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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
Mon Dec 14 2020
Journal Name
Plos One
Healthy lifestyle behaviors are major predictors of mental wellbeing during COVID-19 pandemic confinement: A study on adult Arabs in higher educational institutions
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Background

In the past infectious diseases affected the quality of lifestyle during home confinement. The study conducted examines the influence of home confinement during the COVID-19 pandemic outbreak on lifestyle, mental wellbeing, nutritional status, and sleeping pattern.

Method

An online multicategorical questionnaire was distributed to collect demographic information combined with the following tools: Food Frequency Questionnaire (FFQ), International Physical Activity Questionnaire (IPAQ), WHO-5 wellbeing score, and Pittsburgh Sleep Quality Index (PSQI). A snowball non-discriminate sampling procedure was

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Publication Date
Mon Dec 13 2021
Journal Name
International Journal Of Reproductive Biomedicine (ijrm)
Differences in perinatal outcomes in teenage mothers with their first and third pregnancies and predictors of adverse neonatal events: A cross-sectional study
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Background: Repeated teenage pregnancy is a major burden on the healthcare system worldwide. Objective: We aimed to compare teenagers with their first and third pregnancies and to evaluate the likelihood of neonatal complications. Materials and Methods: This cross-sectional study was performed on female teenagers (aged ≤ 19 yr) with singleton pregnancies. The subjects (n = 298) were screened over 12 months. Ninety-six women were excluded, based on the exclusion criteria. The remaining subjects (n = 202) were divided into two groups: teenagers with first pregnancy (n = 96) and teenagers with third pregnancy (n = 47). The subjects were observed throughout pregnancy and delivery. The final sample size of the first and thi

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Publication Date
Mon Nov 09 2015
Journal Name
Iraqi Journal Of Market Research And Consumer Protection
The effect of different thermal treatments and pH on the stability of a glycyrrhizin which Product from the licorice plant, Glycyrrhiza glabra L: The effect of different thermal treatments and pH on the stability of a glycyrrhizin which Product from the licorice plant, Glycyrrhiza glabra L
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The plant licorice is considered important plants as nutritionally and medically and economically, as a rich in phytochemical, vitamins and minerals, and being widely available, Research indicated the presence of many nutrients such as (proteins, Carbohydrates, vitamins and minerals) as well as presence of Glycyrrhizin which responsible of sweet taste, that allowing the possibility to use it as natural intensity sweetener with few calories in Sweetening of many food. This research is aimed to study the Stability of Glycyrrhizin toward the various manufacturing conditions such as (thermal treatment, pH of foods and microwaves), so three factorial experiments was implemented to find out the Stability as following: 100C° - 121C° - Microwa

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Publication Date
Thu Apr 03 2025
Journal Name
Aip Conference Proceedings
Determining the Optimum Reference Orbits Using Lagrange’s Series for Geocentric Satellite in Low Earth Orbit
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The Taylor series is defined by the f and g series. The solution to the satellite's equation of motion is expanding to generate Taylor series through the coefficients f and g. In this study, the orbit equation in a perifocal system is solved using the Taylor series, which is based on time changing. A program in matlab is designed to apply the results for a geocentric satellite in low orbit (height from perigee, hp= 622 km). The input parameters were the initial distance from perigee, the initial time, eccentricity, true anomaly, position, and finally the velocity. The output parameters were the final distance from perigee and the final time values. The results of radial distance as opposed to time were plotted for dissimilar times in

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Publication Date
Sun Mar 07 2010
Journal Name
Baghdad Science Journal
Determination the concentration for uranium in phosphrous fertilizers by using nuclear track detector CR-39
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The aim of this research was to study the concentrations of Uranium in the phosphorus fertilizers using Nuclear track detector (CR-39). Our present investigation is based on the study of 10 types samples for different kinds of phosphorus fertilizers which were available in the local market Some of them were Iraqi made and the others from different countries like, (Iran, Italy, Holland, Lebanon and Jordan) .. The result obtained shows that the Uranium concentration in phosphorus fertilizers samples varies from (3.59ppm) to(2.59ppm). Based on the radioactive concentration of Uranium in the samples all the results obtained between(3.59ppm) in the Iraqi super phosphate to (2.59ppm) in the mixture Iraqi phosphate fertilizer are withi

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Publication Date
Tue Aug 01 2023
Journal Name
Iop Conference Series: Earth And Environmental Science
Modis Satellite Data Evaluation for Detecting the Dust Storm Using Remote Sensing Techniques Over Iraq
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Abstract<p>The phenomena of Dust storm take place in barren and dry regions all over the world. It may cause by intense ground winds which excite the dust and sand from soft, arid land surfaces resulting it to rise up in the air. These phenomena may cause harmful influences upon health, climate, infrastructure, and transportation. GIS and remote sensing have played a key role in studying dust detection. This study was conducted in Iraq with the objective of validating dust detection. These techniques have been used to derive dust indices using Normalized Difference Dust Index (NDDI) and Middle East Dust Index (MEDI), which are based on images from MODIS and in-situ observation based on hourly wi</p> ... Show More
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Publication Date
Fri Apr 14 2017
Journal Name
Mechanical Engineering
Testing a Locally Assembled Combine Implement Used for Open Furrow, Planting and Fertilizing under Different Machinery Unit Speeds
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Publication Date
Fri Oct 01 2021
Journal Name
International Journal Of Mechanical Engineering And Robotics Research
Proportional-Derivative PD Vibration Control with Adaptive Approximation Compensator for a Nonlinear Smart Thin Beam Interacting with Fluid
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This work is concerned with the vibration attenuation of a smart beam interacting with fluid using proportional-derivative PD control and adaptive approximation compensator AAC. The role of the AAC is to improve the PD performance by compensating for unmodelled dynamics using the concept of function approximation technique FAT. The key idea is to represent the unknown parameters using the weighting coefficient and basis function matrices/vectors. The weighting coefficient vector is updated using Lyapunov theory. This controller is applied to a flexible beam provided with surface bonded piezo-patches while the vibrating beam system is submerged in a fluid. Two main effects are considered: 1) axial stretching of the vibrating beam that leads

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Publication Date
Fri Dec 01 2023
Journal Name
Baghdad Science Journal
A novelty Multi-Step Associated with Laplace Transform Semi Analytic Technique for Solving Generalized Non-linear Differential Equations
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   In this work, a novel technique to obtain an accurate solutions to nonlinear form by multi-step combination with Laplace-variational approach (MSLVIM) is introduced. Compared with the  traditional approach for variational it overcome all difficulties and enable to provide us more an accurate solutions with extended of the convergence region as well as covering to larger intervals which providing us a continuous representation of approximate analytic solution and it give more better information of the solution over the whole time interval. This technique is more easier for obtaining the general Lagrange multiplier with reduces the time and calculations. It converges rapidly to exact formula with simply computable terms wit

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Publication Date
Sun Jun 05 2011
Journal Name
Baghdad Science Journal
Top soil layer equi-electrical conductivity and pollution with salts mapping for a region located within Baghdad city
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This research deals with the study of top soil electrical conductive regions located within Baghdad City. The research included measuring the dissolved soil material extraction Electrical Conductivity (EC) with an aqueous solution for the top (0-30 cm) soil layer of the study area. As the electrical conductivity values increase by increasing the amount of dissolved salts in principle, we can consider that the aim of this research is to predict the amount and distribution of (soil contamination with salts) which is represented by the (Salt Index), this factor calculated for each soil representative sample taken from the region with a depth of (30 cm). Laboratory (EC) test values measured by the use of solutions (EC) digital meter for the ex

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