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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 Jan 01 2016
Journal Name
Journal Of The College Of Languages (jcl)
Linguistic contast between bilateral and trilateral roots in Semitics languages (Arabic and Syriac as a model)
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The present study investigates the relation between the biliteral and triliteral roots which is the introduction to comprehend the nature of the Semitic roots during its early stage of development being unconfirmed to a single pattern. The present research is not meant to decide on the question of the biliteral roots in the Semitic languages, rather it is meant to confirm the predominance of the triliteral roots on these languages which refers, partially, to analogy adopted by the majority of linguists. This tendency is frequently seen in the languages which incline to over generalize the triliteral phenomenon, i. e., to transfer the biliteral roots to the triliteral room, that is, to subject it to the predominant pattern regarding the r

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Publication Date
Thu Mar 30 2017
Journal Name
Iraqi Journal Of Pharmaceutical Sciences ( P-issn 1683 - 3597 E-issn 2521 - 3512)
Cephalothin as a Carrier of 6-Mercaptopurine for Targeting Cancer Tissues
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A lower extracellular pH is one of the few well-documented physiological differences between tumour and normal tissues. On the other hand, elevated glutathione (GSH) level has been detected in many tumours compared with healthy surrounding tissues. The compound II: 3-(9H-purin-6-yl-thio) carbonothionyl methyl-8-oxo-7-(2-thiophen-2-yl) acetamido-5-thia-1-azabicyclo-4-octo-ene-carboxylic acid was a cephalothin derivative contain 6-mercaptopurine (6-MP). Compound II react with general base catalysis in slightly acidic pH or with sulfhydryl nucleophiles to release the chemotherapeutic drug 6-MP. The generation of compound II was accomplished following multistep reaction procedures. The structure of compound II and its intermediate was confir

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Publication Date
Tue Jun 15 2021
Journal Name
Al-academy
The impact of the Arab Islamic environment on contemporary painting" The artist Abdul Rahman Al-Suleiman as a model".: محمود حسين عبد الرحمن
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  This research means a study (the impact of the Arab-Islamic environment on contemporary painting, the artist Abd al-Rahman al-Suleiman as a model). The research falls into two axes: the first: the theoretical axis, and the second: the applied axis. The first axis dealt with an introduction that contained: (the research problem, its importance, its goal, its limits, and the definition of terms). This research aims to uncover (the impact of the Arab-Islamic environment on contemporary painting, and the artist Suleiman was a model). And the research limits spatially: Saudi Arabia, and temporally: 2010-2014. This theme included two topics: The first: the characteristics of the Saudi environment and its impact on art. The second: the s

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Publication Date
Sat Oct 01 2022
Journal Name
Journal Of Pakistan Association Of Dermatologists
Zinc as an essential element for normal immune reactions and as a therapeutic agent for autoimmune diseases
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Publication Date
Mon Nov 30 2020
Journal Name
Journal Of Economics And Administrative Sciences
Strategic leadership skills as a moderate of the impact of environmental challenges on effective management of the environment according to the model (VUCA Prime)
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Purpose – The main purpose of this research is to highlight the main role of strategic leadership skills for top managements in accessing to effective management in accordance with the (VUCA Prime) methodology in (VUCA) environment as Miniature virtual environment, which refers to (Volatility), (Uncertainty), (Complexity), and (Ambiguity).

methodology – To achieve the research objective, this study selected the quantitative approach in research design, Questionnaire was used as the main instrument for data collection, the sample comprised the opinion poll (106) individual who functions as a head department. (Structural equation modelling by (Smart Pls3)

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Publication Date
Mon May 23 2022
Journal Name
The International Journal Of Artificial Organs
Quantitative analysis and control of the torque profile of the upper limb using a kinetic model and motion measurements
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This paper investigates a new approach to the rapid control of an upper limb exoskeleton actuator. We used a mathematical model and motion measurements of a human arm to estimate joint torque as a means to control the exoskeleton’s actuator. The proposed arm model is based on a two-pendulum configuration and is used to obtain instantaneous joint torques which are then passed into control law to regulate the actuator torque. Nine subjects volunteered to take part in the experimental protocol, in which inertial measurement units (IMUs) and a digital goniometer were used to measure and estimate the torque profiles. To validate the control law, a Simscape model was developed to simulate the arm model and control law in which measurem

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Publication Date
Sat Feb 11 2023
Journal Name
Applied Sciences
A Preliminary Study and Implementing Algorithm Using Finite State Automaton for Remote Identification of Drones
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Electronic remote identification (ER-ID) is a new radio frequency (RF) technology that is initiated by the Federal Aviation Authorities (FAA). For security reasons, traffic control, and so on, ER-ID has been applied for drones by the FAA to enable them to transmit their unique identification and location so that unauthorized drones can be identified. The current limitation of the existing ER-ID algorithms is that the application is limited to the Wi-Fi and Bluetooth wireless controllers, which results in a maximum range of 10–20 m for Bluetooth and 50–100 m for Wi-Fi. In this study, a mathematical computing technique based on finite state automaton (FSA) is introduced to expand the range of the ER-ID RF system and reduce the ene

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Publication Date
Wed May 29 2019
Journal Name
Journal Of Legal Sciences
The Extent of the Civil Liability of the Seller or Provider of Alcohol toward Intoxicated Persons and Their Victims – A Comparative Study
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There are many harmful acts that occur from drunkards in this case, especially those resulting from car accidents. The world is witnessing dozens or even hundreds of car accidents due to alcohol consumption. These accidents often result in serious injuries that could lead to the death of the drunk driver and those in the car As well as other persons present in the other vehicles with which the incident occurred or pedestrians on the street, as well as damage to private or public property, and if the order of return of the affected persons on the pretext of civil liability (tort) is made as a direct cause of the harmful act, Is entitled Do they like this refer to the liquor seller or their provider as the culprit? Or are they not related to

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Publication Date
Fri Jul 27 2012
Journal Name
Journal Of Prosthodontics
A Three-Dimensional Finite Element Analysis for Overdenture Attachments Supported by Teeth and/or Mini Dental Implants
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Publication Date
Thu Feb 01 2024
Journal Name
Heliyon
Removal of amoxicillin from contaminated water using modified bentonite as a reactive material
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This study concerns the removal of a trihydrate antibiotic (Amoxicillin) from synthetically contaminated water by adsorption on modified bentonite. The bentonite was modified using hexadecyl trimethyl ammonium bromide (HTAB), which turned it from a hydrophilic to a hydrophobic material. The effects of different parameters were studied in batch experiments. These parameters were contact time, solution pH, agitation speed, initial concentration (C0) of the contaminant, and adsorbent dosage. Maximum removal of amoxicillin (93 %) was achieved at contact time = 240 min, pH = 10, agitation speed = 200 rpm, initial concentration = 30 ppm, and adsorbent dosage = 3 g bentonite per 1L of pollutant solution. The characterization of the adsorbent, modi

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