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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
Mon Sep 09 2024
Journal Name
مداد الاداب
Lexical Stylistic Analysis of Two ‎Extracts from Tale of Two Cities: ‎A Contrastive Study
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Since the time it emerged, stylistics, as a field of knowledge which ‎combines both linguistics and literature, acquired a special status in the ‎linguistic arena. Its significance in complementing the meaning ‎delivered by linguistic means has been proven and acknowledged ‎through numerous stylistic analytic attempts of different literary works ‎and in different languages. The question put forward in this paper is ‎whether or not the stylistic analysis can work as effectively on translated ‎texts as it does on the original ones without having the results reached ‎by the analysis distorting the meaning of the original text. An attempt to ‎investigate this question is made herein by conducting a lexical stylistic ‎analysi

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Publication Date
Tue Sep 15 2020
Journal Name
Arab World English Journal
A Cognitive-Semantic Analysis of Preposition on: An Experimental Study at University of Baghdad
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Publication Date
Mon Jan 01 2018
Journal Name
International Journal Of Surgery Open
Effectiveness of conservative management of uncomplicated acute appendicitis: A single hospital based prospective study
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<bold>ABSTRACT</bold> <sec> <title>Background:

Acute appendicitis is one of the commonest causes of acute abdomen. There is a wide discussion and controversy on the surgical and nonsurgical treatment of acute uncomplicated appendicitis. The aim of this study was to evaluate the efficacy and outcomes of the conservative management of selected cases of acute appendicitis with an antibiotic first plan.

Patients and methods:

This was a single hospital-based prospective study with a durat

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Publication Date
Wed Jun 01 2022
Journal Name
Canadian Journal Of Chemistry
Hydrogenation of pyridine and hydrogenolysis of piperidine over $γ$-Mo2N catalyst: a DFT study
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Increasing demands on producing environmentally friendly products are becoming a driving force for designing highly active catalysts. Thus, surfaces that efficiently catalyse the nitrogen reduction reactions are greatly sought in moderating air-pollutant emissions. This contribution aims to computationally investigate the hydrodenitrogenation (HDN) networks of pyridine over the γ-Mo2N(111) surface using a density functional theory (DFT) approach. Various adsorption configurations have been considered for the molecularly adsorbed pyridine. Findings indicate that pyridine can be adsorbed via side-on and end-on modes in six geometries in which one adsorption site is revealed to have the lowest adsorption energy (–45.3 kcal/mol). Over a nitr

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Publication Date
Wed Oct 03 2012
Journal Name
Journal Of Kufa For Chemical Science
A study of Adsorption of Acetone and 2- Butanone on Iraqi Siliceouns Rocks Powder
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Adsorption of Acetone and 2-Butanone on Iraqi siliceouns rocks powder have been investigated. UV technique has been used to determine the adsorption isotherms. The results showed that the adsorption isotherms obeyed Freundlich adsorption equation. The results showed that the adsorption increases with increasing acidity of solutions. The adsorption was exothermic process, increasing temperature leads to decreasing adsorption. H,  S, G were calculated

Publication Date
Sat Mar 02 2019
Journal Name
World Heart Journal
The Effects of Chronic Cigarette Smoking on the Right Ventricular Functions in Healthy Young Male Subjects: A Speckle Tracking Echocardiographic Study
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Background: Chronic cigarette smoking is one of the major risk factors for coronary artery disease. However, it has additional cardiac adverse effects independent of coronary atherosclerosis. Patient and Methods: After informed consent and perm- ission from the review board of the hospital, 80 healthy subjects who were classified as smokers or non-smokers were included in the study. They were examined by standard echocardiography protocol which was followed by two-dimensional speckle tracking to assess the functions of the right ventricle. Results: The tricuspid annular plane systolic excursion (TAPSE) was significantly reduced in smokers as compared to non-smokers (P < 0.05). The tricuspid flow peak late diastolic velocity (A wave) was sig

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Publication Date
Sat Oct 01 2022
Journal Name
Al–bahith Al–a'alami
Language communication, and the impact of journalism after 2003 AD (a study in the two newspapers, Al-Takahi and Al-Sabah)
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The methods used by the print media (press) is varied in conveying its messages and its orientations to the readers. But language takes the leading method among these methods, or a real competitor - so far - due to the characteristics and advantages of languages, including: ease, abbreviation, and development, etc.

In the midst of such events, political tensions, and what they carry of the global developments, and among which was the most important the fall of the former Iraqi regime in the spring of 2003, the press had the greatest share, and a large portion on the level of monitoring, analyzing, and interpreting the various consequences of the event. The interpreting of the news varies according to the evolving political trends

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Publication Date
Sun Sep 01 2013
Journal Name
Baghdad Science Journal
Synthesis ,spectroscopic study of Antipyryl azo 2-Naphthol and use it as new reagent for determination of Co(II) and Cu(II)
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A simple ,accurate and sensitive spectrophotometric method has been developed the determination of Cobalt(II) and Cupper (II) .The method is based on the chelation of Co(II) and Cu(II) ions with 4-(4´-pyrazolon azo) -2-Naphthol(APAN) in aqueous medium . The complexes have a maximum absorption at (513) and (506) nm and ? max 0.531×10 4 and 0.12×10 5 L.mol -1.cm -1 for Co(II) and Cu(II) respectively .The reagent and two complexes have been prepared in ethanolic solution.The stoichiometry of both complexes were found to be 1:2 (metal :legend) .The effects of various cations and anions on Co(II) and Cu(II) determination have been investigated .The stability constants and standard deviations for Co(II) and Cu(II) 0.291 x107 ,0.909X108 L.mol

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Publication Date
Thu Apr 30 2020
Journal Name
Journal Of Economics And Administrative Sciences
Banking liquidity and the possibility of invested it in enhancing the solvency For a number of commercial banks in Iraq
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The primary function of commercial banks is the process of converting liquid liabilities such as deposits to illiquid assets, (also known as a loan), liquid assets, (aka cash and cash equivalent) in a balanced manner between liquid and illiquid assets, that guaranteed the preservation of the rights of depositors and the bank and not by converting liquid liabilities into liquid assets in a very large percentage. This comes from its role as depository and intermediary institutions between supply and demand, therefore, we find that the high indicators of bank liquidity and solvency may reflect a misleading picture of the status of commercial banks, to some extent in terms of the strength of their balance sheets and

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Publication Date
Fri Mar 31 2017
Journal Name
Iraqi Journal Of Pharmaceutical Sciences ( P-issn 1683 - 3597 E-issn 2521 - 3512)
INVESTIGATION OF BENTONITE CLAY SURFACE AS A PHYSICAL ANTIDOTE IN ADSORPTION OF AMITRIPTYLINE-HCl, CHLORPROMAZINE-HCl AND CHLORDIAZEPOXIDE-HCl FROM SOLUTION
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A detailed study of adsorption from solution of amitriptyline-HCl, chlorpromazine-HCl and
chlordiazepoxide-HCl on bentonite clay surface has been performed at variable conditions of
temperature, pH and ionic strength. It is aimed in this work to explore the capability of this clay in
treatment of poisoning by the mentioned drugs if taken in quantities higher than the usual doses.
Quantities of drugs adsorbed have been determined by UV spectrophotometric technique. The
sequence of adsorption in neutral media at 37.5 CÙ’ followed the order:
Amitriptyline-HCl > chlorpromazine-HCl > chlordiazepoxide-HCl.
The results were discussed in the light of Langmuir and Freundich adsorption isotherms. The usual
basic th

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