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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 Sep 17 2014
Journal Name
African Journal Of Microbiology Research
Xylanase production using fruit waste as cost effective carbon source from thermo-tolerant Bacillus megaterium
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Publication Date
Mon Sep 06 2021
Journal Name
Journal Of Mechanical Engineering Research And Developments
Using Micro-Ceramic as an Abrasive Material to Remove Surface Roughness by Magnetic Abrasive Finishing
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Due to the rapid advancement of technology and the technology of things, modern industries start to need a highprecision equipment and surface finishing, so many finishing processes began to develop. One of the modern processes is Magnetic Abrasive Finishing (MAF), which is a high-precision process for internal and external finishing under the influence of a magnetic field of abrasive particles. Boron Carbide (B4C) ceramics was tested by mixing it with iron (Fe) and produced abrasive particles to reduce the intensity of scraping on the surface, reduce the economic cost and achieve a high finishing addition to remove the edges at the same time. The material selected for the samples was mild steel (ASTM E415) under (Quantity of Abrasives, Mac

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Publication Date
Wed Dec 10 2014
Journal Name
Desalination And Water Treatment
Groundwater protection from lead contamination using granular dead anaerobic sludge biosorbent as permeable reactive barrier
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Publication Date
Tue Oct 25 2022
Journal Name
Vi. International Scientific Congress Of Pure, Applied And Technological Sciences
Study the effect of adding alcoholic and aqueous extract of turmeric to processed chees as natural antioxidant and in improving its physicochemical properties
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Publication Date
Mon Mar 15 2021
Journal Name
Al-academy
Study of the participation of Saudi women in official visual arts exhibitions "Contemporary Saudi Art Exhibition as an Example": حنان بنت سعود الهزاع
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This research studies the Saudi women participation in the visual arts, presents descriptive and analytical overview on their artworks and assess development through their participation in the said exhibition, frequency of participation, and aims to understand the most important stages and changes of the subjects addressed, artistic styles and the factors affecting these results in view of female artist's attitude pertaining to several aspects such as administrative organization, judging committees etc.

Interviews were held with a sample of female artists, 17 artists from different regions and generations out of 182 participants and reviewed relevant exhibition literature during the period 1979-2018. The research problem is to id

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Publication Date
Thu Jun 25 2020
Journal Name
International Journal Of Drug Delivery Technology
The Effects of Salvia officinalis Gel as an Adjunct to Scaling and Root Planning in Patients with Periodontitis (Clinical and Immunological Study)
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Background: Phytotherapy is the usage of herbal species with medicinal properties for the management of various diseases. Gingivitis and periodontitis are diseases that involve the role of both the bacteria and the host immune response. Over the years, various researches have shown the importance of herbal products in the management of periodontal diseases. Aims of the study: To evaluate the efficacy of locally applied Salvia officinalis gel as adjunctive in the treatment of chronic periodontitis. Subjects and methods: Fourteen patients (10 males and 4 females) with chronic periodontitis were enrolled in the present study with total number of twenty-eight periodontal pockets utilizing a split mouth design, the pockets were divided i

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Publication Date
Sun Feb 18 2024
Journal Name
Migration Letters
Knee Injuries And Rehabilitation: A Comprehensive Review Of The Psychological Landscape
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MT Suhail, SA Hussein, MN Abdulhussein, WQ Abdaullateef, M khairallah Aid…, Migration Letters, 2024

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Publication Date
Mon Jan 03 2022
Journal Name
International Education And Culture Studies
A Future Vision of Mathematics Teacher Preparation Program at the Universities
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Publication Date
Mon Sep 14 2020
Journal Name
British Journal Of Neurosurgery
Head injuries caused by the ritual of ‘Tatbir’: a neurosurgical perspective
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Publication Date
Fri Jul 01 2022
Journal Name
Journal Of Engineering
A Review of the Asphalt Mixtures Containing Recycled Solid Waste Materials
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Landfill and incineration are the most common and widely used methods to dispose of solid wastes; both of these techniques are considered the main sources of pollution in the world due to the harmful toxic emissions that are considered an environmental problem. Because of the large areas used by landfills, they are not always considered an economical method. With the increase in the production of solid materials, solid wastes increase the pressure on incinerators and landfills, making the environmental pollution hazard more serious. Instead, these waste materials can be used in some other applications. One of the most important of these applications is asphalt pavements, which are the most used types of pavements in the

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