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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 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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Publication Date
Fri Feb 27 2026
Journal Name
Journal Of Baghdad College Of Dentistry
An Assessment of Alpha-Amylase as Salivary Psychological Stress Marker in Relation to Temporomandibular Disorders among a Sample of Dental Students
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Background: University dental students perceived a higher level of stress prior to the final exam associated with raised salivary alpha-amylase levels which could be considered as a useful noninvasive biomarker for measuring acute stress. Using a Helkimo anamnestic and clinical dysfunction scoring for temporomandibular disorders can give a better insight about the association of this marker and temporomandibular disorders. The aim of this study was to evaluation level of salivary alpha-amylase in stressor students with temporomandibular disorders and the relation between the marker in relation to temporomandibular disorders severity. This might give a better understanding to the role of psychological stress as an etiological factor for deve

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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
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
Sat Mar 01 2008
Journal Name
Journal Of Economics And Administrative Sciences
PART 3 New Experiments Three Factors On The Box plot, Box notch & Outlier Values
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New two experiments of the three factors, in this study were constructed to investigate the effects, of the fixed variations to the box plot on subjects' judgments of the box lengths. These two experiments were constructed as an extension to the group B experiments, the ratio experiments the experiments with two variables carried out previously by Hussin, M.M. (1989, 2006, 2007). The first experiment box notch experiment, and the second experiment outlier values experiment. Subjects were asked to judge what percentage the shorter represented of the longer length in pairs of box lengths and give an estimate of percentage, one being a standard plot and the other being of a different box lengths and

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Publication Date
Wed Sep 08 2021
Journal Name
Journal Of Accounting And Financial Studies ( Jafs )
Obstacles facing the application of electronic banking An exploratory: study of the opinions of a sample of bank employees operating in the city of Nasiriyah
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Electronic banking plays a prominent role in providing the best banking services and upgrading the banking sector for the better, so this study aimed to shed light on the most prominent obstacles that prevent the application of electronic banking in banks operating in the city of Nasiriyah, and in order to achieve this goal the researcher used the descriptive analytical approach And through a questionnaire form that was distributed to a group of employees, numbering (60) employees in the upper, middle and operational departments in a number of branches of private banks operating in the city of Nasiriyah, namely (the Iraqi Trade Bank, the Gulf Commercial Bank, the Bank of Baghdad, the Union Bank of Iraq), which represented The stu

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Publication Date
Sun Jan 05 2020
Journal Name
Annals Of Tropical Medicine And Public Health
THE EFFECT OF THE TRAINING CURRICULUM ON DEVELOPING KINETIC AND TRANSITIONAL RESPONSE SPEED, ACCURACY OF THE STOPPING WALL PERFORMANCE, AND DEFENDING THE STADIUM IN VOLLEYBALL
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Scopus
Publication Date
Tue Dec 30 2008
Journal Name
Al-kindy College Medical Journal
Three Years Experience in the Management of Uterine Rupture at Al-Battool Teaching Hospital Mosul-Iraq
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Background: Ruptured uterus is a catastrophic event to both
mother and her fetus. Apart from maternal and fetal mortality
rates, the incidence of rupture of uterus is often taken as an
index of the standard of obstetric care.
Objective: To determine the frequency, causes, management
outcome of ruptured uterus at Al Batool maternity hospital.
Method: The study was conducted in the department of
obstetrics and gynecology at Al Batool maternity hospital
Mosul-Iraq over a period of three years from October 1st 2002
to August 30th 2005. All the cases of uterine rupture presented
during the study period were recorded and managed in the
department. Data was recorded on designed forms.
Results: Thirty nine cas

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Publication Date
Mon Mar 08 2021
Journal Name
Baghdad Science Journal
The analytical potentiality of three different liquid stationary phases in analysing rathylchlorosilanes by gas - liquid ehromatography
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Organohalosilanes conslitute an important subject ١٦؛ the chemistry oforganosilicon compound؛. Being starting materials and intermediates in the synthesis of a large number of various compounds so it is very important to get such materials in its highest purity ,but the separation of rathylchlorosilanes was still a big^oblem, duet^the great similarity in their physical and chemical properties, making its analysing verydifficult, ^or this reason tteir must be a good method o^e^r^iondealing^ththe^compounds, gas- liquid chromatography proved that it was the best, specially when (m- nitrotoluene) was used as a stationary liquid phase, it gave a complete separation and a good statistical results

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Publication Date
Thu Jan 01 2015
Journal Name
Algebra Letters
THE GRAPH OF A COMMUTATIVE KU-ALGEBRA
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In This paper, we introduce the associated graphs of commutative KU-algebra. Firstly, we define the KU-graph which is determined by all the elements of commutative KU-algebra as vertices. Secondly, the graph of equivalence classes of commutative KU-algebra is studied and several examples are presented. Also, by using the definition of graph folding, we prove that the graph of equivalence classes and the graph folding of commutative KU-algebra are the same, where the graph is complete bipartite graph.