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A Comparative Study for the Accuracy of Three Molecular Docking Programs Using HIV-1 Protease Inhibitors as a Model
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Flexible molecular docking is a computational method of structure-based drug design to evaluate binding interactions between receptor and ligand and identify the ligand conformation within the receptor pocket. Currently, various molecular docking programs are extensively applied; therefore, realizing accuracy and performance of the various docking programs could have a significant value. In this comparative study, the performance and accuracy of three widely used non-commercial docking software (AutoDock Vina, 1-Click Docking, and UCSF DOCK) was evaluated through investigations of the predicted binding affinity and binding conformation of the same set of small molecules (HIV-1 protease inhibitors) and a protein target HIV-1 protease enzyme. The tested sets are composed of eight receptor-ligand complexes with high resolution crystal structures downloaded from Protein Data Bank website. Molecular dockings were applied between approved HIV-1 protease inhibitors and the HIV-1 protease using AutoDock Vina, 1-Click Docking, and DOCK6. Then, docking poses of the top-ranked solution was realized using UCSF Chimera. Furthermore, Pearson correlation coefficient (r) and coefficient of determination (r2) between the experimental results and the top scored docking results of each program were calculated using Graphpad prism V9.2. After comparing saquinavir top scored binding poses of each docking program with the crystal structure, various conformational changes were observed. Moreover, according to the relative comparison between the top ranked calculated ?Gbinding values against the experimental results, r2 value of AutoDock Vina, 1-Click Docking, and DOCK6 were 0.65, 0.41, and 0.005, respectively. The outcome of this study shows that the top scored binding free energy could not produce the best pose prediction. In addition, AutoDock Vina results have the highest correlation with the experimental results.

 

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Publication Date
Tue Jun 01 2021
Journal Name
Journal Of Engineering
Designing a Secure Software-Defined Radio Transceiver using the Logistic Map
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The need to exchange large amounts of real-time data is constantly increasing in wireless communication. While traditional radio transceivers are not cost-effective and their components should be integrated, software-defined radio (SDR) ones have opened up a new class of wireless technologies with high security.  This study aims to design an  SDR  transceiver was built using one type of modulation, which is 16 QAM, and adding a  security subsystem using one type of chaos map, which is a  logistic map, because it is a very simple nonlinear dynamical equations that generate a random key and  EXCLUSIVE  OR with the originally transmitted data to protect data through the transmission. At th

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Publication Date
Thu Jun 01 2023
Journal Name
International Journal Of Agricultural And Statistical Sciences
Forecasting the Saudi Crude Oil Price Using MS-GARCH Model
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Publication Date
Thu Apr 30 2020
Journal Name
Journal Of Economics And Administrative Sciences
Estimate the Partial Linear Model Using Wavelet and Kernel Smoothers
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This article aims to estimate the partially linear model by using two methods, which are the Wavelet and Kernel Smoothers. Simulation experiments are used to study the small sample behavior depending on different functions, sample sizes, and variances. Results explained that the wavelet smoother is the best depending on the mean average squares error criterion for all cases that used.

 

 

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Publication Date
Sun Jun 03 2012
Journal Name
Baghdad Science Journal
A Biochemical Study for Evaluation and Analysis of Serum Protein of Patients with Different Kidney Tumors
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The amount of protein in the serum depends on the balance between the rate of its synthesis, and that of its catabolism or loss. Abnormal metabolism may result from nutritional deficiency, enzyme deficiency, abnormal secretion of hormones, or the actions of drugs and toxins. Renal cancer is the third most common malignancy of the genitourinary system, and accounts for 3% of adult malignancies globally. Total serum proteins were measured in malignant kidney tumor, benign kidney tumors, and non tumoral kidney diseases patient groups, as well as in healthy individuals. A significant decrease (p< 0.001) of total serum protein levels in patients with malignant kidney tumors when compared with those of benign tumors, non tumoral diseases, and hea

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Publication Date
Mon Oct 01 2018
Journal Name
Journal Of Economics And Administrative Sciences
measure the relationship between imported inflation and foreign trade in the Iraqi economy for long 1990-2015 using model nardl
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The study aims to discuss the relation between imported inflation and international trade of Iraqi economy for the period (1990-2015) by using annual data. To achieve the study aim, statistical and Econometrics methods are used through NARDL model to explain non-linear relation because it’s a model assigned to measure non-linear relations and as we know most economic relations are non-linear, beside explaining positive and negative effects of imported inflation, and to reach the research aim deductive approach was adopted through using descriptive method to describe and determine phenomenon. Beside the inductive approach by g statistical and standard tools to get the standard model explains the

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Publication Date
Sun Dec 01 2024
Journal Name
Journal Of Economics And Administrative Sciences
Nadaraya-Watson Estimation of a Circular Regression Model on Peak Systolic Blood Pressure Data
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Purpose: The research aims to estimate models representing phenomena that follow the logic of circular (angular) data, accounting for the 24-hour periodicity in measurement. Theoretical framework: The regression model is developed to account for the periodic nature of the circular scale, considering the periodicity in the dependent variable y, the explanatory variables x, or both. Design/methodology/approach: Two estimation methods were applied: a parametric model, represented by the Simple Circular Regression (SCR) model, and a nonparametric model, represented by the Nadaraya-Watson Circular Regression (NW) model. The analysis used real data from 50 patients at Al-Kindi Teaching Hospital in Baghdad. Findings: The Mean Circular Erro

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Publication Date
Mon Feb 01 2021
Journal Name
Iop Conference Series: Materials Science And Engineering
On modelling and adaptive control of a linear smart beam model interacting with fluid
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Abstract<p>This paper deals with modelling and control of Euler-Bernoulli smart beam interacting with a fluid medium. Several distributed piezo-patches (actuators and/or sensors) are bonded on the surface of the target beam. To model the vibrating beam properly, the effect of the piezo-patches and the hydrodynamic loads should be taken into account carefully. The partial differential equation PDE for the target oscillating beam is derived considering the piezo-actuators as input controls. Fluid forces are decomposed into two components: 1) hydrodynamic forces due to the beam oscillations, and 2) external (disturbance) hydrodynamic loads independent of beam motion. Then the PDE is discretized usi</p> ... Show More
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Publication Date
Sun Sep 01 2019
Journal Name
Baghdad Science Journal
An Analysis of a Partial Temporary Immunity SIR Epidemic Model with Nonlinear Treatment Rate
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     A partial temporary immunity SIR epidemic model involv nonlinear treatment rate is proposed and studied. The basic reproduction number  is determined. The local and global stability of all equilibria of the model are analyzed. The conditions for occurrence of local bifurcation in the proposed epidemic model are established. Finally, numerical simulation is used to confirm our obtained analytical results and specify the control set of parameters that affect the dynamics of the model.

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Publication Date
Mon Nov 06 2023
Journal Name
Communications In Mathematical Biology And Neuroscience
Effect of hunting cooperation and fear in a food chain model with intraspecific competition
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Taking into account the significance of food chains in the environment, it demonstrates the interdependence of all living things and has economic implications for people. Hunting cooperation, fear, and intraspecific competition are all included in a food chain model that has been developed and researched. The study tries to comprehend how these elements affect the behavior of species along the food chain. We first examined the suggested model's solution properties before calculating every potential equilibrium point and examining the stability and bifurcation nearby. We have identified the factors that guarantee the global stability of the positive equilibrium point using the geometric approach. Additionally, the circumstances that would gu

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Publication Date
Sat Sep 30 2023
Journal Name
Journal Of Accounting And Financial Studies ( Jafs )
A model of a proposed audit program to audit the strategies of municipal institutions and its impact on achieving sustainable development: An applied research in the municipal institutions of Karbala Governorate
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Abstract

                  The study aimed to prepare a practical guide for procedures for auditing the strategies of municipal institutions in achieving sustainable development by adopting the idea of ​​the audit matrix through which a classified report is prepared according to the dimensions of sustainable development, by preparing a specialized audit program for the purpose of auditing strategies for achieving sustainable development and emptying the results of the application of each of the paragraphs The program in the audit matrix that was prepared for the purpose of determining the impact of each observation and linkin

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