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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 Jan 01 2013
Journal Name
Journal Of Geochemical Exploration
Geochemical exploration using surveys of spring water, hydrocarbon and gas seepage, and geobotany for determining the surface extension of Abu-Jir Fault Zone in Iraq: A new way for determining geometrical shapes of computational simulation models
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Publication Date
Fri Dec 01 2023
Journal Name
Al-khwarizmi Engineering Journal
The Remediation of Congo Red-Contaminated Groundwater by using a Permeable Reactive Barrier Through Modified Waterworks Sludge MgAl-LDH
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This investigation aims to explore the potential of waterworks sludge (WS), low-cost byproduct of water treatment processes, as a sorbent for removing Congo Red (CR) dyes. This will be achieved by precipitating nano-sized (MgAl-LDH)-layered double hydroxide onto the surface of the sludge. The efficiency of utilizing MgAl-LDH to modify waterworks sludge (MWS) for use in permeable reactive barrier technology was confirmed through analysis with Fourier transform infrared and X-ray diffraction. The isotherm model was employed to elucidate the adsorption mechanisms involved in the process. Furthermore, the COMSOL model was utilized to establish a continuous testing model for the analysis of contaminant transport under diverse conditions.

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Publication Date
Wed Dec 30 2020
Journal Name
Modern Sport
The effect of special exercises using rubber ropes to develop special endurance and achieve a 200-meter freestyle swimming
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Swimming has now become the focus of attention of specialists, which has led to the search for the best methods and various methods of training, which rely heavily on scientific research and studies, through the use of proper planning and a comprehensive scientific and practical vision in the preparation and training process for this game. Some studies have proven that  The use of training methods has a positive role in the athletic training of the swimmer, provided that these methods are used in the correct way according to the scientific principles of training and with the loads and stresses that serve the specialized activity, i.e. the swimming distance. The study aimed at the follow 1- Preparing exercises using elastic ro

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Publication Date
Fri Dec 01 2023
Journal Name
Al-khwarizmi Engineering Journal
The Remediation of Congo Red-Contaminated Groundwater by using a Permeable Reactive Barrier Through Modified Waterworks Sludge MgAl-LDH
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This investigation aims to explore the potential of waterworks sludge (WS), low-cost byproduct of water treatment processes, as a sorbent for removing Congo Red (CR) dyes. This will be achieved by precipitating nano-sized (MgAl-LDH)-layered double hydroxide onto the surface of the sludge. The efficiency of utilizing MgAl-LDH to modify waterworks sludge (MWS) for use in permeable reactive barrier technology was confirmed through analysis with Fourier transform infrared and X-ray diffraction. The isotherm model was employed to elucidate the adsorption mechanisms involved in the process. Furthermore, the COMSOL model was utilized to establish a continuous testing model for the analysis of contaminant transport under diverse conditions. A st

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Publication Date
Fri Jan 01 2021
Journal Name
Aip Conference Proceedings
The study of water quality changes using GIS and remote sensing for Tigris River through Salah Al-Din province, Iraq
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The most significant water supply, which is the basis of agriculture, industry and human and wildlife needs, is the river. In order to determine its suitability for drinking purposes, this study aims to measure the Water Quality Index (WQI) of the Tigris River in the Salah Al-Din Province (center of Tikrit), north of Baghdad. For ten (9) physio-chemical parameters, namely turbidity, total suspended sediments, PH, electrical conductivity, total dissolved solids, alkalinity, chloride, nitrogen as nitrate, sulphate, and then transported for examination to the laboratory, water samples were collected from 13 locations along the Tigris river. Using the weighted arithmetic index method, the WQI was measured and found to be 105,87 in up-stream, wh

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Publication Date
Tue Mar 21 2023
Journal Name
International Journal Of Interactive Mobile Technologies (ijim)
Study the Effect of Using Google Classroom on the Academic Performance Under the Covid19 Pandemic Using Data Mining Technique
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— In light of the pandemic that has swept the world, the use of e-learning in educational institutions has become an urgent necessity for continued knowledge communication with students. Educational institutions can benefit from the free tools that Google provide and from these applications, Google classroom which is characterized by ease of use, but the efficiency of using Google classroom is affected by several variables not studied in previous studies Clearly, this study aimed to identify the use of Google classroom as a system for managing e-learning and the factors affecting the performance of students and lecturer. The data of this study were collected from 219 members of the faculty and students at the College of Administra

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Publication Date
Sun Dec 03 2017
Journal Name
Baghdad Science Journal
A Study of Zooplankton Community in Dukan Lake, Kurdistan Region-Iraq, with a New Record of Craspedacusta sowerbii Lankester (1880) Medusa (Cnidaria: Hydrozoa)
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A study of Zooplankton community has been carried out at four selected sites on Dukan Lake. Samples of water and zooplankton were collected monthly for the period from July 2015 to February 2016. Some physical and chemical properties of water were studied and the results showed that the air temperature were ranged from 0 to 36.16 °C, water temperature ranged from 2.83 to 34.66 °C, hydrogen ion concentration of studied sites were found to lie in alkaline side, it was ranged between 6.87 to 8.57, electrical conductivity ranged from 190.79 to 850.08 µs.cm­¹, turbidity ranged from 0.9-7.7 NTU, and dissolved oxygen from 3.3 to 6.8 mg.l-¹ while BOD5 were ranged from 0.53 to 34.66 mg.l-¹. Concerning to the zooplankton, 37 species were ident

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Publication Date
Wed Jan 01 2025
Journal Name
Smart Innovation, Systems And Technologies
The Effect of Bulgarian Bag Exercises to Develop Explosive Force, Characterized by Speed and Accuracy of the Spiking Performance of Volleyball Players
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The purpose of this study is to develop and assess the effectiveness of exercises using heavy and hanging ropes for handball players, focusing on enhancing specific physical abilities and shooting accuracy. The research addresses the gap in training methodologies by comparing the effects of heavy rope exercises versus hanging rope exercises. An experimental design was used in two equal groups, besides pre-testing and post-testing. The study involved 16 players from the School of Handball for the season 2022–2023. The sample included 14 players, who were then randomly divided into two experimental groups of 7 each. The first group performed heavy rope exercises, while hanging rope exercises were included in the plan of the second group. Th

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Publication Date
Sun Apr 30 2017
Journal Name
Journal Of Engineering
Experimental Study on Heat Transfer and Friction Factor Characteristics of Single Layer Graphene Based DI-water Nanofluid in a Circular Tube under Laminar Flow and Different Heat Fluxes as Boundary Conditions
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An experimental study was performed to estimate the forced convection heat transfer performance and the pressure drop of a single layer graphene (GNPs) based DI-water nanofluid in a circular tube under a laminar flow and a uniform heat flux boundary conditions. The viscosity and thermal conductivity of nanofluid at weight concentrations of (0.1 to 1 wt%) were measured. The effects of the velocity of flow, heat flux and nanoparticle weight concentrations on the  enhancement of the heat transfer are examined. The Nusselt number of the GNPs nanofluid was enhanced as the heat flux and the velocity of flow rate  increased, and the maximum Nusselt number  ratio (Nu nanofluid/ Nu base fluid)   and thermal performance factor

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Publication Date
Sat Dec 02 2017
Journal Name
Al-khwarizmi Engineering Journal
e Timoshenko Three-Beams Technique To Estimate The Main Elastic Moduli Of Orthotropic Homogeneous Materials
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 A New developed technique to estimate the necessary six elastic constants of homogeneous laminate of special orthotropic properties are presented in this paper for the first time. The new approach utilizes the elasto-static deflection behavior of composite cantilever beam employing the famous theory of Timoshenko. Three extracted strips of the composite plate are tested for measuring the bending deflection at two locations. Each strip is associated to a preferred principal axis and the deflection is measured in two orthogonal planes of the beam domain. A total of five trails of testing is accomplished and the numerical results of the stiffness coefficients are evaluated correctly under the contribution of the macromechanic

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