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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 Sep 07 2020
Journal Name
Environmental Science And Pollution Research
The biosorption of reactive red dye onto orange peel waste: a study on the isotherm and kinetic processes and sensitivity analysis using the artificial neural network approach
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Publication Date
Sun Mar 02 2008
Journal Name
Baghdad Science Journal
A study of analysis and comparison to the low nutrient density foods that more normality for children age (3 –5 years)
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Through the early childhood and after the ablactating the child learns acquired food habbits that might studying with him throughout his life. Here the parents role arises: teaching the child the sound food habits and hygienic styles and whatever beneficial to the health and with the sufficient quantities for the body. In this way the experiences the child learns at home will be of great help in his future life in choosing the suitable food after becoming more dependent in making his decisions and choices away from his parents. The results in this study showed that the averages of the children’s consumption of the high energy foods in comparison with the other highest consumption average , after that comes the con sumption of soft drills

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Publication Date
Wed Oct 01 2014
Journal Name
Al–bahith Al–a'alami
Student Survey in Public Relations Services, Registration and Counseling, A Case Study of Petra University for the academic year 2013/2014.
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The research discusses the public relations services, registration, and academic advising at Petra University for the years 2013-2014. Using a field study and surveying Petra University students to be informed about the services and to cover the tiny details that have to do with public relations role in the university as a specialized department interested in serving public and gaining their trust in terms of what is legal and possible to build and enhance the university reputation. And gain mutual trust between the university and its publics.
The public relations is consi

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Publication Date
Wed Jan 01 2014
Journal Name
International Journal Of Medical Physics, Clinical Engineering And Radiation Oncology
The Use of Left Ventricular Myocardial Stiffness Index as a Predictor of Myocardial Performance in Patients with Systemic Hypertension
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Our aim was to investigate the changes in the myocardium stiffness index for patients suffering from systemic hypertension, and to assess their left ventricular performance. We studied 263 hypertensive patients and 166 healthy subjects as a control group. By using conventional Doppler echocardiography, the following parameters were measured—Left ventricular end diastolic diameter, left ventricular end systolic diameter, transmitral early velocity, isovolumic relaxation time, and isovolumic contraction time. Tissue Doppler imaging (TDI) was used in the measurements of the early mitral annular velocity (Ea) and the diastolic stiffness was obtained by calculating the ratio E\Ea\LVIDd. Index myocardial performance (IMP) was calculated

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Publication Date
Fri Mar 29 2024
Journal Name
Molecular Biology Reports
Role of endoplasmic reticulum aminopeptidase-1 gene polymorphism (rs13167972) in occurrence susceptibility of ankylosing spondylitis in a sample of Iraqi male patients
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Publication Date
Tue Oct 29 2024
Journal Name
Retos
The effect of special exercises using some auxiliary tools to develop some bio-kinetic abilities and the accuracy of the crushing and snatch forehand strikes among badminton players
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The best means and ways to develop an athlete's physical and skill capabilities, and among these means is the use of training aids that help develop some bio-kinetic abilities, and prepared exercises have had an important role in improving athletic performance in badminton, where the player must possess physical fitness, explosive power, and strength. Characterized by speed as well as accuracy, awareness, and focus while playing on the court, the badminton player must be physically fit through a continuous movement of small and large muscles to achieve good performance, which requires special physical abilities and skills, and the most important of these bio-kinetic abilities are agility, coordination, and measuring the coordination

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Publication Date
Thu Jan 04 2024
Journal Name
Journal Of Accounting And Financial Studies ( Jafs )
Using the Sherrod model in predicting financial failure in Iraqi private banks: an applied study in the Iraqi commercial and Iraqi Islamic banks
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Abstract:

              The phenomenon of financial failure is one of the phenomena that requires special attention and in-depth study due to its significant impact on various parties, whether they are internal or external and those who benefit from financial performance reports. With the increase in cases of bankruptcy and default facing companies and banks, interest has increased in understanding the reasons that led to this financial failure. This growing interest should be a reason to develop models and analytical methods that help in the early detection of this increasing phenomenon in recent year   . The research examines the use of

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Publication Date
Sun Mar 07 2010
Journal Name
Baghdad Science Journal
A systematical study about the genus Lycopus L. (Labiatae) in Iraq
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The study included gross morphology and pollen of plants – which collected during field trips , and dry ones for most specimen preserved with the Iraqi herbaria – related to the genus Lycopus L. , and to identify the unidentified species and rectify the error there in , so according to that the species L. europaeus L. only were specified for the genus . Through this work the varity L. europaeus var. glabrescens Schmidely were found at the first time , and suggested to record anew for Iraq . Pollen were of medium size, and had an ellipsoid shape in the equatorial view , and hexagonal in the polar view. The ecological and soil quality where these genus plants grows were specified , and were geographically distribut

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Publication Date
Wed Aug 19 2020
Journal Name
International Journal Of Research In Social Sciences And Humanities
HUMOUR IN THE AMERICAN AND BRITISH COMEDYEPISODES: A DISCOURSE ANALYSIS STUDY
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DBNRAAK Mohammed, International Journal of Research in Social Sciences and Humanities, 2020

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Publication Date
Fri Jul 04 2025
Journal Name
Al-rafidain Journal Of Medical Sciences ( Issn 2789-3219 )
Exploring the Relationship Between Urolithiasis and Hypertension: A Cross-Sectional Study
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Background: Urolithiasis and hypertension are prevalent and clinically significant conditions in the Middle East, both influenced by shared metabolic and environmental risk factors. Understanding the potential association between them is important for guiding prevention strategies. Objective: To explore the relationship between urolithiasis and hypertension in a sample of Iraqi adult patients. Methods: A cross-sectional observational study was conducted at Alkindy Teaching Hospital, Baghdad, from September 2024 to March 2025. Participants included 237 patients with confirmed urinary tract stones and 244 controls confirmed to be stone-free, matched for age and sex. Exclusion criteria included secondary hypertension, chronic kidney di

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