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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
Tue Mar 15 2022
Journal Name
Journal Of Baghdad College Of Dentistry
In vitro cytotoxic effect of annona squamosa pulp ex-tract as a mouthwash for children on human normal cell line
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Background: Fruits and their by-products are the primary sources of bioactive chemicals in plants. Because of its phytochemical richness, Annona squamosa fruits have gained the alertness of people willing in health-promoting diets. The purpose of this in vitro study was to evaluate the cytocompatibility effect of ethanolic crude extract of Annona squamosa pulp against a human normal cell line as a mouthwash for children. Material and method: The ethanolic extract of Annona squamosa pulp was extracted using the ultrasonic method and then lyophilized to make it powder. The MTT (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl-2H-tetrazolium bromide) test was performed to investigate the cytotoxic activity of the pulp extract on a human normal cell l

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Publication Date
Mon Mar 25 2019
Journal Name
Al-academy
Direction Structure of the Imaginary and Interpretation Controversy in the Theatre Reception "Mukashafat" Play -A Model: ثابت رسول جواد
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The current research deals with the argument of delusion and interpretation in the direction structure and its reflected impact in the reception activity and the amount of conceptual displacement it is subjected to in an aesthetic approach to abstract conceptual definitions of the reception activity , by the effect of this dialectic in the direction structure, which can be summed up by the following question: (What are the characteristics of the direction structure of the imaginary and what is the argument of interpretation in the theatre reception activity?) in order to stand on the aesthetic framework and conceptual definition of the direction structure in the controversy of interpretation and imagination, and its impact on the concept

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Publication Date
Tue Dec 15 2020
Journal Name
Al-academy
Acculturation and its Evolutionary Tendency in the Design of the Prayer Space Elements / Niche – A model: آلاء طالب كريم
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The peculiarity of worship spaces in the Islamic architecture is evident by its symbolic connotations with doctrinal connections, thus the niche has a major status in that symbolic connotation, which transformed due to the cultural interaction from a rock on the wall directed towards Mecca into an element of integrated structural entity with performative and aesthetic characteristics. The spread of the Islamic religion contributed to subjecting it to a design acculturation process, thus the problem of the research was raised by the following question: has the evolutionary tendency of acculturation been able to effect a major transformation in the niche design? The research aims at identifying the design acculturation and its translation

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Publication Date
Fri Aug 10 2018
Journal Name
In Book: Challenges In Mechanics Of Time-dependent Materials, Volume 2edition: 1stchapter: 11
A Case Study to Evaluate Live Load Distributions for Pre-stressed RC Bridge
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Publication Date
Tue Jan 23 2024
Journal Name
Journal Of Applied Mathematics
Dynamics Analysis of a Delayed Crimean-Congo Hemorrhagic Fever Virus Model in Humans
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Given that the Crimean and Congo hemorrhagic fever is one of the deadly viral diseases that occur seasonally due to the activity of the carrier “tick,” studying and developing a mathematical model simulating this illness are crucial. Due to the delay in the disease’s incubation time in the sick individual, the paper involved the development of a mathematical model modeling the transmission of the disease from the carrier to humans and its spread among them. The major objective is to comprehend the dynamics of illness transmission so that it may be controlled, as well as how time delay affects this. The discussion of every one of the solution’s qualitative attributes is included. According to the established basic reproductio

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Publication Date
Tue Feb 27 2024
Journal Name
Mathematical Modelling Of Engineering Problems
Dynamics of a Fractional-Order Prey-Predator Model with Fear Effect and Harvesting
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Publication Date
Fri Dec 08 2023
Journal Name
Frontiers In Endocrinology
Estrobolome dysregulation is associated with altered immunometabolism in a mouse model of endometriosis
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Introduction

Endometriosis is a painful disease that affects around 5% of women of reproductive age. In endometriosis, ectopic endometrial cells or seeded endometrial debris grow in abnormal locations including the peritoneal cavity. Common manifestations of endometriosis include dyspareunia, dysmenorrhea, chronic pelvic pain and often infertility and symptomatic relief or surgical removal are mainstays of treatment. Endometriosis both promotes and responds to estrogen imbalance, leading to intestinal bacterial estrobolome dysregulation and a subsequent induction of inflammation.

Methods

In the current study, we investigated the linkage be

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Publication Date
Thu Jun 29 2023
Journal Name
International Journal Of Nonlinear Analysis And Applications (ijnaa)
Applying a suitable approximate-simulation technique of an epidemic model with random parameters
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Because the Coronavirus epidemic spread in Iraq, the COVID-19 epidemic of people quarantined due to infection is our application in this work. The numerical simulation methods used in this research are more suitable than other analytical and numerical methods because they solve random systems. Since the Covid-19 epidemic system has random variables coefficients, these methods are used. Suitable numerical simulation methods have been applied to solve the COVID-19 epidemic model in Iraq. The analytical results of the Variation iteration method (VIM) are executed to compare the results. One numerical method which is the Finite difference method (FD) has been used to solve the Coronavirus model and for comparison purposes. The numerical simulat

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Publication Date
Wed Sep 30 2015
Journal Name
College Of Islamic Sciences
Trends of poetic purposes towards praise: Dabal al-Khuzai's poetry is a model
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Poetic objects may go towards a specific purpose and dissolve and interact with them to produce
A purpose characterized by the title but belongs to the U from afar.
The yarn goes towards praise with a purely horizontal relationship that mentions virtues but crowns them towards women.
In lamentation remember the virtues but crown them towards the dead.
In wisdom remember the virtues but crown them towards time.
In the description remember the virtues but crown them towards nature. All objects are inline
Horizontal We will prove this in the axes of research has required the plan to be a blind, five
The preamble, a brief overview of the life of Dabal All Khuzaie and the works and poets of the first axis
The direction

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Publication Date
Tue Feb 01 2022
Journal Name
Civil Engineering Journal
Calibration of a New Concrete Damage Plasticity Theoretical Model Based on Experimental Parameters
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The introduction of concrete damage plasticity material models has significantly improved the accuracy with which the concrete structural elements can be predicted in terms of their structural response. Research into this method's accuracy in analyzing complex concrete forms has been limited. A damage model combined with a plasticity model, based on continuum damage mechanics, is recommended for effectively predicting and simulating concrete behaviour. The damage parameters, such as compressive and tensile damages, can be defined to simulate concrete behavior in a damaged-plasticity model accurately. This research aims to propose an analytical model for assessing concrete compressive damage based on stiffness deterioration. The prop

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