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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
Thu Jun 16 2022
Journal Name
Comparative Parasitology
A Comparative Study of Some Intestinal Parasites in Fecal Samples of Domestic and Stray Cats in Baghdad, Iraq
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Some feline intestinal parasites such as Toxocara, Giardia, and Cryptosporidium can spread to humans through feces. Therefore, it is important to prevent exposure of family members by screening cat fecal samples twice per year for potential treatment regimes. This study was initiated to compare and identify gastrointestinal parasites of domestic and stray cats (Felis domesticus) in Baghdad City, Iraq. Parasite eggs and oocysts were identified under light microscopy by applying standard laboratory techniques (flotation and sedimentation). Overall, 59 of 121 (48.7%) fecal samples were positive for intestinal parasites. The rate of infection by Toxoplasma gondii was (3.31%), Isospora spp. (6.61%), Cryptosporidium spp. (31.4%), and Toxocara spp

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Publication Date
Tue Jun 01 2010
Journal Name
Journal Of The College Of Languages (jcl)
Nature as a holy book
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Nature and natural beauty have always been the source of inspiration for poets and mystics.  For them, nature is one of the most recurrent and celebrated themes. It is a significant symbol of the beauty, righteousness and freshness they are looking for. For religious and mystical poets, it is a reference to God, his beauty, and splendour. Comparing it with the scripture, Thomas Ryan, a Catholic priest and a mystical writer, says ''The Bible is the 'small book', the world of nature is the 'big book'. Both reveal the Creator.''1

     For Muslim mystics, God does exist everywhere as the Qur'an states:   ''Wherever (Whithersoever)  you turn, there is God's face” (Chapter (Surah): 2

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Publication Date
Wed Aug 01 2018
Journal Name
Journal Of Economics And Administrative Sciences
A Comparative Study of Some Methods of Estimating Robust Variance Covariance Matrix of the Parameters Estimated by (OLS) in Cross-Sectional Data
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Abstract

The Classical Normal Linear Regression Model Based on Several hypotheses, one of them is Heteroscedasticity as it is known that the wing of least squares method (OLS), under the existence of these two problems make the estimators, lose their desirable properties, in addition the statistical inference becomes unaccepted table. According that we put tow alternative,  the first one is  (Generalized Least Square) Which is denoted by (GLS), and the second alternative is to (Robust covariance matrix estimation) the estimated parameters method(OLS), and that the way (GLS) method neat and certified, if the capabilities (Efficient) and the statistical inference Thread on the basis of an acceptable

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Publication Date
Fri Dec 15 2017
Journal Name
Journal Of Baghdad College Of Dentistry
In Vitro Comparative Assessment Of The Effect Of Gutta-Fusion Obturation On The Push Out Bond Strenght Of Three Types Of Sealers
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Background: The bond strength of the root canal sealers to dentin is very important property for maintaining the integrity and the seal of root canal filling. The aim of this study was to evaluate and compare the push-out bond strength of root filled with total fill Bioceramic, AH Plus and Gutta-flow®2 sealers using GuttaFusion®obturation system versus single cone obturation technique. Materials and method: sixty of mandibular premolars teeth with straight roots were used in this study, these roots were instrumented using Reciproc system, instrumentation were done with copious irrigation of 3 mL 5.25% sodium hypochlorite solution (NaOCl) during all the steps of preparation, and smear layer will be removed with 1 ml of 17% EDTA kept in

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Publication Date
Fri Dec 01 2017
Journal Name
Journal Of Baghdad College Of Dentistry
In Vitro Comparative Assessment of the Effect of Gutta-Fusion Obturation on the Push Out Bond Strength of Three Types of Sealers
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Background: The bond strength of the root canal sealers to dentin is very important property for maintaining the integrity and the seal of root canal filling. The aim of this study was to evaluate and compare the push-out bond strength of root filled with total fill Bioceramic, AH Plus and Gutta-flow®2 sealers using GuttaFusion®obturation system versus single cone obturation technique. Materials and method: sixty of mandibular premolars teeth with straight roots were used in this study, these roots were instrumented using Reciproc system, instrumentation were done with copious irrigation of 3 mL 5.25% sodium hypochlorite solution (NaOCl) during all the steps of preparation, and smear layer will be removed with 1 ml of 17% EDTA kept in

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Publication Date
Sun Mar 26 2017
Journal Name
Iraqi Journal Of Pharmaceutical Sciences ( P-issn 1683 - 3597 E-issn 2521 - 3512)
Spectrophotometric Determination of Nitrofurantoin Drug in its Pharmaceutical Formulations Using MBTH as a Coupling Reagent
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A direct, sensitive and efficient spectrophotometric method for the determination of nitrofurantoin
drug (NIT) in pure as well as in dosage form (capsules) was described. The suggested method was
based on reduction NIT drug using Zn/HCl and then coupling with 3-methyl-2-benzothiazolinone
hydrazone hydrochloride (MBTH) in the presence of ammonium ceric sulfate. Spectrophotometric
measurement was established by recording the absorbance of the green colored product at 610 nm.
Using the optimized reaction conditions, beer’s law was obeyed in the range of 0.5-30 μg/mL, with
good correlation coefficient of 0.9998 and limits of detection and quantitation of 0.163 and 0.544
μg/mL, respectively. The accuracy and

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Publication Date
Sat Jul 01 2023
Journal Name
Journal Of Engineering
Performance of Solar Adsorption Cooling System Using Methanol and Activated Carbon as a Working Pair
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The need for renewable energy sources is higher than ever due to rising global warming, climate change, and ozone depletion. For refrigeration and air conditioning applications, adsorption refrigeration systems are viable alternatives cooling techniques. This study is a topic and part of the M.Sc. thesis. A field solar-powered ice maker unit was created, studied, tested, and evaluated on the 13th and 30th of May, 2022. Activated carbon and methanol pair was used to set up a refrigeration system in Baghdad (Al Dora). Experimental tests were carried out outdoors to determine the coefficient of performance COP and specific cooling power SCP of the system. The results showed that the lowest temperature

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Publication Date
Mon Jan 13 2020
Journal Name
Day 3 Wed, January 15, 2020
Numerical Simulation of Gas Lift Optimization Using Genetic Algorithm for a Middle East Oil Field: Feasibility Study
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<p>Gas-lift technique plays an important role in sustaining oil production, especially from a mature field when the reservoirs’ natural energy becomes insufficient. However, optimally allocation of the gas injection rate in a large field through its gas-lift network system towards maximization of oil production rate is a challenging task. The conventional gas-lift optimization problems may become inefficient and incapable of modelling the gas-lift optimization in a large network system with problems associated with multi-objective, multi-constrained, and limited gas injection rate. The key objective of this study is to assess the feasibility of utilizing the Genetic Algorithm (GA) technique to optimize t</p> ... Show More
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Publication Date
Mon Jul 10 2023
Journal Name
Journal Of Engineering
Rhythm As Creative System In Houses Architecture Comparative Application Study Between Heritage And Contemporary Houses
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Rhythm is considered one of the creative concepts in the recent architectural thought; it has emerged clearly as a mean of creating the highest levels of creativity in architecture, especially in contemporary architectural movements. The importance of rhythm has  emerged, especially, when the architecture , its beginnings concentrated on the principle of the links with poetic structures. Many architectural studies deal with concept of rhythm in architecture with different ways various according to the trend of each study, this show the importance of studying the concept of rhythm in the architectural field in general. This study try to focus on the utilization of rhythm as creative system in architecture of heritage and contemporary

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Publication Date
Sun Jan 02 2011
Journal Name
Journal Of The Faculty Of Medicine Baghdad
Relation-ships of neonatal septicemia with the mean serum levels of IL-8 and IL-1 in three large hospitals in Baghdad
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