Now showing items 1-20 of 21

  • Applications of machine learning in classification of biological data 

    Authors:Sonlu, Aylin
    Publisher and Date:(Kadir Has University, 2018)
    Machine learning enables computers learn from the data. it has a wide range of application areas. Computational biology and bioinformatics are some areas in which machine learning applications provide accurate solutions to problems. Different types of machine learning tasks are summarized as supervised semi-supervised unsupervised and reinforcement learning. in this thesis we focus on supervised machine learning tasks on biological datasets. We applied multiple machine learning approaches to ...

  • Classification of distinct conformers of beta-2 adrenergic receptor based on binding affinity of ligands through docking studies 

    Authors:Dilcan, Gonca
    Publisher and Date:(Kadir Has University, 2017)
    ?2AR is an important drug target and plays a critical role in the relaxation of pulmonary tissues and cardiovascular physiology. We have developed a strategy for classifying various ?2AR conformers as active or inactive states based on binding mode of selected ligands with known activities. Previously distinct conformational states of the ligand’s binding pocket were obtained from a 2.8 µs MD simulation. Snapshots were clustered based on RMSD value of five key residues at the binding site. Clustering ...

  • Deep learning applications on biological data 

    Authors:Kurt, Zeynep
    Publisher and Date:(Kadir Has University, 2018)
    Biological sciences and medicine have been rapidly becoming data-intensive disciplines. Machine learning algorithms in particular deep learning methods are becoming essential tools of data analysis to facilitate our understanding of complex biological systems by extracting highly non-trivial patterns in data. The focus of this master thesis is to develop a working understanding of general deep learning approach and apply these approaches on a variety of biological and medical data classes. More ...

  • Designing inhibitors via molecular modelling methods for monoamine oxidase isozymes a and b 

    Authors:Varnalı, Filiz
    Publisher and Date:(Kadir Has University, 2012)
    in drug development studies a large number of new drug candidates (leads)have to be synthesized and optimized by changing several moieties of the leads in order to increase efficacies and decrease toxicities. Each synthesis of these new drug candidates include multi-steps procedures. -- Abstract'dan.

  • Docking study of resveratrol like molecules on histone deacetylase 

    Authors:Alnemsi, Fatma
    Publisher and Date:(Kadir Has University, 2016)
    The modulation of histone acetylation plays a pivotal role in the regulation of gene expression by governing the state of lysine residues located on the amino – terminal tails of histone proteins. A dynamic balance of histone acetylation /deacetylation is maintained by histone acetyl transferases(HAT) and histone deacetylases(HDACs) . Due to their fundamental role in gene expression HDAC family have been associated with basic cellular events and disease states such as cell growth differentiation ...

  • In silico design and modeling of coumarin derivatives as selective monoamine oxidase a inhibitors 

    Authors:Karaman, Dilara
    Publisher and Date:(Kadir Has University, 2014)
    Selective and reversible inhibition of Monoamine Oxidase (MAO) isoenzymes has an important place in treatment of various neurological disorders. Out of the two isoforms of Monoamine Oxidase enzymes inhibition of MAO-A have been giving positive results in treatment of depression and inhibition of MAO-B in cure of Parkinson’s disease. The difference in treatment is due to the fact that these two enzymes have different substrate specificities. in this study 125 different coumarin derivatives were ...

  • In silico design of selective monoamine Oxidase B inhibitors using indane ring 

    Authors:Altuntas, Serkan
    Publisher and Date:(Kadir Has University, 2013)
    in the present work 209952 analogs of an indane scaffold were created using various fragment moieties at different position of indane ring. CHEMPLP module of GOLD program is utilized in the screening process. in order to obtain additional validation of selectivity and scoring values the first 100 best selective MAO inhibitor candidates are also tested via ChemScore and ASP scoring fuctions of Gold docking software AutoDock 4.2 and AutoDock Vina. inhibition constants and their poses in the active ...

  • In silico identification of physiological substrates and inhibitors of serum paraoxonase 1 enzyme 

    Authors:Karabıyık, Talha
    Publisher and Date:(Kadir Has University, 2014)
    Paraoxonase 1 (PON1) as an important antioxidant enzyme against oxidative stress has been implicated in the pathogenesis of a number of disorders including cancer cardiovascular and several other diseases. Although there has been considerable progress in understanding the PON1 enzyme its precise physiological substrate and function still remain inconclusive. Discovery of new PON1 substrates or inhibitors will provide better understanding of PON1’s cardiovascular protective and antioxidant effects. ...

  • In Silico Inhibitor Design For Monomine Oxidase A And B Isozymes 

    Authors:Mıdık, Çağla
    Publisher and Date:(Kadir Has University, 2012)
    in this thesis study MAO-A and MAO-B isozymes are selected as target enzymes that have important role of regulation of diseases such as ..Parkinson Alzheimer and depression... MAO isozymes which catalyze the oxidation of monoamines in the body stand out in these diseases. Today explicitly known that MAO enzymes oxidize the neurological amines such as serotonine dopamine neuroadrenaline more than usual way and result in the reduction of the level of these important monoamines creating disease state. ...

  • In silico screening of neuronal nitric oxide synthase enzyme inhibitors 

    Authors:Örtmen, Bahanur
    Publisher and Date:(Kadir Has University, 2014)
    Three closely related isoforms of nitric oxide synthases (NOS) catalyze an important secondary messenger nitric oxide (NO) synthesis through oxidation of L-arginine to L-citrulline. These three NOS isoforms takes parts in different tissues for various physiological and pathological processes. Neuronal NOS (nNOS) produce NO in central and peripheral nervous system endothelial NOS (eNOS) plays role in endothelial cells and NO in macrophage cells is produced by inducible NOS (iNOS). Excessive NO ...

  • In silico screening of tangible-potential inhibitor of methionine aminopeptidase 2 for the treatment of cancer 

    Authors:Weako, Jackson
    Publisher and Date:(Kadir Has University, 2017)
    Methionine Aminopeptidases (MetAPs) are divalent-cofactor dependent enzymes that are responsible for cleaving the initiator Methionine from the newly synthesized polypeptides. These metalloproteases are classified into two distinct isoforms- MetAP1 and MetAP2. The MetAP2 isoform is upregulated in many cancerous cells. A selective inhibition of MetAP2 is an effective means of suppressing vascularization and limiting both the size and metastasis of solid tumors in a model organism. A selective and ...

  • Loop modeling and molecular dynamics simulations of apo and ligand-bound human glun1-hlun2A nmda type receptors 

    Authors:Aktolun, Muhammed
    Publisher and Date:(Kadir Has University, 2017)
    N-Methyl-D-Aspartate receptors (NMDARs) are glutamate-gated ion channels found in the nerve cell membranes. The functioning of the receptor is of crucial importance in consciousness and normal brain functions. As a result of overexcitation of NMDARs neuronal death occurs and may lead to diseases such as epilepsy stroke Alzheimer's and Parkinson's. Understanding the molecular mechanism and structure function relationships of the receptor might lead to discovery of new drug target mechanisms. Recently ...

  • Molacilar Dynamics Studies oh human dat and its natural ligand dopamine 

    Authors:Demirci, Seda
    Publisher and Date:(Kadir Has University, 2012)
    The dopamine transporter (DAT) which is a member of Neurotransmitter sodium symporters (NSSs) family takes place in dopaminergic neurotransmission. Therefore it is a major molecular target for numerous drugs including the widely abused psychostimulants cocaine and amphetamine as well as antidepressants. in this study to understand the dynamics behavior of structure-function relationship of the human dopamine transporter (DAT) we performed MD studies. The dopamine DAT interactions were investigated ...

  • Pharmacophore- based screening and docking for the discovery of novel antagonists of Beta-2 adrenergic receptor 

    Authors:Yakar, Rüya
    Publisher and Date:(Kadir Has University, 2013)
    ß2AR which is the member of rhodopsin-like GPCR is the target system for the discovery of novel antagonists using structure-based pharmacophore modeling and docking methods. initially a shared pharmacophore model is obtained using the structure of five known inactive ß2AR complex (PDB ids: 2HR1 3D4S 3NY8 3NY9 and 3NYA). in order to test the discriminatory power of pharmacophore model a small database consisting of 117 known molecules (53 antagonists against 64 agonists) was screened using LigandScout ...

  • Potent inhibitors designed for methionine aminopeptidase II using pharmocophore modeling 

    Authors:Al Bayati, Safanah A.
    Publisher and Date:(Kadir Has University, 2019)
    Methionine Aminopeptidase (Metap2) is a metalloenzyme that is responsible of removing of the N-terminal of newly synthesized protein. The inhibition of the enzyme was found to be crucial in diminishing tumor's nourishment, growth, and metastasis. It is directly related to incurable diseases such as Cancer, Rheumatoid Arthritis, etc. Over the year, different compounds were developed to inhibit that enzyme. Fumagillin, a natural irreversible inhibitor of MetAP2 and its derivatives, has been showing ...

  • The prediction of 3d structure of the dimeric state of human β2-adrenergic receptor 

    Authors:Koroğlu, Ayça
    Publisher and Date:(Kadir Has University, 2016)
    A significant amount of experimental and computational data points out a possible role of TM6 in the dimerization of ?2-adrenergic receptor (?2AR). Peptide– and protein–protein docking experiments guided by this assumption were conducted in order to confirm the potential participation of TM6 at the interface region of ?2AR dimers. Firstly a derived peptide consisting of 23 residues of TM6 was blindly docked to ?2AR monomer using a rigid body approach. The resulting complexes in which the peptide ...

  • Sonsuz Uzay : Invisible woman in the man's world 

    Authors:Eletreby, Sahar
    Publisher and Date:(Kadir Has University, 2017)
    Bu tezde başlangıç noktam, feminist film teorisyenlerinin kadının sinemada nasıl temsil edildiği ve kadın hakları gerçekliğinin filmlere nasıl yansıtıldığıyla ilgili çalışmaları oldu. Buradan hareketle tezimde, geçmiş yüzyıllardan günümüze sinemada kadın gerçekliğinin nasıl temsil edildiğini tartıştım. Hollywood sinemasının Western türünden ve Orta Doğu Sinemasının Mısır filmlerinden örnekler vererek, sinemanın bu konuda ne denli haklı olduğunu ve sosyal olarak filmler ve gerçeklik arasında nasıl ...

  • Structural studies of nmda receptor and xanthine oxidase enzyme 

    Authors:Gencel, Melis
    Publisher and Date:(Kadir Has University, 2019)
    The first part of the thesis deals with the structural studies of N-Methyl-D-Aspartate receptors (NMDARs). NMDARs are ionotropic ligand-gated receptors that have pivotal roles at the central neuronal system but hyperactivity of NMDARs could contribute to neurodegenerative diseases. Therefore understanding the activation mechanism of NMDARs is important as it may lead to the development of new treatments for neurodegenerative diseases. in this thesis human GluN1/GluN2A type NMDAR is modeled based ...

  • Structural studies of nmda receptor and xanthine oxidase enzyme 

    Authors:Gencel, Melis
    Publisher and Date:(Kadir Has University, 2019)
    The first part of the thesis deals with the structural studies of N-Methyl-D-Aspartate receptors (NMDARs). NMDARs are ionotropic ligand-gated receptors that have pivotal roles at the central neuronal system but, hyperactivity of NMDARs could contribute to neurodegenerative diseases. Therefore, understanding the activation mechanism of NMDARs is important as it may lead to the development of new treatments for neurodegenerative diseases. In this thesis, human GluN1/GluN2A type NMDAR is modeled ...

  • Structural study of gaba type a receptor : the effect of intrasubunit disulphide bridges on dynamics 

    Authors:Ayan, Meral
    Publisher and Date:(Kadir Has University, 2014)
    In the mammalian brain the gamma-aminobutyric acid type A receptor is the most commonly expressed subtype of receptor family. Although there is a rich pharmacological activity of R, specific molecular features are still not well known. In this study, we developed a new homology model based on a recently available X-Ray structure of the glutamate-gated chloride channel. When it is compared with previous homology models of the based on lower sequence identity templates, there are three additional ...