Examination of vibrational motions of energy hot spots and conserved residues

scientific article

Independent and cooperative motions of the Kv1.2 channel: voltage sensing and gating

scientific article published on May 2010

Interactions of cationic-hydrophobic peptides with lipid bilayers: a Monte Carlo simulation method

scientific article published on 11 May 2007

Interactions of hydrophobic peptides with lipid bilayers: Monte Carlo simulations with M2delta

scientific article published in December 2003

Interactions of the M2delta segment of the acetylcholine receptor with lipid bilayers: a continuum-solvent model study

scientific article

Local and Global Motions Underlying Antibiotic Binding in Bacterial Ribosome

scientific article published on 24 November 2020

MCPath: Monte Carlo path generation approach to predict likely allosteric pathways and functional residues.

scientific article

Machine learning integration for predicting the effect of single amino acid substitutions on protein stability

scientific article

Molecular dynamics simulations on constraint metal binding peptides

article

Monte Carlo simulations of peptide-membrane interactions with the MCPep web server

scientific article published on 13 June 2012

Monte Carlo studies of folding, dynamics, and stability in alpha-helices

scientific article published on 14 January 2005

MuD: an interactive web server for the prediction of non-neutral substitutions using protein structural data

scientific article

MuD: an interactive web server for the prediction of non-neutral substitutions using protein structural data.

scientific article published on 23 November 2010

NhaA antiporter functions using 10 helices, and an additional 2 contribute to assembly/stability

scientific article

Predicting important residues and interaction pathways in proteins using Gaussian Network Model: binding and stability of HLA proteins

scientific article

Prediction of binding sites in receptor-ligand complexes with the Gaussian Network Model

scientific article published on 03 June 2008

Protein dynamics analysis reveals that missense mutations in cancer-related genes appear frequently on hinge-neighboring residues

article

Rationale for More Diverse Inhibitors in Competition with Substrates in HIV-1 Protease ⬇️

scientific article published on September 8, 2010

Single-molecule probing of the conformational homogeneity of the ABC transporter BtuCD

scientific article published on 18 June 2018

Structural and dynamics aspects of ASC speck assembly.

scientific article published on 6 November 2014

Structure, dynamics and implied gating mechanism of a human cyclic nucleotide-gated channel

scientific article (publication date: December 2014)

Structure-based prediction of potential binding and nonbinding peptides to HIV-1 protease

scientific article

Substrate specificity in HIV-1 protease by a biased sequence search method

scientific article published in August 2006

The Transmembrane Helix Tilt May Be Determined by the Balance between Precession Entropy and Lipid Perturbation

scientific article published on 6 June 2012

Use of residual dipolar couplings as restraints in ab initio protein structure prediction.

scientific article

What can we learn from highly connected beta-rich structures for structural interface design?

scientific article published on January 2008

List of works by Türkan Haliloğlu

A mechanistic view of the role of E3 in sumoylation

A model-structure of a periplasm-facing state of the NhaA antiporter suggests the molecular underpinnings of pH-induced conformational changes

Adaptability of protein structures to enable functional interactions and evolutionary implications

Allosteric Dynamic Control of Binding.

Alternative allosteric mechanisms can regulate the substrate and E2 in SUMO conjugation

Analysis of correlations between energy and residue fluctuations in native proteins and determination of specific sites for binding

Association of putative concave protein-binding sites with the fluctuation behavior of residues

C(alpha)-trace model of the transmembrane domain of human copper transporter 1, motion and functional implications

Cataloging and organizing p73 interactions in cell cycle arrest and apoptosis

Changes to the dynamic nature of hemagglutinin and the emergence of the 2009 pandemic H1N1 influenza virus

Community-wide assessment of protein-interface modeling suggests improvements to design methodology

Conformational control of the binding of the transactivation domain of the MLL protein and c-Myb to the KIX domain of CREB

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

Cooperative fluctuations of unliganded and substrate-bound HIV-1 protease: a structure-based analysis on a variety of conformations from crystallography and molecular dynamics simulations

Cooperative fluctuations point to the dimerization interface of p53 core domain

Cooperative transition between open and closed conformations in potassium channels

Cullin neddylation may allosterically tune polyubiquitin chain length and topology

DNABINDPROT: fluctuation-based predictor of DNA-binding residues within a network of interacting residues.

Detection of the onset of demixing in simulations of polypropylene melts in which the chains differ only in stereochemical composition

Distinct Allosteric Networks Underlie Mechanistic Speciation of ABC Transporters

Drug-resistant HIV-1 protease regains functional dynamics through cleavage site coevolution.

DynaFace: Discrimination between Obligatory and Non-obligatory Protein-Protein Interactions Based on the Complex's Dynamics

Dynamic allostery: linkers are not merely flexible

Dynamic fluctuations provide the basis of a conformational switch mechanism in apo cyclic AMP receptor protein

Dynamics of preferential substrate recognition in HIV-1 protease: redefining the substrate envelope

Emergence and transmission of arbovirus evolutionary intermediates with epidemic potential

Extreme Entropy–Enthalpy Compensation in a Drug-Resistant Variant of HIV-1 Protease ⬇️

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

Gaussian Dynamics of Folded Proteins

HIV-1 Protease and Substrate Coevolution Validates the Substrate Envelope As the Substrate Recognition Pattern.

HingeProt: automated prediction of hinges in protein structures

Hot spots in a network of functional sites

How Does KCNE1 Regulate the Kv7.1 Potassium Channel? Model-Structure, Mutations, and Dynamics of the Kv7.1-KCNE1 Complex

How similar are protein folding and protein binding nuclei? Examination of vibrational motions of energy hot spots and conserved residues

Independent and cooperative motions of the Kv1.2 channel: voltage sensing and gating

Interactions of cationic-hydrophobic peptides with lipid bilayers: a Monte Carlo simulation method

Interactions of hydrophobic peptides with lipid bilayers: Monte Carlo simulations with M2delta

Interactions of the M2delta segment of the acetylcholine receptor with lipid bilayers: a continuum-solvent model study

Local and Global Motions Underlying Antibiotic Binding in Bacterial Ribosome

MCPath: Monte Carlo path generation approach to predict likely allosteric pathways and functional residues.

Machine learning integration for predicting the effect of single amino acid substitutions on protein stability

Molecular dynamics simulations on constraint metal binding peptides

Monte Carlo simulations of peptide-membrane interactions with the MCPep web server

Monte Carlo studies of folding, dynamics, and stability in alpha-helices

MuD: an interactive web server for the prediction of non-neutral substitutions using protein structural data

MuD: an interactive web server for the prediction of non-neutral substitutions using protein structural data.

NhaA antiporter functions using 10 helices, and an additional 2 contribute to assembly/stability

Predicting important residues and interaction pathways in proteins using Gaussian Network Model: binding and stability of HLA proteins

Prediction of binding sites in receptor-ligand complexes with the Gaussian Network Model

Protein dynamics analysis reveals that missense mutations in cancer-related genes appear frequently on hinge-neighboring residues

Rationale for More Diverse Inhibitors in Competition with Substrates in HIV-1 Protease ⬇️

Single-molecule probing of the conformational homogeneity of the ABC transporter BtuCD

Structural and dynamics aspects of ASC speck assembly.

Structure, dynamics and implied gating mechanism of a human cyclic nucleotide-gated channel

Structure-based prediction of potential binding and nonbinding peptides to HIV-1 protease

Substrate specificity in HIV-1 protease by a biased sequence search method

The Transmembrane Helix Tilt May Be Determined by the Balance between Precession Entropy and Lipid Perturbation

Use of residual dipolar couplings as restraints in ab initio protein structure prediction.

What can we learn from highly connected beta-rich structures for structural interface design?