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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
Fri Sep 15 2023
Journal Name
Al-academy
The effectiveness of change and transformation of formal displacement in the internal space (historical passenger stations as a model)
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Intellectual and material displacement is one of the design strategies through many mechanisms and means, and depends on the idea of changing the shape within the internal spaces at times and has concepts related to the transformation at other times. And represented by the boxes for travelers, the research problem emerged through the following question: (What is the effectiveness of displacement in the formal structures in the interior design of historical sites), and the aim of the study is to reveal the reality of the use of historical internal spaces and to determine the formal displacement that occurs as a result of change and transformation, and it included two topics, the first topic Transformation and the effectiveness of formal d

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Publication Date
Wed Jun 11 2008
Journal Name
Journal Of Al-nahrain University
ANALYSIS OF A MOLECULAR DYNAMICS SIMULATION OF THE ACETYLCHOLINESTERASE ENZYME AND ITS COMPLEX WITH (AXILLARIDINE-A) INHIBITOR
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Molecular dynamics (MD) simulations were carried out in order to investigate the binding mode of axillaridine-A at the active site of human acetylcholinesterase (AChE) enzyme. 2.0 nanosecond of MD simulations was made for the protein and the complex to dynamically explore the active site and the behavior of the ligand at the peripheral AChE binding site. These calculations for the enzyme alone showed that the active site of AChE is located at the bottom of a deep and narrow cavity whose surface is lined with rings of aromatic residues and Tyr72 is almost perpendicular to the Trp286 ring and forms a stable - interaction. The size of the active site of the complex decreases with time due to increase the interaction. Axillaridine-A forms

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Publication Date
Wed Feb 01 2017
Journal Name
Journal Of Economics And Administrative Sciences
A comparison between the logistic regression model and Linear Discriminant analysis using Principal Component unemployment data for the province of Baghdad
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     The objective of the study is to demonstrate the predictive ability is better between the logistic regression model and Linear Discriminant function using the original data first and then the Home vehicles to reduce the dimensions of the variables for data and socio-economic survey of the family to the province of Baghdad in 2012 and included a sample of 615 observation with 13 variable, 12 of them is an explanatory variable and the depended variable is number of workers and the unemployed.

     Was conducted to compare the two methods above and it became clear by comparing the  logistic regression model best of a Linear Discriminant  function written

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Publication Date
Sun Feb 15 2026
Journal Name
Al–bahith Al–a'alami
Preferences of the Iraqi Public towards Arab News Channels Programs and Materials (Al Jazeera, Al Arabiya, Al Ekhbariya Satellite Channels: a field Study)
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Broadcasting across satellites has become an important media phenomenon and largely available for watchers. As the receiver can see the events at the very moment and at any spot in the world. This study aims to discover the degree of the extent of exposure of Iraqi people to the news broadcasting satellites in Arabic language, (Al Jazeera, Al Arabiya, Al Ekhbariya Satellite Channels) as one of the media that serves the public; and to discover the range of these Satellite Channels in covering the local Iraqi situation in different sides and aspects; and to know the significance of the Iraqi people in watching those news programmers; and state the motives behind the Iraqi public's dependence on these channels.

The

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Publication Date
Mon Mar 01 2021
Journal Name
Microporous And Mesoporous Materials
Using the ash of common water reeds as a silica source for producing high purity ZSM-5 zeolite microspheres
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Publication Date
Thu Apr 14 2016
Journal Name
Iraqi Journal Of Market Research And Consumer Protection
Study The Effect of α-amylase Inhibitors Isolated from Plant Sources on Some Mold.: Study The Effect of α-amylase Inhibitors Isolated from Plant Sources on Some Mold.
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Activity test of the inhibitors purified from barley and broad beans crop proved the inhibition activity against 6 types of rots Pencillium ssp and Aspergellusflavus and Aspergillus niger and Fusarium solani and Fusarium semitectum and Mucor with three concentrations 0.1 and 0.2 and 0.3 mg/ml, where the inhibitor purified from the second peak of broad beans proved that it had a higher inhibition activity against the growth of test rots which were 53.75 and 62.5 and 78.5 and 76.25 and 84 and 18.8% respectively, at 0.3 mg/ ml followed by the first peak of the inhibitor purified from broad beans the inhibition activity were 43.75 and 50 and 62.96 and 75 and 80 and 12.5 then the inhibitor purified from barley in which the inhibition activity

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Publication Date
Tue Apr 18 2023
Journal Name
Al–bahith Al–a'alami
Public relations programs and its role to enhance the morale of employees in the Ministry of Transportation: A survey study on the State land Transport Company
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This research aims to learn about public relations programs and their role to enhance the morale of the State land Transport Company employees.The researcher relied on the survey method and use a questionnaire and scale tools to collect information from workers in the Department of Relations and Media and employees in all departments.
The research reached several conclusions, including:
1- Public relations seek to increase workers’ confidence in senior management and motivate them to improve their production, as well as their relentless endeavor to bring workers closer by following multiple and varied forms of communication with them.
2- The results of the study showed that there was a negative i

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Publication Date
Thu Dec 15 2022
Journal Name
Engineering, Technology & Applied Science Research
Numerical Modeling of a Pile Group Subjected to Seismic Loading Using the Hypoplasticity Model
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Various simple and complicated models have been utilized to simulate the stress-strain behavior of the soil. These models are used in Finite Element Modeling (FEM) for geotechnical engineering applications and analysis of dynamic soil-structure interaction problems. These models either can't adequately describe some features, such as the strain-softening of dense sand, or they require several parameters that are difficult to gather by conventional laboratory testing. Furthermore, soils are not completely linearly elastic and perfectly plastic for the whole range of loads. Soil behavior is quite difficult to comprehend and exhibits a variety of behaviors under various circumstances. As a result, a more realistic constitutive model is

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Publication Date
Thu Dec 15 2022
Journal Name
Engineering, Technology & Applied Science Research (etasr)
Numerical Modeling of a Pile Group Subjected to Seismic Loading Using the Hypoplasticity Model
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Various simple and complicated models have been utilized to simulate the stress-strain behavior of the soil. These models are used in Finite Element Modeling (FEM) for geotechnical engineering applications and analysis of dynamic soil-structure interaction problems. These models either can't adequately describe some features, such as the strain-softening of dense sand, or they require several parameters that are difficult to gather by conventional laboratory testing. Furthermore, soils are not completely linearly elastic and perfectly plastic for the whole range of loads. Soil behavior is quite difficult to comprehend and exhibits a variety of behaviors under various circumstances. As a result, a more realistic constitutive model is

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Publication Date
Sun Dec 07 2008
Journal Name
Baghdad Science Journal
Optium Conditions for the Production of Neutral Protease from local strain Aspergillus niger var cabonarius
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The optimum conditions for the production of neutral protease from local strain Aspergillus niger var carbonarius by solid – state fermentation system (Wheat bran) moisted with 0.2 M phosphate buffer (PH7.0) . the hydration ratio was 1:5 (V:W) . the concentration of inoculum was 1×106 spores per 10 gram of solid materials , initial P H 6.5 and 96 hours of incubation period at 30? C .the enzyme activity was 1300 unit / ml and specific activity was 1550 unit / mg protein .

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