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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
Wed Jun 06 2001
Journal Name
مجلة العلوم الاقتصادية والادارية
Double cross-over and cross-over with extra period designs -comparative study-
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The goal of the research is to find the optimization in the test of the appropriate cross-over design for the experiment that the researcher is carrying out (under assumption that there are carry-over effects of the treatments) to posterior periods after the application period (which is often assumed to be the first period). The comparison between the double cross-over design and the cross-over design with extra period. The similarities and differences between the two designs were studied by measuring the Relative Efficiency (RE) of the experiment.

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Publication Date
Thu Mar 01 2007
Journal Name
Al-khwarizmi Engineering Journal
An experimental comparative study between polypropylene and laminated lower limb prosthetic socket
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Most researchers concentrate their studies on the design, stress and pressure distributions of the prosthetic socket. A little attention is considered for the stiffness of the various materials of the prosthetic sockets. Prosthetic laminated sockets in Iraq are costly to be manufactured while polypropylene socket is relatively cheap in comparing with the laminates.

Experimental study is conducted to compare the stiffness of five prosthetic sockets made of different materials. Compression, three point flexural and tensile tests are implemented by the Testometric machine. The laminate sockets give better results in compression than polypropylene. Polypropylene gives good results in bending compared with the laminate sockets. When t

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Publication Date
Tue Jun 20 2023
Journal Name
Baghdad Science Journal
Determination of Molecular Weight and Viscosity of Irradiated Polystyrene
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The varied applications of polystyrene in various fields of life led to examining the cause of radiation influence on some rheological behavior of commercial Polystyrene (PS) solution in the chloroform (CHCl3) solvent. Polystyrene grains shape samples were irradiated using the radioactive element Cesium- 137 with (9 µci) activity for 10, 20, and 30 minutes. The viscosity of the polymer solution depends on the concentration and size (i.e. molecular weight) of the dissolved polymer. Experimental data showed that the radiation dose affected the value of viscosity (shear, relative, specific, and reduced). The viscosity value significantly reduced at 10 min radiation dose and when increasing the dose, the viscosity value increased

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Publication Date
Sat Dec 01 2012
Journal Name
Journal Of Economics And Administrative Sciences
A comparison Some of Methods for Estimating Survival Function for Truncated Exponential Distribution
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Exponential distribution is one of most common distributions in studies and scientific researches with wide application in the fields of reliability, engineering and in analyzing survival function therefore the researcher has carried on extended studies in the characteristics of this distribution.

In this research, estimation of survival function for truncated exponential distribution in the maximum likelihood  methods and Bayes first and second method, least square method and Jackknife dependent in the first place on the maximum likelihood method, then on Bayes first method then comparing then using simulation, thus to accomplish this task, different size samples have been adopted by the searcher us

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Publication Date
Mon Jan 28 2019
Journal Name
Journal Of The College Of Education For Women
Apply the gravity model for trips between Najaf center and its settlements
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The study showed flow rates and the interaction between the settlements served by applying the model of gravity theory to measure depending on the number of the population between city Najaf and the rest of the other settlements served and using three functions of disability, time and cost, as recorded an increase in the interaction index with some settlements like them Kufa, Abbasid and Manathira, while the indicator contrast was in other settlements, either when the application of the gravity model depending on trips and socio-economic characteristics accuracy rate was more pronounced.

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Publication Date
Thu Dec 01 2016
Journal Name
Journal Of Economics And Administrative Sciences
Use the le'vy Model on stock returns for some Iraqi banks estimate
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In this article we  study a single stochastic process model for the evaluate the assets pricing and stock.,On of the models le'vy . depending on the so –called Brownian subordinate as it has been depending on the so-called Normal Inverse Gaussian (NIG). this article aims as the estimate that the parameters of his model using my way (MME,MLE) and then employ those  estimate of the parameters is the study of stock returns and evaluate asset pricing for both the united Bank and Bank of North which their data were taken from the Iraq stock Exchange.

which showed the results to a preference MLE on MME based on the standard of comparison the average square e

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Publication Date
Mon Oct 07 2019
Journal Name
Journal Of Global Pharma Technology
Contribution of Equilibrium Variables with the High Spike Accuracy of the Position Diagonal Center (4) in the National Volleyball Team Players
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What is important about this study is whether there is a relationship between the ability to balance and beating overwhelming for the Iraqi national team volleyball? The study aims to identify the percentage of the equilibrium contribution and its variables with the accuracy of the skill of beating the high spike Diagonal center (4) in the players. In the national volleyball team season (2016-2017), the researchers used the descriptive approach in the style of associative relationships to suit the problem of research. The research community included all the players specialized in the high beating of the Iraqi national team applicants in the ball The researchers concluded that the equilibrium variables contributed accurately and quickly to t

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Publication Date
Thu Jan 01 2009
Journal Name
Journal Of Global Pharma Technology
Contribution of Equilibrium Variables with the High Spike Accuracy of the Position Diagonal Center (4) in the National Volleyball Team Players
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Publication Date
Fri Sep 09 2022
Journal Name
Surgical Neurology International
WhatsApp as a remote patient-monitoring tool in low- and middle-income countries: Experience from the cerebrovascular surgery service in Iraq
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Publication Date
Tue Jan 01 2019
Journal Name
Journal Of Global Pharma Technology
A morphological study and a new species registration of genus Xerophloea Germa, 1839 sp.nov. From sub-family Ledrinae Fairmai, 1855 of the leafhopper (Hemiptera: Cicadellidae) in Iraq
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