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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
Wed Aug 30 2023
Journal Name
Al-kindy College Medical Journal
Pancreatic Stone Protein/ regenerating Protein (PSP/reg) as a Biochemical Marker for prediction of Microvascular Complications of Type 2 Diabetes Mellitus
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Background: Type 2 diabetes mellitus (T2DM) characterized by insulin resistance (IR) and progressive decline in functional beta (β) cell mass partially due to increased β cell apoptosis rate. Pancreatic stone protein /regenerating protein (PSP/reg) is produced mainly by the pancreas and elevated drastically during pancreatic disorder. Beta cells are experiencing apoptosis that stimulate the expression of PSP/reg gene in surviving neighboring cells, and that PSP/reg protein is subsequently secreted from these cells which could play a role in their regeneration.

Objectives: To analyze serum levels of PSP/reg protein in T2DM patients and evaluate its correlation with the microvasc

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Publication Date
Tue Feb 28 2023
Journal Name
Iraqi Geological Journal
Development of 3D Geological Model and Analysis of the Uncertainty in a Tight Oil Reservoir in the Halfaya Oil Field
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A geological model was built for the Sadi reservoir, located at the Halfaya oil field. It is regarded as one of the most significant oilfields in Iraq. The study includes several steps, the most essential of which was importing well logs from six oil wells to the Interactive Petrophysics software for conducting interpretation and analysis to calculate the petrophysical properties such as permeability, porosity, shale volume, water saturation, and NTG and then importing maps and the well tops to the Petrel software to build the 3D-Geological model and to calculate the value of the original oil in place. Three geological surfaces were produced for all Sadi units based on well-top data and the top Sadi structural map. The reservoir has

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Publication Date
Mon Dec 30 2024
Journal Name
Iraqi Journal Of Science
The Impact of Fear and Anti-Predator Behavior on the Dynamics of Stage-Structure Prey–Predator Model With a Harvesting
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In this paper, an ecological model with stage-structure in prey population, fear, anti-predator and harvesting are suggested. Lotka-Volterra and Holling type II functional responses have been assumed to describe the feeding processes . The local and global stability of steady points of this model are established. Finally, the global dynamics are studied numerically to investigate the influence of the parameters on the solutions of the system, especially the effect of fear and anti-predation.

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Publication Date
Sat Jul 27 2024
Journal Name
International Journal Of Economic Perspectives
The impact of strategic leadership on the building of intelligent organizations: A field study of a group of economic institutions in Algeria
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This study aims to highlight the role of strategic leadership in adopting the intelligent organization model. The study was conducted on 7 economic organizations in Algeria. The study population consisted of 354 leaders, of whom a random sample of 176 leaders (managers, department heads, division heads, engineers) was selected. The researcher used a questionnaire as the main tool of the study. Statistical analysis and hypothesis testing were conducted using SEM (Structural Equation Modeling) with the aid of SPSS.v26 and AMOS.v24 software. The study concluded with a set of results, most notably: there is a statistically significant direct positive effect between strategic leadership and building intelligent organizations at a significance le

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Publication Date
Wed Aug 30 2023
Journal Name
Al-kindy College Medical Journal
Serum Pseudocholinesterase as a Biomarker in the Differentiation between Gastric Cancer and Benign Gastric Diseases
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Background: Worldwide gastric cancer is the fifth most common cancer with poor prognosis. In early stages, it is hard to distinguish gastric cancer from benign gastric diseases, resulting in delayed diagnosis. There is a need to develop a biomarker for differentiating between gastric cancer and benign gastric diseases. Serum cholinesterase is synthesized in liver and released into plasma, and it has an important role in oncogenesis.

Objectives: To determine the correlation between serum cholinesterase activity and gastric cancer, in comparison to benign gastric diseases.

Subjects and Methods: A case control study carried out at Medical City Direct

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Publication Date
Sun Dec 02 2012
Journal Name
Baghdad Science Journal
The Dissolution Study For Sodium Selenite Tablets Using Atomic Absorption Spectrophotometer
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The development of a meaningful dissolution procedure for drug products with limited water solubility has been a challenge to both the pharmaceutical industry and the agencies that regulate them. Natural surfactants aid in the dissolution and subsequent absorption of drugs with limited aqueous solubility. In vitro, various techniques have been used to achieve adequate dissolution of the sparingly water – soluble or water insoluble drug products such as the use of mechanical methods (i.e., increased agitation and the disintegration method) or hydro alcoholic medium or large volumes of medium. The necessity of assuring the quality of drugs , especially those with low aqueous solubility and in vivo absorption , has led to the development and

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Publication Date
Wed Aug 01 2018
Journal Name
Engineering And Technology Journal
A Proposed Method for the Sound Recognition Process
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Publication Date
Wed Feb 04 2026
Journal Name
Journal Of Physical Education
Agility and its relationship with of scoring accuracy for young footballers aged (14-16) years
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Publication Date
Sun Feb 28 2021
Journal Name
Journal Of Economics And Administrative Sciences
Effects of Macroeconomic Variables on Gross Domestic Product in Saudi Arabia using ARDL model for the period 1993-2019
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This paper analyses the relationship between selected macroeconomic variables and gross domestic product (GDP) in Saudi Arabia for the period 1993-2019. Specifically, it measures the effects of interest rate, oil price, inflation rate, budget deficit and money supply on the GDP of Saudi Arabia. The method employs in this paper is based on a descriptive analysis approach and ARDL model through the Bounds testing approach to cointegration. The results of the research reveal that the budget deficit, oil price and money supply have positive significant effects on GDP, while other variables have no effects on GDP and turned out to be insignificant. The findings suggest that both fiscal and monetary policies should be fo

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Publication Date
Wed Jun 15 2016
Journal Name
Iraqi National Journal Of Chemistry
Physical and Electrical Study of Different Carbone Nanomaterials as Modifying Material for SPCE
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In this work was prepared three different types of modified screen printed carbon electrode (SPCEs) with drops casted method, the used carbone nanomaterials were the MWCNT, functionalized –MWCNT (f-MWCNT) and After several experiments were made to find an appropriate ratio to make good GOT/f-MWCNT nanocomposite, and found the suspension mixture (1:1) from GOT/f-MWCNT (f-MWCNT-GOT). The electrical and physical properties were performed with cyclic voltammeter technique, and studied the maximum current response, the effective surface area, effect of the pH value and the determination of active surface area for MWCNT-SPCE , f-MWCNT-SPCE and f-MWCNT-GOT/SPCE as (0.04 cm2), (0.119 cm2) and (0.115 cm2) respectively, the surface coverage concent

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