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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 Jan 01 2024
Journal Name
Baghdad Science Journal
Using Wild Plant Species Grown in Wadi Al – Tib Region North East of Al – Ammara, Iraq, as Indicators of Heavy Metals Accumulation
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The current study included, studying the ability of eight genera of plants belong to Brassicaceae family, Brassica tournifortii, Cakile Arabica, Capsella bursa – pastoris,Carrichtera annua, Diplotaxis acris, Diplotaxis haru , Eruca sativa and Erucaria hispanica to accumulate ten heavy metals Cadmium, Chromium , Copper, Mercury, Manganese ,Nickel ,Lead ,and Zinc . Plant leaves samples were collected from Al-Tib area during spring of 2021.The data demonstrated that, the highest conc. of Cd was 2.7 mg/kg in Diplotaxis acris leaves and lower value was 0.3 mg/kg in Cakile Arabica leaves. For Co, the highest conc.was 1.3 mg/kg in Capsella bursa – pastoris leaves, whereas the lower value was 0.5 mg/kg in Cakile arabica leaves. As for Cr ele

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Publication Date
Sun Jun 12 2011
Journal Name
Baghdad Science Journal
Study the effective of annealing on the structural and sensitivity properties for SnO2 thin films to CO2 Gas
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In this research thin films from SnO2 semiconductor have been prepared by using chemical pyrolysis spray method from solution SnCl2.2H2O at 0.125M concentration on glass at substrate temperature (723K ).Annealing was preformed for prepared thin film at (823K) temperature. The structural and sensing properties of SnO2 thin films for CO2 gas was studied before and after annealing ,as well as we studied the effect temperature annealing on grain size for prepared thin films .

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Publication Date
Sun Sep 01 2013
Journal Name
Journal Of Economics And Administrative Sciences
The Impact of Sharing knowledge on organizational innovation Field study in the arab company , for detergents and chemical
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ABSTRACT

Impkact  of  Knowledge  sharing  on  organizational  innovation  Impriscal  study in Arabic company . 

of  Knowledge Management is  the  main  component  Knowledge  sharing  system, it mean the exchange if  Knowledge, ideas, and good  practice with  another  individual . Knowledge sharing between persons, then its values can growth .

It is vry important because it can provide us with the contention between virus peoples . the interaction among the people can pass all kind of Knowledge among them. the connection and interaction and interaction enabl

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Publication Date
Sun Dec 07 2008
Journal Name
Baghdad Science Journal
Nahrwan Clays Study for Brick Industry
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Nahrawan clay deposits lies in Diyala governorate , 65 Km, NE of Baghdad , according to the previous work in this field, in which they study the reserve belong to category of investigation ( C2 & C1 ) , we choice the proper area to investigation of category (B) with drill net( 200x 200m ) to rise the amount of reserve. The investigation work included drilling (116) boreholes of total depth ranges from (10.0-12.55m) , showed mainly clayey and silty deposits with little sand , and the typical borehole (648) represents all types of sediment in the area , and most of boreholes without sandy deposits , and all of these deposits is Quaternary sediment which is consist of two main sedimentary cycles ( the Pleistocene & Holocene ) . Chemical a

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Publication Date
Sun Feb 01 2026
Journal Name
Bulletin Of Pharmaceutical Sciences Assiut University
Synthesis and Characterization a New Schiff Base Ligand Derived from O-vanillin with Some Transition Metal Complexes and Study of Antimicrobial Activity
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Publication Date
Mon Mar 13 2017
Journal Name
Journal Of Baghdad College Of Dentistry
Gingival health condition and salivary physical properties among a group of patients with intermaxillary fixation in tow times intervals (Follow up study)
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ABSTRACT Background: One of the methods used in the treatment of maxillofacial fracture is intermaxillary fixation(IMF), the most common type is the Erich arch bar with interdental wiring. This study was conducted to investigate the impact of intermaxillary fixation on gingival health condition among a group of patients with facial fracture in relation to salivary physical properties. Materials and methods: Thirty patients with an age range of (17-37) years old with facial fractures and indicated for IMF. Plaque index and gingival index (Loe, 1967) were used to assess both of them before application and after removal of IMF. Unstimulated saliva sample collection was carried out under standardized conditions according to Navazesh and Kum

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Publication Date
Tue Dec 01 2009
Journal Name
Journal Of Economics And Administrative Sciences
Measuring the impact of interest rates on the movement of international financial flows (Japan case study) for the period 1985-2005
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يعد الاقتصاد الياباني احد اكبر الاقتصادات الرأسمالية المتقدمة ويحتل المرتبة الثالثة بعد الاقتصاد الأمريكي واقتصاد الاتحاد الاوربي من حيث حجم الناتج المحلي الإجمالي والذي يكاد يقترب من (5) تريليون دولار سنويا.

لقد ادت التطورات المتلاحقة التي شهدها الاقتصاد العالمي وخاصة في حقل التمويل الدولي خلال العشرين سنة الاخيرة الى تصاعد وارتفاع في حجم وحركه رؤوس الاموال الدولية على اوسع نطاق بحيث ا

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Publication Date
Sun Jan 01 2023
Journal Name
Material Science And Semiconductor Processing
Photocatalytic degradation of Congo red dye using magnetic silica-coated Ag2WO4/Ag2S as Type I heterojunction photocatalyst: Stability and mechanisms studies
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In the present study, magnet silica-coated Ag2WO4/Ag2S nanocomposites (FOSOAWAS) were fabricated via a multistep method to address the drawbacks related to single photocatalysts (pure Ag2WO4 and pure Ag2S) and to clarify the significant influence of semiconductor heterojunction on the enhancement of visible-light-driven organic degradation. Different techniques were performed to investigate the elemental composition, morphology, magnetic and photoelectrochemical properties of the fabricated FOSOAWAS photocatalyst. The FOSOAWAS photocatalyst (1 g/L) exhibited excellent photodegradation efficiency (99.5%) against Congo red dye (CR = 20 ppm) after 140 min of visible-light illumination. This result confirmed the ability of the heterojunction be

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Publication Date
Fri Jun 01 2018
Journal Name
أ.م. حسين علي خضير بهاري
Symbolism of Jekor Village in the Poetry of the Iraqi Poet Badr Shakir as-Sayyab
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The paper aims at making the Russian reader acquainted with the Iraqi Poet Badr Shakir as-Sayyab, and showing the effect of the village and the city in his soul, the theme which is reflected in his poetry. Therefore, the researcher has translated the verses pertaining to this topic from Arabic into Russian so as to make the Russian reader know the important phases that talk about the village and city. The researcher has concluded that the theme of place, village and city has occupied a good portion of As-Sayyab's poetry, and that he (the poet) hated the city and expressed his wrath against it, because he viewed the city as embodiment of money and the degeneration of man. As opposed to this, As-Sayyab he loved being a farmer, and was

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Publication Date
Sun Apr 16 2023
Journal Name
Iraqi Journal For Computer Science And Mathematics
Some Methods to Estimate the Parameters of Generalized Exponential Rayleigh Model by Simulation
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This paper shews how to estimate the parameter of generalized exponential Rayleigh (GER) distribution by three estimation methods. The first one is maximum likelihood estimator method the second one is moment employing estimation method (MEM), the third one is rank set sampling estimator method (RSSEM)The simulation technique is used for all these estimation methods to find the parameters for generalized exponential Rayleigh distribution. Finally using the mean squares error criterion to compare between these estimation methods to find which of these methods are best to the others

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