Yaman Arkun
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Explore the profile of Yaman Arkun including associated specialties, affiliations and a list of published articles.
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10
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83
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Recent Articles
1.
Arkun Y
BMC Bioinformatics
. 2019 Nov;
20(1):615.
PMID: 31779580
Background: Bistability and ability to switch between two stable states is the hallmark of cellular responses. Cellular signaling pathways often contain bistable switches that regulate the transmission of the extracellular...
2.
Arkun Y, Yasemi M
PLoS One
. 2018 Apr;
13(4):e0195513.
PMID: 29630631
Cell signaling is the process by which extracellular information is transmitted into the cell to perform useful biological functions. The ERK (extracellular-signal-regulated kinase) signaling controls several cellular processes such as...
3.
Arkun Y
PLoS One
. 2016 Mar;
11(3):e0149684.
PMID: 26930065
Feedback loops play a key role in the regulation of the complex interactions in signal transduction networks. By studying the network of interactions among the biomolecules present in signaling pathways...
4.
Cizmeci D, Arkun Y
PLoS One
. 2014 Jan;
8(12):e83640.
PMID: 24400038
The cross-talk between insulin and angiotensin II signalling pathways plays a significant role in the co-occurrence of diabetes and hypertension. We developed a mathematical model of the system of interactions...
5.
Arkun Y, Gur M
PLoS One
. 2012 Jan;
7(1):e29628.
PMID: 22238629
A new method to develop low-energy folding routes for proteins is presented. The novel aspect of the proposed approach is the synergistic use of optimal control theory with Molecular Dynamics...
6.
Arkun Y, Erman B
PLoS One
. 2010 Oct;
5(10):e13275.
PMID: 20967269
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...
7.
Baday S, Erman B, Arkun Y
Phys Chem Chem Phys
. 2009 Mar;
11(12):1949-61.
PMID: 19280006
Interaction forces among residue pairs are determined from optimum folding pathways along which a protein represented as a coarse-grained chain of alpha-carbons goes from different initial configurations to a known...
8.
Senturk S, Baday S, Arkun Y, Erman B
Phys Biol
. 2008 Jan;
4(4):305-16.
PMID: 18185008
The folding of a protein is studied as it grows residue by residue from the N-terminus and enters an environment that stabilizes the folded state. This mode of folding of...
9.
Guner U, Arkun Y, Erman B
J Chem Phys
. 2006 Apr;
124(13):134911.
PMID: 16613481
We develop a dynamic optimization technique for determining optimum folding pathways of proteins starting from different initial configurations. A coarse-grained Go model is used. Forces acting on each bead are...
10.
Palazoglu A, Gursoy A, Arkun Y, Erman B
J Comput Biol
. 2005 Jan;
11(6):1149-68.
PMID: 15662203
Several trajectories starting from random configurations and ending in the native state for chymotrypsin inhibitor 2, CI2, are generated using a Go-type model where the backbone torsional angles execute random...