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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
Thu Oct 01 2020
Journal Name
Palarch's Journal Of Archaeology Of Egypt / Egyptology
"Guarantees of Disciplinary Punishment on University Service Employee and Mechanisms for their Cancellation" Comparative study
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The university Service employee is considered one of the categories of public employees, However, The academic and administrative tasks duties that undertakes have made him a special importance and a distinguished legal status, Therefore, we find That the Iraqi legislatures assigned this category a special Law, it is the university Service law No (23) of 2008 as amended who dealt with some aspects related to serving this category, such as duties, right, condition for appointment and award of academic titles, and financial allocation, such as university service allocation, academic title allocations, and some other Provisions leaving other matters to the general service laws and employee discipline, among the matters that the legislator negl

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Publication Date
Tue Aug 03 2021
Journal Name
Key Engineering Materials
Comparative Study of Structural Behavior for Asymmetrical Castellated (Concavely - Curved Soffit) Steel Beams with Different Strengthening Techniques
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The Asymmetrical Castellated concavely – curved soffit Steel Beams with RPC and Lacing Reinforcement improves compactness and local buckling (web and flange local buckling), vertical shear strength at gross section (web crippling and web yielding at the fillet), and net section ( net vertical shear strength proportioned between the top and bottom tees relative to their areas (Yielding)), horizontal shear strength in web post (Yielding), web post-buckling strength, overall beam flexure strength, tee Vierendeel bending moment and lateral-torsional buckling, as a result of steel section encasement. This study presents two concentrated loads test results for seven specimens Asymmetrical Castellated concavely – curved soffit Steel Be

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Publication Date
Tue Oct 22 2024
Journal Name
Iraqi Statisticians Journal
Inferential Methods for the Dagum Regression Model
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The Dagum Regression Model, introduced to address limitations in traditional econometric models, provides enhanced flexibility for analyzing data characterized by heavy tails and asymmetry, which is common in income and wealth distributions. This paper develops and applies the Dagum model, demonstrating its advantages over other distributions such as the Log-Normal and Gamma distributions. The model's parameters are estimated using Maximum Likelihood Estimation (MLE) and the Method of Moments (MoM). A simulation study evaluates both methods' performance across various sample sizes, showing that MoM tends to offer more robust and precise estimates, particularly in small samples. These findings provide valuable insights into the ana

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Publication Date
Tue Dec 05 2023
Journal Name
Baghdad Science Journal
Classification of Diseases in Oil Palm Leaves Using the GoogLeNet Model
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The general health of palm trees, encompassing the roots, stems, and leaves, significantly impacts palm oil production, therefore, meticulous attention is needed to achieve optimal yield. One of the challenges encountered in sustaining productive crops is the prevalence of pests and diseases afflicting oil palm plants. These diseases can detrimentally influence growth and development, leading to decreased productivity. Oil palm productivity is closely related to the conditions of its leaves, which play a vital role in photosynthesis. This research employed a comprehensive dataset of 1,230 images, consisting of 410 showing leaves, another 410 depicting bagworm infestations, and an additional 410 displaying caterpillar infestations. Furthe

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Publication Date
Fri Aug 20 2021
Journal Name
European Journal Of Molecular & Clinical Medicine
Comparative study of obesity between men and women: Review
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Obesity is disorder in a foremost nutritional health it’s developed with countries developing. Also is known as increasingin fat accumulation that lead toproblem in health, besidesmay coin one of the reasons lead toloss of life,the obesity not effect on adults just but effect onoffspringand juveniles. In some ofinhabitants the incidence of obesity is superior in female than in male; on the other hand, the variation degree of the between the genderdifferby country.Obesity is generally measured by body mass index and waist circumference, Obesity are classified according to body mass index into:Pre obesity sort 1 : (25 - 29.9) kg/m2, Obesity sort 2 : (30 - 34.9 kg/m2) and extreme obesity sort 3: (40 kg/m2) or greater. Obesity is described by

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Publication Date
Sat Jan 01 2022
Journal Name
Materials Today: Proceedings
Comparative study between the individual, dual and triple addition of (SF), (TGP) and (PVA) for improving Local Plaster of Paris (LPOP) properties
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Publication Date
Wed Apr 01 2015
Journal Name
Journal Of Economics And Administrative Sciences
Dimensions of performance to provide nursing services: a comparative analytical research in Baghdad of Rusafa Health Organization
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     This research aims to study the performance of operations to provide nursing services, which included dimensions (quality, timeliness, leadership skills, behavioral manifestations, relationships with others, problem-solving and decision-making, job performance) and its effects in nursing performance. The research to prove the value of the performance of service delivery processes dimensions by nursing staffs working in Iraqi hospitals, nursing and measuring performance. To find out the nature of nursing services, and a comparison between hospitals to measure the extent of the application dimensional among themselves, and that by relying on the dimensions of a global study, which was measu

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Publication Date
Wed Jun 15 2016
Journal Name
Iraqi National Journal Of Chemistry
Physical and Electrical Study of Different Carbone Nanomaterials as Modifying Material for SPCE
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In this work was prepared three different types of modified screen printed carbon electrode (SPCEs) with drops casted method, the used carbone nanomaterials were the MWCNT, functionalized –MWCNT (f-MWCNT) and After several experiments were made to find an appropriate ratio to make good GOT/f-MWCNT nanocomposite, and found the suspension mixture (1:1) from GOT/f-MWCNT (f-MWCNT-GOT). The electrical and physical properties were performed with cyclic voltammeter technique, and studied the maximum current response, the effective surface area, effect of the pH value and the determination of active surface area for MWCNT-SPCE , f-MWCNT-SPCE and f-MWCNT-GOT/SPCE as (0.04 cm2), (0.119 cm2) and (0.115 cm2) respectively, the surface coverage concent

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Publication Date
Tue Jun 20 2023
Journal Name
Baghdad Science Journal
Numerical Solutions for the Nonlinear PDEs of Fractional Order by Using a New Double Integral Transform with Variational Iteration Method
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This paper considers a new Double Integral transform called Double Sumudu-Elzaki transform DSET. The combining of the DSET with a semi-analytical method, namely the variational iteration method DSETVIM, to arrive numerical solution of nonlinear PDEs of Fractional Order derivatives. The proposed dual method property decreases the number of calculations required, so combining these two methods leads to calculating the solution's speed. The suggested technique is tested on four problems. The results demonstrated that solving these types of equations using the DSETVIM was more advantageous and efficient

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Publication Date
Tue Jun 20 2023
Journal Name
Baghdad Science Journal
Numerical Solutions for the Nonlinear PDEs of Fractional Order by Using a New Double Integral Transform with Variational Iteration Method
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This paper considers a new Double Integral transform called Double Sumudu-Elzaki transform DSET. The combining of the DSET with a semi-analytical method, namely the variational iteration method DSETVIM, to arrive numerical solution of nonlinear PDEs of Fractional Order derivatives. The proposed dual method property decreases the number of calculations required, so combining these two methods leads to calculating the solution's speed. The suggested technique is tested on four problems. The results demonstrated that solving these types of equations using the DSETVIM was more advantageous and efficient

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Scopus (8)
Crossref (4)
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