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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 Aug 01 2019
Journal Name
Journal Of Economics And Administrative Sciences
Diversity of Management Practices of Human Resources and their Impact on Entrepreneurship in Universities: A Field Study in Public Jordanian Universities
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The purpose of this study is to examine the effect of human resource diversity management practices on achieving entrepreneurship in Jordanian public universities. To achieve the aims of the study, a well-designed questionnaire was used for collecting data. The population of the study was (7433) faculty members (including different ranks such as professors, associate professors, assistant professors and lecturers) in Jordanian public universities. The study sample was selected through the use of a random sample, the questionnaire is distributed to a sample (of 400 with the percentage of 5%) selected by using a random sampling (350) copies of the questionnaire were collected, reaching about (87.5%) out of the sum total of the dist

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Publication Date
Mon Sep 30 2024
Journal Name
South Eastern European Journal Of Public Health
Antimicrobial Efficacy of a Novel Herbal Endodontic Irrigant Against Enterococcus Faecalis in Root Canals of Permanent Teeth: An in Vitro Study
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Background: A successful endodontic treatment is aimed at the sterilization of the entire pulp space. The use of extracts from Rhamnus prinoides as a novel irrigating material for root canal has not been studied . Hence, the antimicrobial efficacy of the alcoholic extract of Rhamnus prinoides as an irrigation material against E. faecalis was evaluated in comparison with the 2.5% sodium hypochlorite (NaOCL) solution used for root canals of permanent teeth. Methods: A total of 30 single-rooted human permanent teeth were thoroughly cleaned, shaped, and disinfected. Then, each tooth was subjected to a two-week infection with Enterococcus faecalis at 37 °C . Afterward, the samples were divided into three groups (10 teeth per group): 0.9

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Publication Date
Fri Jan 01 2021
Journal Name
Journal Of Engineering
Experimental Study of Electrical and Thermal Efficiencies of a Photovoltaic Thermal (PVT) Hybrid Solar Water Collector with and Without Glass Cover
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Investigating the thermal and electrical gains and efficiencies influence the designed photovoltaic thermal hybrid collector (PVT) under different weather conditions. The designed system was manufactured by attaching a fabricated cooling system made of serpentine tubes to a single PV panel and connecting it to an automatic controlling system for measuring, monitoring, and simultaneously collecting the required data. A removable glass cover had been used to study the effects of glazed and unglazed PVT panel situations. The research was conducted in February (winter) and July (summer), and March for daily solar radiation effects on efficiencies. The results indicated that electrical and thermal gains increased by the incre

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Publication Date
Wed Dec 25 2019
Journal Name
Journal Of Accounting And Financial Studies ( Jafs )
The Problem of International Finance and Efficiency of Local Savings in Financing for Development in Algeria: Standard study for the period (1970-2014)
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      The aim of this study is to investigate the nature of the relationship between domestic savings and domestic investment, or rather the efficiency of domestic savings in financing development in Algeria, in order to explain this relationship, identify the challenges to investment, and finance and accelerate economic growth. The economic measurement methodology has estimated the relationship between the savings rate and the local investment rate in the Algerian economy. We have annual data for the period 1970-2014. One of the most important conclusions is that there is no relationship between savings and investment, nor even an integration between them. To illustrate this, the use of some statistical tools, a

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Publication Date
Wed Feb 01 2017
Journal Name
Journal Of Controlled Release
Surface engineering tumor cells with adjuvant-loaded particles for use as cancer vaccines
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Publication Date
Fri Aug 28 2020
Journal Name
Tropical Journal Of Natural Product Research
Red Cell Distribution Width and Neutrophil-Lymphocyte Ratio as Markers for Diabetic Nephropathy
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Diabetic nephropathy (DN) is the foremost cause of end-stage renal disease. Early detection of DN can spare diabetic patients of severe complications. This study aimed to evaluate the diagnostic value of red cell distribution width (RDW) and neutrophil-lymphocyte ratio (NLR) in the detection of DN in patients with type 2 diabetes mellitus (T2DM). This cross-sectional study included a total of 130 patients with T2DM, already diagnosed with T2DM. The albumin creatinine ratio (ACR) in urine samples was calculated for each patient, according to which patients were divided into two groups: with evidence of DN when ACR ? 30 mg/g, and those with no evidence of DN when ACR < 30 mg/g. According to multivariate analysis, each of disease duration (OR

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Publication Date
Mon Aug 01 2022
Journal Name
Monatshefte Für Chemie - Chemical Monthly
Al-, Ga-, and In-decorated BP nanotubes as chemical sensors for 2-chloroethanol
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B3LYP density functional is utilized for probing the effect of decorating Al, Ga, and In on the sensing performance of a boron phosphide nanotube (BPNT) in detecting the 2-chloroethanol (CHE) molecule. We predict that the interaction of pure BPNT with CHE is physisorption, and the sensing response (SR) of BPNT is approximately 6.3. The adsorption energy of CHE is about − 26.3 to − 91.1, − 96.6, and − 100.3 kJ/mol, when the Al, Ga, and In metals are decorated on the BPNT surface, respectively. This indicates that the decorated metals significantly strength the interaction. Also, the corresponding SR meaningfully rises to 19.4, 41.0, and 93.4, indicating that by increasing the atomic number of metals, the sensitivity i

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Publication Date
Wed Jun 28 2023
Journal Name
The Iraqi Journal Of Veterinary Medicine
Hematological Parameters as Indicators for Litter size and Pregnancy Stage in Awassi ‎Ewes
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Physiological status and litter size can indeed have a significant impact on ewes' ‎hematological parameters, which are essential indicators of their health. Therefore, this study ‎examined the hematological profiles of ewes during pregnancy with single and twins in the ‎Awassi ewes. The present study involved 232 ewes in good health and at sexual maturity. ‎Among them, 123 ewes had single pregnancies, while 109 ewes had twin pregnancies. The age ‎range of the ewes included in the study was between 3.5 and 4.5 years. Hematological tests ‎were conducted on the sheep's blood samples promptly following collection. The findings ‎demonstrated variations in hematological parameters among pregnant

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Publication Date
Mon Apr 01 2013
Journal Name
International Journal Of Drug Development And Research
Therapeutic potential effects of pyridoxine and /or ascorbic acid on microalbuminuria in diabetes mellitus patient's: A randomized controlled clinical study
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Objectives: This study aimed to evaluate the therapeutic potential effects of ascorbic acid or and pyridoxine on diabetic renal microalbumiuria. Methods: This was a cross-sectional study on patients with diabetes mellitus at Al-Yarmouk teaching hospital from January to December 2012, Iraq-Baghdad. Twenty one patients with diabetes mellitus (D.M), 8 IDDM and 13 IDDM were selected from, the duration of disease were ranged from 2-12 years for both type (10 females and 11males) and all enrolled patients ages were ranged from 28-65years. The concentration of total protein in urine was calculated by a biuret colorimetric assay and the urine creatinine level was measured by a modified Jaffe test. Statistical analysis: results are expressed as mean

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Publication Date
Sun Dec 06 2015
Journal Name
Baghdad Science Journal
A Qualitative Study of Epiphytic Algae (Diatom) on Some Aquatic Plants in Al-Auda Marshes Within Maysan Province / Southern Iraq
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The study conducted on the compositions of epiphytic diatoms on three taxa of aquatic plants were selected (Phragmites australis Trin ex stand , Ceratophyllum demersum L. and Typha domengensis Pers) in three sites within Al-Auda Marsh, from autumn 2013 to summer 2014 . The study was measured physical and chemical factors of all the study sites, such as: air temperature, power of hydrogen (pH), electrical conductivity (EC), salinity (S‰), total hardness(TH), dissolved oxygen (DO), and plant nutrient. The results showed that water of marsh was oxygenated and it was very hard. A total of 111 taxa of phytoplankton were identified, which belonged to 13 families and 26 genus (one family and two genus of centric diatoms, 12 families and 26 ge

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