List of works - Burak Erman

A comparative molecular dynamics study of methylation state specificity of JMJD2A.

scientific article

A computational model for controlling conformational cooperativity and function in proteins

scientific article published on 25 August 2018

A fast approximate method of identifying paths of allosteric communication in proteins

scientific article published on 20 April 2013

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

Anharmonicity, mode-coupling and entropy in a fluctuating native protein

scientific article published on 26 October 2010

Binding Stability of Peptides on Major Histocompatibility Complex Class I Proteins: Role of Entropy and Dynamics

scientific article published on 16 October 2017

Causality, transfer entropy, and allosteric communication landscapes in proteins with harmonic interactions

scientific article

Collective motions in HIV-1 reverse transcriptase: examination of flexibility and enzyme function.

scientific article

Computational and experimental investigation of DNA repair protein photolyase interactions with low molecular weight drugs.

scientific article published in July 2013

Computational basis of knowledge-based conformational probabilities derived from local- and long-range interactions in proteins.

scientific article

Conformational energies and entropies of peptides, and the peptide-protein binding problem.

scientific article

Conformational transitions in the Ramachandran space of amino acids using the dynamic rotational isomeric state (DRIS) model

scientific article published on 17 January 2014

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

scientific article

Determination of pair-wise inter-residue interaction forces from folding pathways and their implementation in coarse-grained folding prediction.

scientific article published on 20 February 2009

Effects of ligand binding upon flexibility of proteins.

scientific article published on 25 March 2015

Efficient characterization of collective motions and interresidue correlations in proteins by low-resolution simulations.

scientific article published on November 1997

Entropy Transfer between Residue Pairs and Allostery in Proteins: Quantifying Allosteric Communication in Ubiquitin

scientific article (publication date: 17 January 2017)

Eugene Guth

biographical article published in 1991

Folding dynamics of proteins from denatured to native state: principal component analysis.

scientific article published in January 2004

Identification of ligand binding sites of proteins using the Gaussian Network Model

scientific article

MATHEMATICAL MODELING OF BEHÇET'S DISEASE: A DYNAMICAL SYSTEMS APPROACH

Minimum energy configurations of the 2-dimensional HP-model of proteins by self-organizing networks

scientific article published in January 2002

Mode coupling points to functionally important residues in myosin II

scientific article published on 31 March 2014

Molecular dynamics simulations provide molecular insights into the role of HLA-B51 in Behçet's disease pathogenesis

scientific article published on 01 July 2020

Molecular recognition of H3/H4 histone tails by the tudor domains of JMJD2A: a comparative molecular dynamics simulations study

scientific article

Optimum folding pathways of proteins: their determination and properties.

scientific article published in April 2006

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

scientific article

Predicting most probable conformations of a given peptide sequence in the random coil state.

scientific article

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

scientific article published on 03 June 2008

Prediction of optimal folding routes of proteins that satisfy the principle of lowest entropy loss: dynamic contact maps and optimal control

scientific article

Quasi-harmonic analysis of mode coupling in fluctuating native proteins

scientific article published on 26 October 2010

Quasi-harmonic fluctuations of two bound peptides

scientific article published on 15 September 2012

Relating the Structure of HIV-1 Reverse Transcriptase to Its Processing Step.

scientific article

Relationships between amino acid sequence and backbone torsion angle preferences.

scientific article

Relationships between ligand binding sites, protein architecture and correlated paths of energy and conformational fluctuations ⬇️

scientific article published on August 10, 2011

Simulation of temporal stochastic phenomena in electronic and biological systems: A comparative review, examples and synergies

article

Statistical thermodynamics of residue fluctuations in native proteins.

scientific article published in March 2009

The elastic net algorithm and protein structure prediction.

scientific article

The gaussian network model: precise prediction of residue fluctuations and application to binding problems

scientific article

The introduction of hydrogen bond and hydrophobicity effects into the rotational isomeric states model for conformational analysis of unfolded peptides.

scientific article published on 13 January 2009

Turkey must end violent response to protests

scientific article

Understanding the recognition of protein structural classes by amino acid composition ⬇️

scientific article published on October 1, 1997

VitAL: Viterbi algorithm for de novo peptide design

scientific article

List of works by Burak Erman

A comparative molecular dynamics study of methylation state specificity of JMJD2A.

A computational model for controlling conformational cooperativity and function in proteins

A fast approximate method of identifying paths of allosteric communication in proteins

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

Anharmonicity, mode-coupling and entropy in a fluctuating native protein

Binding Stability of Peptides on Major Histocompatibility Complex Class I Proteins: Role of Entropy and Dynamics

Causality, transfer entropy, and allosteric communication landscapes in proteins with harmonic interactions

Collective motions in HIV-1 reverse transcriptase: examination of flexibility and enzyme function.

Computational and experimental investigation of DNA repair protein photolyase interactions with low molecular weight drugs.

Computational basis of knowledge-based conformational probabilities derived from local- and long-range interactions in proteins.

Conformational energies and entropies of peptides, and the peptide-protein binding problem.

Conformational transitions in the Ramachandran space of amino acids using the dynamic rotational isomeric state (DRIS) model

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

Determination of pair-wise inter-residue interaction forces from folding pathways and their implementation in coarse-grained folding prediction.

Effects of ligand binding upon flexibility of proteins.

Efficient characterization of collective motions and interresidue correlations in proteins by low-resolution simulations.

Entropy Transfer between Residue Pairs and Allostery in Proteins: Quantifying Allosteric Communication in Ubiquitin

Eugene Guth

Folding dynamics of proteins from denatured to native state: principal component analysis.

Identification of ligand binding sites of proteins using the Gaussian Network Model

MATHEMATICAL MODELING OF BEHÇET'S DISEASE: A DYNAMICAL SYSTEMS APPROACH

Minimum energy configurations of the 2-dimensional HP-model of proteins by self-organizing networks

Mode coupling points to functionally important residues in myosin II

Molecular dynamics simulations provide molecular insights into the role of HLA-B51 in Behçet's disease pathogenesis

Molecular recognition of H3/H4 histone tails by the tudor domains of JMJD2A: a comparative molecular dynamics simulations study

Optimum folding pathways of proteins: their determination and properties.

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

Predicting most probable conformations of a given peptide sequence in the random coil state.

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

Prediction of optimal folding routes of proteins that satisfy the principle of lowest entropy loss: dynamic contact maps and optimal control

Quasi-harmonic analysis of mode coupling in fluctuating native proteins

Quasi-harmonic fluctuations of two bound peptides

Relating the Structure of HIV-1 Reverse Transcriptase to Its Processing Step.

Relationships between amino acid sequence and backbone torsion angle preferences.

Relationships between ligand binding sites, protein architecture and correlated paths of energy and conformational fluctuations ⬇️

Simulation of temporal stochastic phenomena in electronic and biological systems: A comparative review, examples and synergies

Statistical thermodynamics of residue fluctuations in native proteins.

The elastic net algorithm and protein structure prediction.

The gaussian network model: precise prediction of residue fluctuations and application to binding problems

The introduction of hydrogen bond and hydrophobicity effects into the rotational isomeric states model for conformational analysis of unfolded peptides.

Turkey must end violent response to protests

Understanding the recognition of protein structural classes by amino acid composition ⬇️

VitAL: Viterbi algorithm for de novo peptide design