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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 Jun 01 2015
Journal Name
Journal Of Economics And Administrative Sciences
Using the Logistic Regression Model in Studding the Assistant Factors to Diagnose Bladder Cancer
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The cancer is one of the biggest health problems that facing the world . And  the bladder cancer has a special place among the most spread cancers in Arab countries specially in Iraq and Egypt(2) . It is one of the diseases which can be treated and cured if it is diagnosed early . This research is aimed at studying the assistant factors that diagnose bladder cancer such as (patient's age , gender , and other major complains of hematuria , burning or pain during urination and micturition disorders) and then determine which factors are the most effective in the possibility of diagnosing this disease by using the statistical model (logistic regression model) and depending on a random sample of (128) patients . After

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Publication Date
Thu Dec 01 2011
Journal Name
Iraqi Journal Of Physics
Design of Achromatic Combined Quadrupole Lens Using the Modified Bell-Shaped Field Distribution Model
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The optimization calculations are made to find the optimum properties of combined quadrupole lens consist of electrostatic and magnetic lenses to produce achromatic lens. The modified bell-shaped model is used and the calculation is made by solving the equation of motion and finding the transfer matrices in convergence and divergence planes, these matrices are used to find the properties of lens as the magnification and aberrations coefficients. To find the optimum values of chromatic and spherical aberrations coefficients, the effect of both the excitation parameter of the lens (n) and the effective length of the lens into account as effective parameters in the optimization processing

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Publication Date
Sun Mar 15 2020
Journal Name
Al-academy
Semiotic Transformations in Scenography of the Iraqi Theatre Show "The Play of Ali Al-Wardi and his Opponent- A Model": باسم محمد احمد حسن
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      Semiotics has been through wide experiences in various human sciences, especially in the fields of poetry, novel and myths. But its interest in the theatre and drama was much less and unique despite the richness of the theatrical connection as it is a probable field for the semiotic investigation which may require the semiotic approach in dealing with the theatrical and dramatic show during the two processes of: structural construction and deconstruction starting from a set of overlapping and interconnected texts inside the show, which can be limited in the text, then it would be difficult to semiotically cover all these complex and tricky texts. The theatre in its structural and aesthetic construction is c

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Publication Date
Thu Jun 01 2017
Journal Name
International Journal Of Science And Research
Precise Solutions of a Viscoelastic Fluid Flow in an Annular Pipe under an Impulsive Pressure with the Fractional Generalized Burgers' Model
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This paper deals with an analytical study of the flow of an incompressible generalized Burgers’ fluid (GBF) in an annular pipe. We discussed in this problem the flow induced by an impulsive pressure gradient and compare the results with flow due to a constant pressure gradient. Analytic solutions for velocity is earned by using discrete Laplace transform (DLT) of the sequential fractional derivatives (FD) and finite Hankel transform (FHT). The influences of different parameters are analyzed on a velocity distribution characteristics and a comparison between two cases is also presented, and discussed in details. Eventually, the figures are plotted to exhibit these effects.

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Publication Date
Thu Apr 01 2021
Journal Name
Iop Conference Series: Earth And Environmental Science
Groundwater Quality Study Based on the Existence of Escherichia coli as Bioindicator
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Abstract<p>The research aim was to observe the distribution pattern of <italic>Escherichia coli</italic> as groundwater pollution indicator in the most populous area, Matraman Sub-District Area in Jakarta, Indonesia (106°49’35” EL and 06°10’37” SL) consists of six (6) Urban Villages. The existence of <italic>Escherichia coli</italic> was measured with Most Probable Number (MPN) method as mentioned in Indonesian Standard Number 01-2332.1-2006. This research was also measure pollution parameter of Dissolved Oxygen (DO) and pH, and topography analyses used as well to determine groundwater flow direction. Groundwater sampling was conducted in several housings that have </p> ... Show More
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Publication Date
Fri Jan 01 2021
Journal Name
Revista Iberoamericana De PsicologÍa Del Ejercicio Y El Deporte
SPECIAL EXERCISES IN THE HIERARCHICAL OPPOSING TRAINING METHOD AND ITS EFFECT ON DEVELOPING PHYSICAL ABILITIES AND ACCURACY OF SOCCER SCORING FOR ADVANCED PLAYERS
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Publication Date
Wed Jun 01 2011
Journal Name
Journal Of Economics And Administrative Sciences
Methods of using the periodic chart in the case of the missing values of the stable AR model (2)
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In this study, we investigate the behavior of the estimated spectral density function of stationary time series in the case of missing values, which are generated by the second order Autoregressive (AR (2)) model, when the error term for the AR(2) model has many of continuous distributions. The Classical and Lomb periodograms used to study the behavior of the estimated spectral density function by using  the simulation.

 

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Publication Date
Fri Nov 11 2011
Journal Name
Thesis
Performance Analysis of a New Compact Magneto-Rheological Proportional Control Valve for Hydraulic Actuation Using FEM and Experimental Approach
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One of the main parts in hydraulic system is directional control valve, which is needed in order to operate hydraulic actuator. Practically, a conventional directional control valve has complex construction and moving parts, such as spool. Alternatively, a proposed Magneto-rheological (MR) directional control valve can offer a better solution without any moving parts by means of MR fluid. MR fluid consists of stable suspension of micro-sized magnetic particles dispersed in carrier medium like hydrocarbon oil. The main objectives of this present research are to design a MR directional control valve using MR fluid, to analyse its magnetic circuit using FEMM software, and to study and simulate the performance of this valve. In this research, a

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Publication Date
Sat Jun 01 2024
Journal Name
Case Studies In Chemical And Environmental Engineering
Optimization of photocatalytic process with SnO2 catalyst for COD reduction from petroleum refinery wastewater using a slurry bubble photoreactor
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Publication Date
Tue Apr 14 2020
Journal Name
Modern Sport
The Effect of Using the Bybee Strategy(5ES) according to Brain Control Patterns in Learning a Kinetic Series on Floor exercises in Artistic Gymnastics for men
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The aim of this study to identify patterns of cerebral control (right and left) for second grade students in the collage of physical education and sports science of the University of Baghdad, as well as identify the definition of theThe Effect of Using the Bybee Strategy(5ES) according to Brain Control Patterns in Learning a Kinetic Series on Floor exercises in Artistic Gymnastics for menمجلة الرياضة المعاصرةالمجلد 19 العدد 1 عام 2020effect using the (Bybee) strategy (5ES) according to brain control patterns inlearning a Kinetic series on floor exercises In artistic gymnastics for men, andidentify the best combination between the four research groups learn, use Finderexperimental method research sample consi

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