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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 Sep 03 2020
Journal Name
Al-kindy College Medical Journal
Unusual Location of Giant Cell Tumor of the Tendon Sheath .. A Case Report
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Locking of the knee is a one of the commonest orthopedic outpatient presentation. This patient usually need magnetic resonance imaging (MRI) when there is suspected lesion in the soft tissue clinically. Meniscal tears is the first differential diagnosis when accompany with painful knee. (1, 2)Giant cell tumor (GCT) is benign a localized nodular tenosynovitis often occur in the tendon sheath , Mostly involve the hand tendons in middle age group between 30 and 50 years old , female affect more than male.(3,4) The WHO defines two well-known kinds of giant cell tumor: (1) pigmented villonodular synovitis ( generalized type), which mainly involve the joints of the lower limb and (2) giant cell tumor of the tendon sheath ( localized type)

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Publication Date
Tue Oct 08 2002
Journal Name
Iraqi Journal Of Laser
Effect of Gas Mixture on the Output Characteristics of a CW CO2 Laser
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In this work, the effect of partial amounts of gases in gas mixture of a CW CO2 laser on the output power was investigated. Also their effect on the condition determining the glow-discharge self-sustaining required for pumping the active medium was studied. Two fit relations were derived to predict the output laser power and the electric field to unit pressure ratio as functions to the partial amounts of gases. Results presented in this work could be used fruitfully to determine some of the optimum operational conditions of glow-discharge low-power CW CO2 lasers.

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Publication Date
Thu Oct 06 2011
Journal Name
Fes Journal Of Engineering Sciences
Derivation of a New Equation to Obtain the Permeability Coefficient of Clayey Soils
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The main objective of this research is to find the coefficient of permeability (k) of the soil and especially clayey soil by finding the degree of consolidation (rate of consolidation). New modify procedure is proposed by using the odometer (consolidation) device. The ordinary conventional permeability test usually takes a long time by preparing and by testing and this could cause some problems especially if there is a need to do a large number of this test and there were a limited number of technicians and/or apparatus. From this point of view the importance of this research is clear, since the modified procedure will require a time of 25 minute only. Derivation made to produce an equation which could be used to fined the permeabi

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Publication Date
Thu May 14 2026
Journal Name
Al–bahith Al–a'alami
THE ROLE OF IRAQI SATELLITE TV TOWARDS A CULTURE OF PROTEST AND REMONSTRATION
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The research dealt with a topic that has been practiced and transmitted news in satellite channels in recent years a lot. That is to say the role of satellite channels in the culture of a protest. In general, this study aims to reach to know the extent of the impact of television, especially the impact of the programs that bear the contents of protest and remonstration on the public; and what can be resulted out of these programs as cognitive, emotional and behavioral effects as a result of the individual's exposure to these programs and their impact from the culture of pretense. In addition to that, the research was interested in explaining the role of Iraqi satellite channels in developing and cultivating such culture; and following up

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Publication Date
Tue Mar 01 2022
Journal Name
Iraqi Journal Of Physics
Effect of Carbon Nanoparticles on the Performance Efficiency of a Solar Water Heater
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Carbon nanoparticles are prepared by sonication using carbon black powder. The surface morphology of carbon black (CB) and carbon nanoparticles (CNPs) is investigated using scanning electron microscopy (SEM). The particles size ranges from 100 nm to 400 nm for CB and from 10 nm to 100 nm for CNPs. CNPs and CB are mixed with silicon glue of different ratios of 0.025, 0.2, 0.05, and 0.1 to synthesis films. The optical properties of the prepared films are investigated through reflectance and absorbance analyses. The ratio of 0.05 for CNPs and CB is the best for solar paint because of its higher solar water heater efficiency and is then added to the silicon glue . Temperature of cold water and temperature of hot water in storage tank were ta

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Publication Date
Sun Jun 02 2019
Journal Name
Journal Of The College Of Languages (jcl)
A Pragmatic Analysis of the Use of Intensifiers in Charles Dickens’ Hard Times
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The present study investigates the use of intensifiers as linguisticdevices employed by Charles Dickens in Hard Times. For ease of analysis, the data are obtained by a rigorous observation of spontaneously occurring intensifiers in the text. The study aims at exploring the pragmatic functions and aesthetic impact of using intensifiers in Hard Times.The current study is mainly descriptive analytical and is based on analyzing and interpreting the use of intensifiers in terms ofHolmes (1984) andCacchiani’smodel (2009). From the findings, the novelist overuses intensifiers to the extent that 280 intensifiers are used in the text. These intensifiers(218) are undistinguished

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Publication Date
Sat Aug 01 2015
Journal Name
Journal Of Engineering
Development of a Blueprint Impact System of the risks on construction projects Implementation
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In Production and Operations Management the specialists  have  tried to develop a strategy to counter the risks arising from the activities of the organization and of waste of various types and therefore the risk management in the contemporary framework represents a phenomenon of new quality, and can not be this phenomenon to take practical dimensions, but the development of culture of the organization towards the risks and deal with all aspects and paint ways to address them within an integrated program, and requires new skills and systems provide accurate information capable of coordination between the various parties within the organization.

     The research aims to develop a blu

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Publication Date
Thu Sep 03 2020
Journal Name
Al-kindy College Medical Journal
Unusual Location of Giant Cell Tumor of the Tendon Sheath .. A Case Report
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Locking of the knee is a one of the commonest orthopedic outpatient presentation. This patient usually need magnetic resonance imaging (MRI) when there is suspected lesion in the soft tissue clinically. Meniscal tears is the first differential diagnosis when accompany with painful knee. (1, 2)
Giant cell tumor (GCT) is benign a localized nodular tenosynovitis often occur in the tendon sheath , Mostly involve the hand tendons in middle age group between 30 and 50 years old , female affect more than male.(3,4) The WHO defines two well-known kinds of giant cell tumor: (1) pigmented villonodular synovitis ( generalized type), which mainly involve the joints of the lower limb and (2) giant cell tumor of the tendon sheath ( localized type)

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Publication Date
Sat Jan 25 2020
Journal Name
International Journal Of Research In Pharmaceutical Sciences
Determination of the Dissociation Constants of Metformin from a Second Derivative UV Spectrum
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An environmentally begnin second derivative spectrometric approach was developed for the estimation of the dissociation constants pKa(s) of metformin, a common anti-diabetic drug.  The ultraviolet spectra of the aqueous solution of metformin were measured at different acidities, then the second derivative of each spectrum was graphed. The overlaid second derivative graphs exhibited two isobestic points at 225.5 nm and 244 nm pointing out to the presence of two dissociation constants for metformin pKa1 and pKa2, respectively. The method was validated by evaluating the reproducibility of the acquired results by comparing the estimated values of the dissociation constants of two different strategies that show excellent matching. As we

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Publication Date
Mon Oct 30 2023
Journal Name
Rare Metal Materials And Engineering
The effect of special exercises using the (Blazepod) device to develop the defensive player's movement for advanced basketball players
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The purpose of this paper is to preparing exercises for using the (Blazepod) device for advanced basketball players, and then identifying the effect of using the (Blazepod) device in developing some of the player's defensive movement for advanced basketball players. 12 players from the Adhamiya Sports Club, the category of applicants for the 2022/2023 sports year, where they were chosen in a deliberate manner from the community of origin represented by clubs, and the researchers used the defender player's movement test, and the results of the study showed that the special exercises prepared by the researcher using the (Blazepod) device affected the development Defensive skills (the movement of the defending player) greatly increased among a

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