30 hasil untuk "Burak Erman"
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Prediction of Optimal Folding Routes of Proteins That Satisfy the Principle of Lowest Entropy Loss: Dynamic Contact Maps and Optimal Control
An optimization model is introduced in which proteins try to evade high energy regions of the folding landscape, and prefer low entropy loss routes during folding. We make use of the framework of optimal control whose convenient solution provides practical and useful insight into the sequence of…
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Identification of Ligand Binding Sites of Proteins Using the Gaussian Network Model
The nonlocal nature of the protein-ligand binding problem is investigated via the Gaussian Network Model with which the residues lying along interaction pathways in a protein and the residues at the binding site are predicted. The predictions of the binding site residues are verified by using…
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Entropy Transfer between Residue Pairs and Allostery in Proteins: Quantifying Allosteric Communication in Ubiquitin
It has recently been proposed by Gunasakaran et al. that allostery may be an intrinsic property of all proteins. Here, we develop a computational method that can determine and quantify allosteric activity in any given protein. Based on Schreiber's transfer entropy formulation, our approach leads to…
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Engineering molecular machines
Biological molecular motors use chemical energy, mostly in the form of ATP hydrolysis, and convert it to mechanical energy. Correlated thermal fluctuations are essential for the function of a molecular machine and it is the hydrolysis of ATP that modifies the correlated fluctuations of the system…
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Predicting Important Residues and Interaction Pathways in Proteins Using Gaussian Network Model: Binding and Stability of HLA Proteins
A statistical thermodynamics approach is proposed to determine structurally and functionally important residues in native proteins that are involved in energy exchange with a ligand and other residues along an interaction pathway. The structure-function relationships, ligand binding and allosteric…
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VitAL: Viterbi Algorithm for de novo Peptide Design
Background: Drug design against proteins to cure various diseases has been studied for several years. Numerous design techniques were discovered for small organic molecules for specific protein targets. The specificity, toxicity and selectivity of small molecules are hard problems to solve. The use…
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A Comparative Molecular Dynamics Study of Methylation State Specificity of JMJD2A
Histone modifications have great importance in epigenetic regulation. JMJD2A is a histone demethylase which is selective for di- and trimethyl forms of residues Lys9 and Lys36 of Histone 3 tail (H3K9 and H3K36). We present a molecular dynamics simulations of mono-, di- and trimethylated histone…
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Molecular Recognition of H3/H4 Histone Tails by the Tudor Domains of JMJD2A: A Comparative Molecular Dynamics Simulations Study
Background: Histone demethylase, JMJD2A, specifically recognizes and binds to methylated lysine residues at histone H3 and H4 tails (especially trimethylated H3K4 (H3K4me3), trimethylated H3K9 (H3K9me3) and di,trimethylated H4K20 (H4K20me2, H4K20me3)) via its tandem tudor domains. Crystal…
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Regulation of ryanodine receptor RyR2 by protein-protein interactions: prediction of a PKA binding site on the N-terminal domain of RyR2 and its relation to disease causing mutations [v1; ref status: indexed, http://f1000r.es/4tw]
Protein-protein interactions are the key processes responsible for signaling and function in complex networks. Determining the correct binding partners and predicting the ligand binding sites in the absence of experimental data require predictive models. Hybrid models that combine quantitative…
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Comparative effects of oncogenic mutations G12C, G12V, G13D, and Q61H on local conformations and dynamics of K-Ras
K-Ras is the most frequently mutated protein in human cancers. However, until very recently, its oncogenic mutants were viewed as undruggable. To develop inhibitors that directly target oncogenic K-Ras mutants, we need to understand both their mutant-specific and pan-mutant dynamics and…
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The effects of social media news that users trusted and verified on anxiety level and disease control perception in COVID-19 Pandemic (eng)
INTRODUCTION[|]Since the beginning of the pandemic, social media users have been bombarded with news about the number of cases and deaths, virus origin, vaccine development process, symptoms, transmission ways, prevention and treatment methods of COVID-19. This study was planned considering that…
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Adverse Neuropsychiatric Events Associated with Varenicline: A Case Series
Varenicline is an orally administered α4β2 nicotinic acetylcholine (Ach) receptor, partial agonist. This drug has been known to be more effective in the treatment of nicotine withdrawal than bupropion and nicotine replacement therapies. Besides this effectiveness, it has some systemic and…
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The effect of alcoholics anonymous group participation on flourishing in Turkey: the mediating role of hope and social support
BACKGROUND: Alcohol use disorder (AUD) is a significant public health issue that negatively impacts individuals’ flourishing, social relationships, and life satisfaction. In recent years, the concept of recovery has been approached as encompassing not only the reduction or cessation of alcohol use…