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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 Feb 20 2012
Journal Name
North Africa Technical Conference And Exhibition
Comprehensive Model for Flash Calculations of Heavy Oils Using the Soave - Redlich - Kwong Equation of State
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Abstract<p>One of the main techniques to achieve phase behavior calculations of reservoir fluids is the equation of state. Soave - Redlich - Kwong equation of state can then be used to predict the phase behavior of the petroleum fluids by treating it as a multi-components system of pure and pseudo-components. The use of Soave – Redlich – Kwon equation of state is popular in the calculations of petroleum engineering therefore many researchers used it to perform phase behavior analysis for reservoir fluids (Wang and Orr (2000), Ertekin and Obut (2003), Hasan (2004) and Haghtalab (2011))</p><p>This paper presents a new flash model for reservoir fluids in gas – oil se</p> ... Show More
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Publication Date
Wed Jan 01 2025
Journal Name
Aip Conference Proceedings
Enhanced aerodynamics for sport cars using inverted wings: A comprehensive review
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Publication Date
Wed Mar 10 2021
Journal Name
Baghdad Science Journal
Detection capability Alttafaria for some materials using a bacterial mutagenesis system
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Tested effective Alttafaria some materials used for different purposes, system a bacterial mutagenesis component of three bacterial isolates belonging to different races and materials tested included drug Briaktin

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Publication Date
Tue Jan 01 2008
Journal Name
Journal Of Engineering
USING FUZZY LOGIC CONTROLLER FOR A TWO- TANK LEVEL CONTROL SYSTEM
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This paper presents a fuzzy logic controller for a two-tank level control system, which is a process with a dead time. The fuzzy controller is a proportional-integral (PI-like) fuzzy controller which is suitable for steady state behavior of the system. Transient behavior of the system was improved without the need for a derivative action by suitable change in the rule base of the controller. Simulation results showed the step response of the two-tank level control system when this controller was used to control this plant and the effect of the dead time on the response of the system.

Publication Date
Sun Jun 02 2019
Journal Name
Baghdad Science Journal
Proposing a Scheme for Human Interactive Proof Test using Plasma Effect
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            Human Interactive Proofs (HIPs) are automatic inverse Turing tests, which are intended to differentiate between people and malicious computer programs. The mission of making good HIP system is a challenging issue, since the resultant HIP must be secure against attacks and in the same time it must be practical for humans. Text-based HIPs is one of the most popular HIPs types. It exploits the capability of humans to recite text images more than Optical Character Recognition (OCR), but the current text-based HIPs are not well-matched with rapid development of computer vision techniques, since they are either vey simply passed or very hard to resolve, thus this motivate that

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Publication Date
Sat May 01 2021
Journal Name
Journal Of Physics: Conference Series
Three Weighted Residuals Methods for Solving the Nonlinear Thin Film Flow Problem
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Abstract<p>In this paper, the methods of weighted residuals: Collocation Method (CM), Least Squares Method (LSM) and Galerkin Method (GM) are used to solve the thin film flow (TFF) equation. The weighted residual methods were implemented to get an approximate solution to the TFF equation. The accuracy of the obtained results is checked by calculating the maximum error remainder functions (MER). Moreover, the outcomes were examined in comparison with the 4<sup>th</sup>-order Runge-Kutta method (RK4) and good agreements have been achieved. All the evaluations have been successfully implemented by using the computer system Mathematica®10.</p>
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Publication Date
Fri Mar 01 2013
Journal Name
Applied Mechanics And Materials
Measure and Analyze the Problems of Concrete Mixture Production via Six Sigma DMAIC Tools: Central Concrete Mix Plant as a Case Study
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The aims of this study are to measure the defect rate and analyze the problems of production of ready concrete mixture plant by using Six Sigma methodology which is a business strategy for operations improvement depending basically on the application of its sub-methodology DMAIC improvement cycle and the basic statistical tools where the process sigma level of concrete production in the case study was 2.41 σ.

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Publication Date
Tue Dec 07 2021
Design and numerical verification of a polarization-independent grating coupler using a double-layer approach for visible wavelengths applications
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Publication Date
Wed Apr 01 2015
Journal Name
Journal Of Educational And Psychological Researches
The Effect of Enrichment Programs on the Performance of Gifted Students in KSA
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       The current study aimed at identifying the impact of each of the full and part time summer enrichment programs on the performance of gifted students. Moreover, it aimed to study the difference between the full and part time programs on the performance of gifted students. The study sample consisted of (115) students from the full time programs and (137) students from the part time programs, they have been randomly selected from the gifted students participating in the full and part time summer enrichment programs. The researcher used the scale of student performance. The results indicated that there were statistically significant differences between the averages of the pre and post applications of the

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Publication Date
Thu Oct 01 2009
Journal Name
Iraqi Journal Of Physics
PMMA/ Anthracene Film as a Low Doses Dosimeter
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A prepared PMMA/Anthracene film of thickness 70μm was irradiated under reduced pressure ~10-3 to 60Coγ-ray dose of (0.1mrad-10krad) range. The optical properties of the irradiated films were evaluated spectrophotometrically. The absorption spectrum showed induced absorption changes in the 200-400nm range. At 359nm, where there is a decrease in radiation-induced absorption, the optical density as a function of absorbed dose is linear from 10mrad-10Krad.It can therefore, be used as radiation dosimeter for gamma ray in the range 10mrd-10krad

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