8 hasil untuk "Burak Erman"
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Artikel Jurnal Teks lengkap
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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Artikel Jurnal Teks lengkap
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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Artikel Jurnal Teks lengkap
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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Artikel Jurnal Teks lengkap
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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Artikel Jurnal Teks lengkap
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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Artikel Jurnal Teks lengkap
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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Artikel Jurnal Teks lengkap
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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Artikel Jurnal Teks lengkap
Targeting mitochondrial DNA polymerase gamma for selective inhibition of MLH1 deficient colon cancer growth
Synthetic lethality in DNA repair pathways is an important strategy for the selective treatment of cancer cells without harming healthy cells and developing cancer-specific drugs. The synthetic lethal interaction between the mismatch repair (MMR) protein, MutL homolog 1 (MLH1), and the…