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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 Dec 30 2015
Journal Name
College Of Islamic Sciences
Trees and their impact on humans And the environment from a Qur'anic perspective
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Show the greatness of Allah Almighty when contemplating the benefits of trees and plants in
Life in general and trees mentioned in the Koran in particular, do not have to meditate that
He acknowledges the greatness of the Almighty Creator, and his preference over man, that he is prepared for his livelihood
And give him what he can do in this life to the fullest.
  The study also stressed the need to urge people to this great blessing trees
By preserving them and wasteful wastefulness.
  The study also pointed to the need to guide people towards the aesthetics and improvements of
Look through and enjoy the beauty of trees, flowers, greenery and fruits ..

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Publication Date
Wed Dec 01 2021
Journal Name
Journal Of Engineering
Controlling the Salt Wedge Intrusion in Shatt Al-Arab River by a Barrage
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Shatt Al-Arab River in Al Basrah, Iraq, has recently recorded massive levels of TDS values (Total Dissolved Solids) in the water as a result of reduced fresh water discharge from sources, causing the river to become salinized due to salt wedge intrusion. Therefore, a block dam in the south reach is required to salt intrusion prevention. The main objective of this research is to simulate the hydraulic impact of a suggested barrage in Ras Al Besha on the Shatt Al-Arab River. The HEC-RAS (5.0.7) model was used to develop a one-dimensional unsteady model to gaining an understanding of the proposed barrage's influence on river behaviour. The daily discharges of the Tigris River provided as the upstream boundary conditions, wh

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Publication Date
Fri Oct 10 2025
Journal Name
Pharmakeftiki
Genetic polymorphisms and adverse effects that affect the natalizumab clinical response: a review
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The clinical response to natalizumab in patients with multiple sclerosis (MS) may be significantly influenced by genetic variation. Mutations in genes related to the drug’s mechanism of action or the pathological milieu of MS can contribute substantially to interindividual differences in treatment outcomes. This review aims to provide an overview of previous studies that have examined genetic polymorphisms associated with the clinical efficacy of natalizumab. A systematic literature search was conducted across the PubMed, Google Scholar, and ResearchGate databases using targeted keywords relevant to the subject matter. Several genetic loci were found to be linked to natalizumab responsiveness, including the integrin subunit alpha 4 (ITGA4

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Publication Date
Fri Jun 30 2023
Journal Name
College Of Islamic Sciences
Belief in the Last Day and its impact on building a Muslim's personality
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Research Summary

        The doctrine of belief in the Last Day is one of the pillars of faith, and the doctrine of resurrection and reckoning are part of this day.

 Belief in the Last Day puts a person in constant control over himself, as this control creates in this person happiness and a decent life, and he renounces the world and turns away from all vices and adorns all virtues.

        On the other hand, we find that the person who does not believe in this day does not stand before his eyes anything that prevents him from doing injustices and corruption in the land. The doctrine of belief in the Last Day alone is

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Publication Date
Thu Sep 01 2022
Journal Name
Translational Research In Anatomy
Unusual large central sphenoethmoidal cell separating the two sphenoid sinuses - A case report
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Publication Date
Tue Jan 29 2019
Journal Name
Journal Of The College Of Education For Women
Geopolitical dimensions to build a dam on the downstream Renaissance (Egypt and Sudan)
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Varied uses of international rivers in the past few decades dramatically, resulting in this multiplicity of uses and all associated with it for the occurrence of freshwater scarcity activities, and thus an increase in conflicts and disputes around on the rights of each of the riparian countries to benefit from the waters of the river at various purposes, particularly the establishment of dams on some of them as is the case (Renaissance Ethiopian) big impact on downstream countries Dam (Egypt and Sudan), due to the Oukuahma at the end of the Nile Valley made them vulnerable to environmental fluctuations, political crises facing the Nile basin countries, and any reduction in the proportion of water is not only the Nile River, but for all r

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Publication Date
Thu Dec 15 2022
Journal Name
Heat Transfer
The indirect solar dryers with innovative solar air heaters designs: A review article
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Abstract<p>The drying process is considered an effective technique for preserving foods and agricultural products from spoilage. Moreover, the drying process lessens the products' weight, volume, and packaging, which prompts a reduction in the products' transportation costs. The drying technique with solar energy represents an ancient method, still alluring due to solar energy abundance and cost‐effectiveness. In this article, the previous manuscripts concerned with studying and analyzing indirect solar dryer systems that utilize innovative solar air heaters (SAHs) are reviewed. The results and conclusions are discussed intensively to clarify the significance of utilizing this type of drying technique. The ef</p> ... Show More
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Publication Date
Sun Oct 01 2023
Journal Name
Fuel
Matrix acidizing in carbonate rocks and the impact on geomechanical properties: A review
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Acid treatment is a widely used stimulation technique in the petroleum industry. Matrix acidizing is regarded as an effective and efficient acidizing technique for carbonate formations that leads to increase the fracture propagation, repair formation damage, and increase the permeability of carbonate rocks. Generally, the injected acid dissolves into the rock minerals and generates wormholes that modify the rock structure and enhance hydrocarbon production. However, one of the key issues is the associated degradation in the mechanical properties of carbonate rocks caused by the generated wormholes, which may significantly reduce the elastic properties and hardness of rocks. There have been several experimental and simulation studies regardi

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Publication Date
Wed May 17 2023
Journal Name
Journal Of Engineering
Development of Quality Rating Evaluation of Outgoing Product Case Study Applied at the General Company for Vegetable Oils
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Research covers the uses the method of Quality Rating Evaluation to evaluate the
quality of production through which a determination of product quality of its production in
order to determine the amount of sales hence the profits for the company. The most important
function is to satisfy consumer at reasonable prices. Methods were applied to the product
(toothpaste) in the General Company for Vegetable Oil – Almaamoon Factory .
The company's has obtained ISO-certified (ISO 9001-2008). Random samples of
final product intended for sale were collected from the store during months (February, April ,
June , October and December) for the year 2011 to determine the "quality rating " through
the applicat

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Publication Date
Thu May 18 2023
Journal Name
Journal Of Engineering
An Experimental Study of the Effects of Coolant Fluid on Surface Roughness in Turning Operation for Brass Alloy
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The effect of different cutting fluids on surface roughness of brass alloy workpiece during turning operation was carried out in this research. This was performed with different cutting speed, while other cutting parameters had been regarded as constants(feeding rate , and depth of cut). Surface roughness of machined parts that will be tested by electronic surface roughness tester .The results show that the standard coolant gives the best values of surface roughness for fixed cutting speed ,followed by sun flower oil that has approximately the same effect, while the air stream as a coolant gave unsatisfied results for the evaluation of surface roughness.

In the other hand the best values of surface roughness were recorded for max

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