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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
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
Sun Jan 01 2017
Journal Name
Journal Of The College Of Languages (jcl)
השואה והשלכותיה על אהרון אפלפלד - עיון בשלושה סיפורים קצרים עוזר למורה – עלי מוחמד רשיד The Holocaust and its impact on Aharon Bielefeld - A Study in Three Short Stories
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מטרת המחקר הזה היא לבדוק את שלושה סיפורים קצרים מהקובץ הראשון של אהרון אפלפלד , שנחשב ההצהרה הרשמית על היותו סופר השואה הראשון בישראל , המשותף לשלושת הסיפורים הוא הנימה של הגיבורים היוצאים למסע פיזי ונפשי לגלות את אשר אירע להם , מגמתו של המחקר היא לבדוק את הצורה המיוחדת שבה אפיין אפלפלד את גיבוריו שמעידים על כך , כי השואה היא החוויה המרה והקשה בקרב היהודים והשלכותיה נשארה טמונה בקרבם גם אחרי המלחמה ואחרי שנים

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Publication Date
Wed Mar 10 2021
Journal Name
Baghdad Science Journal
Production of fibrinolytic protease from various fungal isolates and species 2.Determination of optimum conditions for enzyme production from Pleurotus ostreatus
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The optimum conditions for production of fibrinolytic protease from an edible mushroom Pleurotus ostreatus grown on the solid medium , Sus medium, composed of Sus wastes (produced from extracted medicinal plant Glycyrrhiza glabra) were determined. Addition of 5% of Soya bean seeds meal in Sus medium recorded a maximum fibrinolytic protease activity resulting in 7.7 units / ml. The optimum moisture content of Sus medium supplemented with 5% Soya bean seeds meal was 60% resulting in 7.2 units / ml.Pleurotus ostreatus produced a maximum fibrinolytic protease activity when the spawn rate,pH of medium and incubation temperature were 2,6 and 30°C, respectively. The maximum fibrinolytic protease activity was 7.6 units / ml when incubat

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Publication Date
Thu Feb 29 2024
Journal Name
Sabrao Journal Of Breeding And Genetics
LOW-‎COST SOIL ‎MOISTURE SENSORS’ ASSESSMENT FOR THEIR ACCURACY AFTER CALIBRATION THROUGH THE ‎GRAVIMETRIC METHOD
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The existing study aimed to assess four soil moisture sensors’ capacitive (WH51 and SKU: S EN0193) and resistive (Yl69 and IC Station) abilities, which are affordable and medium-priced for their accuracy in six common soil types in the central region of Iraq. The readings’ calibration for the soil moisture sensor devices continued through two gravimetric methods. The first depended on the protocols’ database, while the second was the traditional calibration method. The second method recorded the lowest analysis error compared with the first. The moderate-cost sensor WH51 showed the lowest standard error (SE), MAD , and RMSE and the highest R² in both methods. The performance accuracy of WH51 was close to readings shown by the manufac

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Publication Date
Mon Dec 01 2014
Journal Name
2014 Ieee Symposium On Differential Evolution (sde)
Comparative analysis of a modified differential evolution algorithm based on bacterial mutation scheme
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A new modified differential evolution algorithm DE-BEA, is proposed to improve the reliability of the standard DE/current-to-rand/1/bin by implementing a new mutation scheme inspired by the bacterial evolutionary algorithm (BEA). The crossover and the selection schemes of the DE method are also modified to fit the new DE-BEA mechanism. The new scheme diversifies the population by applying to all the individuals a segment based scheme that generates multiple copies (clones) from each individual one-by-one and applies the BEA segment-wise mechanism. These new steps are embedded in the DE/current-to-rand/bin scheme. The performance of the new algorithm has been compared with several DE variants over eighteen benchmark functions including sever

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Publication Date
Sun May 10 2015
Journal Name
Al-academy
Performing processors of view between impressionism & superrealism (A comparative analysis): فريد خالد علوان
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Addressed the problem of the research is marked: (Performing processors for the time between Impressionism and superrealism) the concept of time and how to submit artwork. The search came in four sections: general framework for research and identified the research problem and the need for him. With an indication of the importance of his presence. Then determine the research objectives of (detection processors performing to the concept of time in works of art in each of Impressionism and superrealism. And a comparison between them to reveal similarities and differences), followed by the establishment of boundaries Find three (objectivity, the temporal and spatial) were then determine the terms related to the title. Then provide the theore

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Publication Date
Mon Jul 01 2019
Journal Name
Journal Of Engineering
Speed Controller of Three Phase Induction Motor Using Sliding Mode Controller
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In this paper, an adaptive integral Sliding Mode Control (SMC) is employed to control the speed of Three-Phase Induction Motor. The strategy used is the field oriented control as ac drive system. The SMC is used to estimate the frequency that required to generates three phase voltage of Space Vector Pulse Width Modulation (SVPWM) invertor . When the SMC is used with current controller, the quadratic component of stator current is estimated by the controller. Instead of using current controller, this paper proposed estimating the frequency of stator voltage since that the slip speed is function of the quadratic current . The simulation results of using the SMC showed that a good dynamic response can be obtained under load

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Publication Date
Fri May 01 2020
Journal Name
Journal Of Engineering
A Study of the Hydrodynamics Behavior of Cylindrical Gas-Solid Fluidized Beds for pharmaceutical material “Paracetamol “
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The hydrodynamics behavior of gas - solid fluidized beds is complex and it should be analyzed  and understood due to its importance in the design and operating of the units. The effect of column inside diameter and static bed height on the minimum fluidization velocity, minimum bubbling velocity, fluidization index, minimum slugging velocity and slug index have been studied experimentally and theoretically for three cylindrical columns of 0.0762, 0.15 and 0.18 m inside diameters  and 0.05, 0.07 and 0.09 m static bed heights .The experimental results showed that the minimum fluidization and bubbling velocities had a direct relation with column diameter and static bed height .The minimum slugging velocity had an

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Publication Date
Sat Jan 01 2022
Journal Name
Journal Of Intelligent Systems
Trip generation modeling for a selected sector in Baghdad city using the artificial neural network
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Abstract<p>This study is planned with the aim of constructing models that can be used to forecast trip production in the Al-Karada region in Baghdad city incorporating the socioeconomic features, through the use of various statistical approaches to the modeling of trip generation, such as artificial neural network (ANN) and multiple linear regression (MLR). The research region was split into 11 zones to accomplish the study aim. Forms were issued based on the needed sample size of 1,170. Only 1,050 forms with responses were received, giving a response rate of 89.74% for the research region. The collected data were processed using the ANN technique in MATLAB v20. The same database was utilized to</p> ... Show More
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Publication Date
Thu Mar 09 2017
Journal Name
Ibn Al-haitham Journal For Pure And Applied Sciences
IFN-γ T/A +874 Gene Polymorphism in Type 1 Diabetes Mellitus of Iraqi Children
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This study included 50 blood samples collected from children with mean age 8-12 years. Thirty five blood samples were collected from children with Type 1 Diabetes Mellitus (T1D) with mean age 9.4±0.34 years, and 15 blood samples collected from healthy children as a control sample with mean age 10.9±0.38 years. Immunogenetic study was done on collected blood samples. Concentrations of IFN-γ were estimated from T1D patient and control samples by using Elisa instrument. The concentration of this interferon was 1.575 pg/ml in T1D patient sample in comparison with 0.921 pg/ml in control sample. Significant differences of this interferon concentration were found between T1D patient and control samples when Mann-Whitney U test was used

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