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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
Sat Jan 01 2022
Journal Name
Journal Of Intelligent Systems
Trip generation modeling for a selected sector in Baghdad city using the artificial neural network
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Abstract<p>This study is planned with the aim of constructing models that can be used to forecast trip production in the Al-Karada region in Baghdad city incorporating the socioeconomic features, through the use of various statistical approaches to the modeling of trip generation, such as artificial neural network (ANN) and multiple linear regression (MLR). The research region was split into 11 zones to accomplish the study aim. Forms were issued based on the needed sample size of 1,170. Only 1,050 forms with responses were received, giving a response rate of 89.74% for the research region. The collected data were processed using the ANN technique in MATLAB v20. The same database was utilized to</p> ... Show More
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Publication Date
Fri Mar 01 2013
Journal Name
Applied Mechanics And Materials
Measure and Analyze the Problems of Concrete Mixture Production via Six Sigma DMAIC Tools: Central Concrete Mix Plant as a Case Study
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The aims of this study are to measure the defect rate and analyze the problems of production of ready concrete mixture plant by using Six Sigma methodology which is a business strategy for operations improvement depending basically on the application of its sub-methodology DMAIC improvement cycle and the basic statistical tools where the process sigma level of concrete production in the case study was 2.41 σ.

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Publication Date
Tue Jan 01 2019
Journal Name
Journal Of International Oral Health
Endothelin-1 is a surrogate biomarker link severe periodontitis and endothelial dysfunction in hypertensive patients: The potential nexus
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Aim and Objectives: The objective of this study was to illustrate the link between periodontitis (PO) and endothelial dysfunction in hypertensive patients. Materials and Methods: This cross‑sectional study involved 53 hypertensive patients with or without PO compared with 28 healthy controls. On the basis of the study protocol, the participants were divided into three groups: Group (1): 24 patients with hypertension only, Group (2): 29 patients with hypertension and PO, and Group (3): 28 healthy controls. Lipid profile, endothelin‑1 (ET‑1), and high‑sensitivity C‑reactive protein (hs‑CRP) were measured. Blood pressure and body mass index (BMI) were evaluated. Diagnostic criteria of severe PO periodontal indices including plaque

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Publication Date
Tue Dec 07 2021
Design and numerical verification of a polarization-independent grating coupler using a double-layer approach for visible wavelengths applications
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Publication Date
Sat Jul 01 2017
Journal Name
Bulletin Of The Iraq Natural History Museum (p-issn: 1017-8678 , E-issn: 2311-9799)
THE SPOTTED SANDGROUSE, PTEROCLES SENEGALLUS (LINNAEUS, 1771) AS A NEW HOST FOR THE SPIRURID NEMATODE HARTERTIA GALLINARUM (THEILER, 1919) IN IRAQ
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    In this work, the spirurid nematode Hartertia gallinarum was reported in the intestine of the spotted sandgrouse, Pterocles senegallus, collected in three different locations: Ga'ara Depression, Iraqi Western Desert, Zurbatiyah and Al-Attariyah, Middle of Iraq. Description and measurements of the nematode were given. The role of termites in the infection of P. senegallus with H. gallinarum was discussed. Occurrence of H. gallinarum in P. senegallus represents a new host record.

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Publication Date
Sat May 01 2021
Journal Name
Journal Of Physics: Conference Series
Three Weighted Residuals Methods for Solving the Nonlinear Thin Film Flow Problem
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Abstract<p>In this paper, the methods of weighted residuals: Collocation Method (CM), Least Squares Method (LSM) and Galerkin Method (GM) are used to solve the thin film flow (TFF) equation. The weighted residual methods were implemented to get an approximate solution to the TFF equation. The accuracy of the obtained results is checked by calculating the maximum error remainder functions (MER). Moreover, the outcomes were examined in comparison with the 4<sup>th</sup>-order Runge-Kutta method (RK4) and good agreements have been achieved. All the evaluations have been successfully implemented by using the computer system Mathematica®10.</p>
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Publication Date
Sat Oct 01 2016
Journal Name
Journal Of Economics And Administrative Sciences
Suggestive Framework for Applying Performance and Programs Budget in Iraqi Government Units Environment
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This research  aims to reform the Iraqi public budget through going into the challenges the budget faces in applying item-line budget in its preparation, implementation and control; which encourage extravagance and waste instead of rationalizing expenditures. This  is shown in the data analysis of Federal public budget laws in Iraq for the years from 2005 till 2013; there was a continuous increase in the aggregate public expenditures in the public budget for the years previously mentioned, as the public expenditures growth has reached into the percent 284.71% in 2013. In addition the public budget for these years (2005-2013) is being prepared with planned deficit without confirming that

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Publication Date
Sun Jun 26 2022
Journal Name
International Journal Of Corrosion And Scale Inhibition
Theoretical and experimental studies of copper(II) and nickel(II) complexes derived from the ligand N-benzyl benzimidazole as corrosion inhibitors in ionic and bacterial media
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Publication Date
Mon Jan 01 2018
Journal Name
Biochemical Cellular Archive
Immunological and molecular detection of herpes simplex virus type 1 and 2 in patients clinically diagnosed with parkinson’s disease and multiple sclerosis
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To determine the relationship between herpes simplex virus 1, 2 and neurological disorders, sixty samples from patients with neurological diseases were collected (40 patients with Multiple sclerosis and 20 patients with Parkinson’s disease) all of whom attended both the Neurological science Hospital as well as the Neuropathology consultation Department in Baghdad Hospital In Iraq. The samples were collected in the time frame between November 2017 and April 2018. The ages of the patients that were investigated were between (17-76) years and compared to a control group consisting of 25 samples collected from apparently healthy individuals. All the studied groups were subjected to the measurement of anti-HSV 1, 2 IgG antibodies by the means

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Publication Date
Mon Dec 01 2014
Journal Name
2014 Ieee Symposium On Differential Evolution (sde)
Comparative analysis of a modified differential evolution algorithm based on bacterial mutation scheme
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A new modified differential evolution algorithm DE-BEA, is proposed to improve the reliability of the standard DE/current-to-rand/1/bin by implementing a new mutation scheme inspired by the bacterial evolutionary algorithm (BEA). The crossover and the selection schemes of the DE method are also modified to fit the new DE-BEA mechanism. The new scheme diversifies the population by applying to all the individuals a segment based scheme that generates multiple copies (clones) from each individual one-by-one and applies the BEA segment-wise mechanism. These new steps are embedded in the DE/current-to-rand/bin scheme. The performance of the new algorithm has been compared with several DE variants over eighteen benchmark functions including sever

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