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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
Sun Sep 06 2009
Journal Name
Baghdad Science Journal
A Study of the Nutritional Behavior and Body Mass Indexes for Students of Age (17-25) Years In Baghdad, Iraq.
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The aim of this study was to assess the nutritional status for samples at the age of 17-15 years. These samples were taken from secondary schools and universities in Baghdad area, 123 of them were male and 261 were female. Data on weight, height and body mass index (BMI) were determined in each individual. Smaller sample of 215 individuals (male and female) from the original sample was taken in order to record their nutritional behavior and daily food intake during the 24 hours prior to the visit through personal meeting using special questionnaire. The results showed that the weight and the height were within the range of the people of neighboring Arab countries, who are in the same age. Beside 44.4- 55.95% of these samples were within t

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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
Sat Jul 15 2023
Journal Name
2023 6th International Conference On Engineering Technology And Its Applications (iiceta)
Methodology for the Design and Programming Methods for a Smart Home
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Publication Date
Wed Jun 29 2022
Journal Name
Iraqi Journal Of Chemical And Petroleum Engineering
A Comparison Study for The Performance of Polyethersulfone Ultrafiltration Mixed Matrix Membranes in The Removal of Heavy Metal Ions from Aqueous Solutions
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Polyethersulfone (PES) ultrafiltration membrane blending NaX zeolite crystals as a hydrophilic additive was examined for zinc (II) and lead ions Pb (II) removal from aqueous solutions. The effect of NaX zeolite content on the permeation flux and removal efficiency was studied. The results showed that adding zeolite to the polymer matrix enhanced the permeation flux. The permeation flux of all the zeolite/PES matrix membranes was higher than the pristine membrane. No significant improvement was observed in the removal of Zn (II) ions using all prepared membranes as the removal percentage did not raise above 29.2%. However, the removal percentage of Pb (II) ions was enhanced to 97% using a membrane containing 0.9%wt. zeolite. Also, it was

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Publication Date
Sat Oct 22 2022
Journal Name
Aro-the Scientific Journal Of Koya University
Classification of Different Shoulder Girdle Motions for Prosthesis Control Using a Time-Domain Feature Extraction Technique
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Abstract—The upper limb amputation exerts a significant burden on the amputee, limiting their ability to perform everyday activities, and degrading their quality of life. Amputee patients’ quality of life can be improved if they have natural control over their prosthetic hands. Among the biological signals, most commonly used to predict upper limb motor intentions, surface electromyography (sEMG), and axial acceleration sensor signals are essential components of shoulder-level upper limb prosthetic hand control systems. In this work, a pattern recognition system is proposed to create a plan for categorizing high-level upper limb prostheses in seven various types of shoulder girdle motions. Thus, combining seven feature groups, w

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Publication Date
Thu Aug 01 2024
Journal Name
Advances In Science And Technology Research Journal
Power Predicting for Power Take-Off Shaft of a Disc Maize Silage Harvester Using Machine Learning
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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
Mon Mar 25 2019
Journal Name
Al-academy
Melodic Characteristics of Oud Instrument Compositions with the Iraqi Symphony Orchestra (Saleem Salim) A Model: رعد عدنان علوان
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The variety of ideas and freedom of expression among the authors who are looking for everything new that serves the goals of musical and aesthetic expression, which calls for the use of traditional musical instruments with the great composition of musical instruments known as the orchestra represents a great challenge in several aspects. The incompetence of some of these instruments or limited capabilities or its costly method of performance sometimes forbids its use permanently in this great composition. It was necessary to have some problems facing the composer and the player on the one hand and the recipient on the other hand, who must be looking for perfection. Among those instruments that are used regularly in the works of the orche

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Publication Date
Wed Aug 01 2018
Journal Name
Journal Of Economics And Administrative Sciences
The impact of governmental consumer spending on the development of the current account balance in Iraq for the period (1990-2014) using ARDL model
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To avoid the negative effects due to inflexibility of the domestic production inresponse to the increase in government consumption expenditure leads to more  imports to meet the increase in domestic demand resulting from the increase in government consumption expenditure. Since the Iraqi economy economy yield unilateral depends on oil revenues to finance spending, and the fact government consumer spending is a progressive high flexibility the increase in overall revenues, while being a regressive flexibility is very low in the event of reduced public revenues, and therefore lead to a deficit in the current account position. And that caused the deficit for imbalance are the disruption of the

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Publication Date
Mon Feb 01 2016
Journal Name
Journal Of Economics And Administrative Sciences
The impact of strategic innovation components of the application Business process re-engineering: A survey Study of the consultant of a sample of managers and their assistants and consultants in the General Company for Post & Telecommunications
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Abstract:

        Organizations need today to move towards strategic innovation, which means the analysis of positions, especially the challenges faced by the change in the external environment, which makes it imperative for the organization that you reconsider their strategies and orientations and operations, a so-called re-engineering to meet those challenges and pressures. Now this research dilemma intellectual two-dimensional, yet my account in not Take writings and researchers effect strategic innovation in re-engineering business processes, according to science and to inform the researcher, and after the application represented in the non-application of such resear

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