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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 Mar 01 2023
Journal Name
Baghdad Science Journal
A Study on Co – odd (even) Sum Degree Edge Domination Number in Graphs
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 An edge dominating set    of a graph  is said to be an odd (even) sum degree edge dominating set (osded (esded) - set) of G if the sum of the degree of all edges in X is an odd (even) number. The odd (even) sum degree edge domination number  is the minimum cardinality taken over all odd (even) sum degree edge dominating sets of G and is defined as zero if no such odd (even) sum degree edge dominating set exists in G. In this paper, the odd (even) sum degree domination concept is extended on the co-dominating set E-T of a graph G, where T is an edge dominating set of G.  The corresponding parameters co-odd (even) sum degree edge dominating set, co-odd (even) sum degree edge domination number and co-odd (even) sum degree edge domin

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Publication Date
Thu Nov 30 2023
Journal Name
Iraqi Geological Journal
A Review on Pressure Transient Analysis in Multilayer Reservoir: South Iraq Case Study
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Multilayer reservoirs are currently modeled as a single zone system by averaging the reservoir parameters associated with each reservoir zone. However, this type of modeling is rarely accurate because a single zone system does not account for the fact that each zone's pressure decreases independently. Pressure drop for each zone has an effect on the total output and would result in inter-flow and the premature depletion of one of the zones. Understanding reservoir performance requires a precise estimation of each layer's permeability and skin factor. The Multilayer Transient Analysis is a well-testing technique designed to determine formation properties in more than one layer, and its effectiveness over the past two decades has been

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Publication Date
Tue Feb 14 2023
Journal Name
Journal Of Educational And Psychological Researches
Panic Attacks Over COVID 19 : A Survey Study on An Iraqi University Sample
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Abstract

The present paper attempts to detect the level of (COVID-19) pandemic panic attacks among university students, according to gender and stage variables.

To achieve this objective, the present paper adopts the scale set up by (Fathallah et al., 2021), which has been applied electronically to a previous cross-cultural sample consisting of (2285) participants from Arab countries, including Iraq. The scale includes, in its final form, (69) optional items distributed on (6) dimensions:  physical symptoms (13) items, psychological and emotional symptoms (12) items, cognitive and mental symptoms (11) items, social symptoms (8) items, general symptoms (13) items and daily living practices (12) items

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Publication Date
Sun Jan 01 2017
Journal Name
Journal Of Engineering
Two – Dimensional Mathematical Model to Study Erosion Problem of Tigris River Banks at Nu’maniyah
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The high and low water levels in Tigris River threaten the banks of the river. The study area is located on the main stream of Tigris River at Nu’maniyah City and the length of the considered reach is 5.4 km, especially the region from 400 m upstream Nu’maniyah Bridge and downstream of the bridge up to 1250 mwhich increased the risk ofthe problemthat itheading towardsthe streetand causingdanger tonearbyareas.

The aim of this research is to identify the reason of slope collapse and find proper treatments for erosion problem in the river banks with the least cost. The modeling approach consisted of several steps, the first of which  is by using “mini” JET (Jet Erosion Test) d

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Publication Date
Fri Jul 01 2016
Journal Name
Al–bahith Al–a'alami
A Semiotic Approach to the Analysis of the News Story
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This study attempts to provide an approach analysis for the news, depending on the bases and principles which conceptuality semiotic researchers of this field first of them «A. J. Gremas» for the theory of «narrative discourse analysis», to more clarify we tried to apply it on a published press- news, to concludes the most important steps and methods that are necessary to follows gain more understanding of the press- news.

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Publication Date
Wed May 17 2023
Journal Name
College Of Islamic Sciences
A stylistic vision of the objection in the Quranic discourse
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The modern stylistic lesson has become more committed to the scientific limits in which it believed, and more confident in itself, and it is no longer just a scientific procedure that helps other curricula and sciences that preceded it.

Based on this, our modest research ((a stylistic vision of the objection in the Quranic discourse)) arose to explore an artistic rhetorical phenomenon that was included in the Holy Quran text. ; Because analysis is a situation that allows us to see a lot and absorb the stranger more clearly.

And since the horizontal arrangement of the linguistic elements in which stylistically undistinguished elements meet with distinct ones, the other trend has emerged that believes that the stylistic dis

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Publication Date
Sun Oct 15 2023
Journal Name
Bionatura
Examining how PMMA and polyamide denture base materials' physical characteristics are affected by electrolyzed water used as a denture cleaner
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Denture cleansing is an essential step that can stop cross‑contamination and adds to the health of the patient, denture durability, and the general quality of life. A disinfection technique must be practical and devoid of damaging effects on the material's properties used to construct the denture base. The main aim of this study is to evaluate the effect of three concentrations of electrolyzed water denture cleanser on heat cure acrylic and polyamide after immersion in electrolyzed water. The evaluation is based on their efficacy on surface hardness, wettability, and color stability compared with one submerged in distilled water as a control group. The method consists of eighty samples of heat-cured acrylic and polyamide material.

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Publication Date
Fri Feb 26 2021
Journal Name
Life-cycle Civil Engineering: Innovation, Theory And Practice
Shear performance of a novel demountable connector for reusable steel-concrete composite structures
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A novel demountable shear connector is proposed to link a concrete slab to steel sections in a way that resulting steel-concrete composite floor is demountable, i.e. it can be easily dismantled at the end of its service life. The proposed connectors consist of two parts: the first part is a hollow steel tube with internal threads at its lower end. The second part is a compatible partially threaded bolted stud. After linking the stud to the steel section, the hollow steel tube can be fastened over the threaded stud, which create a complete demountable shear connector. The connector is suitable for use in both composite bridges and buildings, and using cast in-situ slabs, precast solid slabs, or hollow-core precast slabs. A series of push-off

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Publication Date
Fri May 18 2018
Journal Name
International Journal Of Simulation: Systems, Science & Technology
A Review of Advances in Pressurizer Response Research for Pressurized Water Reactor Systems
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Publication Date
Sun Mar 01 2020
Journal Name
Baghdad Science Journal
Dynamic Response of a Nonlinear Fabry-Perot Etalon for Various Medium Response Times
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     In this work, the switching nonlinear dynamics of a Fabry-Perot etalon are studied. The method used to complete the solution of the differential equations for the nonlinear medium. The Debye relaxation equations solved numerically to predict the behavior of the cavity for modulated input power. The response of the cavity filled with materials of different response time is depicted. For a material with a response time equal to = 50 ns, the cavity switches after about (100 ns). Notice that there is always a finite time delay before the cavity switches. The switch up time is much longer than the cavity build-up time of the corresponding linear cavity which was found to be of the order of a few round-trip ti

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