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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
Sat Jan 01 2022
Journal Name
Materials Today: Proceedings
Studying the impact of condensate blockage on gas production: A review
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When the drawdown pressure amounts to a value below the dew point pressure, a minor droplet of condensate is shaped and accumulated in the close area of wellbore. As the accumulation happens, the saturation of the liquid will grow and a reduction in gas relative permeability will happen, therefore it will affect the productivity. Generally, condensate baking problem in gas wells is being deliberated and studied and numerous techniques have been suggested to solve the problem. The studying of condensate banking dynamics is essential to evaluate the productivity and behavior of the wells of the gas fields.

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Publication Date
Sun Jan 01 2023
Journal Name
Ath-thaqafa Al-ajnabiah
Sufi Tafsir Reconsidered: Exploring the Development of a genre, Foreign Culture
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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
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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Publication Date
Tue Jan 01 2019
Journal Name
Plant Archives
The role and importance of amino acids within plants: A review
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Publication Date
Tue Jan 05 2021
Journal Name
International Journal Of Research In Social Sciences & Humanities
THE SCIENCES OF THE QUR’AN IN THE INTERPRETATION OF A BRIGHTENING OF THE QUR’AN BY AL-TALAQANI
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The paper deals with the study of the sciences of the Qur’an according to the interpreter, Ayatollah Sayyid Mahmoud al-Talaqani, a religious jihadist figure from Iran. He is the author of the exegesis (Ishraq from Al-Quran), which consists of six parts, which he wrote inside the prisons of the Shah and in exile. Mr. Al-Talaqani agreed with some of the commentators in his positions on the sciences of the Qur’an, and some of them disagreed with others.

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Publication Date
Fri Sep 01 2017
Journal Name
Journal Of Baghdad College Of Dentistry
In Vitro the Effect of Canals Instrumented with Three Rotary Ni-Ti Systems on the Dislocation Resistanceo Guttafusion ® versus Single Cone Obturation Technique
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Background: Complete seal of the root canal system following its chemo-mechanical debridement plays a pivotal role for achieving successful endodontic treatment. This can be established by reducing the gaps between the core filling material and root canal wall. Aim: To assess and compare the dislocation resistance of root canals obturated with GuttaFusion® and TotalFill BC sealer versus single cone obturation technique and TotalFill BC sealer after instrumentation of the canals with WaveOne, ProTaper Next and ProTaper Universal system. Material and Method: Sixty extracted human permanent mandibular premolars were conducted in the current study. The teeth were decorated and left the root with 15mm length; the roots were divided randomly i

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Publication Date
Sat Feb 01 2020
Journal Name
Journal Of Economics And Administrative Sciences
Applying some hybrid models for modeling bivariate time series assuming different distributions for random error with a practical application
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Abstract

  Bivariate time series modeling and forecasting have become a promising field of applied studies in recent times. For this purpose, the Linear Autoregressive Moving Average with exogenous variable ARMAX model is the most widely used technique over the past few years in modeling and forecasting this type of data. The most important assumptions of this model are linearity and homogenous for random error variance of the appropriate model. In practice, these two assumptions are often violated, so the Generalized Autoregressive Conditional Heteroscedasticity (ARCH) and (GARCH) with exogenous varia

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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 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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