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bijps-1604
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
Sun Oct 01 2017
Journal Name
Journal Of Economics And Administrative Sciences
The role of organizational change in easing the organizational conflict: an exploratory study of the opinions of a sample of managers and workers in Iraq to EarthLink Network Services Company And communications
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Research on the role of organizational change in easing the organizational conflict focuses for being one of the important topics and relatively modern and which have a significant impact on the future of organizations, so this study was to identify the relationship and the impact of organizational change and of deportation (technological, organizational structure, human resources, the change in the task) at the organizational conflict in the Earth company link Iraq, in order to reach the goals of the research, it has been the development of a questionnaire distributed to a random sample of (100) composed employees from managers and heads of departments and the people and staff at the Earth company link Iraq, the study found: the

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Publication Date
Mon Nov 30 2020
Journal Name
Journal Of Economics And Administrative Sciences
The correlation between identifying needs and choosing the appropriate productive art for use / primary health care centers as an example
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        The purpose of the study is to identify the need to improve health services in Iraq by determining the efficiency of service in health care centres and working on exploiting limited resources through choosing the most efficient technological art represented by using precast concrete technology to fill the shortfall in the establishment health centres for primary care and to explain the impact of this on saving resources, time, and increasing production efficiency. To achieve this, the quantitative analysis adopted as a methodology in the study by determining the size of the deficit in the infrastructure of health centres for primary care according to the standard of a he

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Publication Date
Sat Jul 27 2024
Journal Name
Scientific Journal Of Sport And Performance
effect of a laser device on some biomechanical variables of the rotational phase in the achievement of 100 m freestyle swimming for the Iraqi team (16-18 years old)
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The researchers have discovered weaknesses in the rotational phase of the 100-meter freestyle event, including a lack of proper movement direction and control of biomechanical variables necessary for swimmers to achieve high rotational accuracy, which leads to outperforming competitors. The objective of this study was to investigate the effect of using a laser device on improving the performance of the rotational phase among swimmers on the Iraqi national team. The experimental approach was conducted on a sample of 6 swimmers, representing 100% of the target population. The researchers concluded that the utilization of a proposed laser device in the rotational phase resulted in positive differences in biomechanical variables, contri

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Publication Date
Sat Dec 15 2018
Journal Name
Research Journal Of Pharmaceutical, Biological And Chemical Sciences
Synthesis, Spectroscopic and Antimicrobial Studies of Mixed Ligand Metal (II) Complexes with three amino acids
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The research includes synthesis and identification of novel three amino acids ligands complexes of some heavy metal (II) ions by using the amino acids like glycine, L-alanine and L-valine. New metal mixed ligand complexes with amino acids are prepared the reaction by reacting the three amino acids with the metals(II) chloride by using 50% ethanolic solution and 50% distall water in the molar ratio [1:1:1:1] ( M:Gly:Ala:Val) except for Co(II) and Ni(II) complexes were found after diagnosis the coordination with both Lalanine and L-valine. The prepared complexes identified by using physical properties, flame atomic absorption and conductivity measurements, in addition, mass, FT.IR and UV.vis spectrum as well magnetic moment data. The general

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Publication Date
Sat Mar 31 2018
Journal Name
Iraqi Journal Of Chemical And Petroleum Engineering
Experimental Study for the Influence of Operating Parameters on Copper Electrorefining Process
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Copper electrodeposition by electrorefining process in acidic sulfate media contains 40 g/l of cupric ions and 160 g/l of sulfuric acid was achieved to study the influence of the operating parameters on cathode purity, surface morphology, deposition rate, current efficiency and power consumption. These operating parameters and there ranges are: current density 200, 300 and 400 A/m2, electrolyte temperature 35, 50 and 65 oC, electrodes spacing 15, 30 and 45 mm and electrolyte residence time 6, 4 and 2 h were utilized. XRF, SEM and EDX analyses were attained to clarify the properties of the produced cathode.

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Publication Date
Sun Jul 09 2023
Journal Name
Journal Of Engineering
Study the Application of Ultrasonic Technology for Phenol Removal in Petroleum Industry
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In this study, the sonochemical degradation of phenol in water was investigated using two types of ultrasonic wave generators; 20 kHz ultrasonic processor and 40 kHz ultrasonic cleaner bath. Mineralization rates were determined as a function of phenol concentration, contact time, pH, power density, and type of ultrasonic generator. Results revealed that sonochemical degradation of the phenol conversion was enhanced at increased applied power densities and acidic conditions. At 10 mg/L initial concentration of phenol, pH 7, and applied power density of 3000 W/L, the maximum removal efficiency of phenol was 93% using ultrasonic processor at 2h contact time. Whereby, it was 87% using and ultrasonic cleaner bath at 16h contact time and 150 W

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Publication Date
Thu Aug 01 2024
Journal Name
Iop Conference Series: Earth And Environmental Science
Assessing the Environmental Footprint of the Cement Industry: A Pathway to Sustainable Development
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Abstract<p>Achieving a connection between sustainability processes and environmental protection, or what is known as sustainable development, requires paying more attention to environmental and sustainability issues for various projects and their effects on environmental problems. It involves determining the most appropriate ways to deal with them within pillars of sustainability (environmental, social, economic, and natural resources. As cement is a fundamental component of industrial services and construction in cities, it has a direct and significant interaction with the development process, making it one of the most important industries in Iraq. Because of the clinker particles and combustio</p> ... Show More
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Publication Date
Thu Feb 01 2018
Journal Name
Comparative Medicine
Model of traumatic spinal cord injury for evaluating pharmacologic treatments in cynomolgus macaques (Macaca fasicularis)
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Here we present the results of experiments involving cynomolgus macaques, in which a model of traumatic spinal cord injury (TSCI) was created by using a balloon catheter inserted into the epidural space. Prior to the creation of the lesion, we inserted an EMG recording device to facilitate measurement of tail movement and muscle activity before and after TSCI. This model is unique in that the impairment is limited to the tail: the subjects do not experience limb weakness, bladder impairment, or bowel dysfunction. In addition, 4 of the 6 subjects received a combination treatment comprising thyrotropin releasing hormone, selenium, and vitamin E after induction of experimental TSCI. The subjects tolerated the implantation of the recording devi

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Publication Date
Tue Jan 31 2023
Journal Name
Iraqi Geological Journal
Geological Model for Jeribe/Euphrates Formation, Tertiary Reservoir in Qaiyarah Oil Field, North of Iraq
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Visualization of subsurface geology is mainly considered as the framework of the required structure to provide distribution of petrophysical properties. The geological model helps to understand the behavior of the fluid flow in the porous media that is affected by heterogeneity of the reservoir and helps in calculating the initial oil in place as well as selecting accurate new well location. In this study, a geological model is built for Qaiyarah field, tertiary reservoir, relying on well data from 48 wells, including the location of wells, formation tops and contour map. The structural model is constructed for the tertiary reservoir, which is an asymmetrical anticline consisting of two domes separated by a saddle. It is found that

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Publication Date
Sat Jan 01 2011
Journal Name
Iraqi Journal Of Physics
Calculation of Particle Emission Rates for Nucleon-Induced Reactions with non-Equidistance Spacing Model Dependence
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Nuclear emission rates for nucleon-induced reactions are theoretically calculated based on the one-component exciton model that uses state density with non-Equidistance Spacing Model (non-ESM). Fair comparison is made from different state density values that assumed various degrees of approximation formulae, beside the zeroth-order formula corresponding to the ESM. Calculations were made for 96Mo nucleus subjected to (N,N) reaction at Emax=50 MeV. The results showed that the non-ESM treatment for the state density will significantly improve the emission rates calculated for various exciton configurations. Three terms might suffice a proper calculation, but the results kept changing even for ten terms. However, five terms is found to give

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