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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
Sat Feb 01 2020
Journal Name
Indian Journal Of Science And Technology
Improvement of the Accuracy of the Perturbed Orbital Elements for LEO Satellite by Improving 4th Order Runge–Kutta’s Method
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Background/objectives: To study the motion equation under all perturbations effect for Low Earth Orbit (LEO) satellite. Predicting a satellite’s orbit is an important part of mission exploration. Methodology: Using 4th order Runge–Kutta’s method this equation was integrated numerically. In this study, the accurate perturbed value of orbital elements was calculated by using sub-steps number m during one revolution, also different step numbers nnn during 400 revolutions. The predication algorithm was applied and orbital elements changing were analyzed. The satellite in LEO influences by drag more than other perturbations regardless nnn through semi-major axis and eccentricity reducing. Findings and novelty/improvement: The results demo

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Publication Date
Thu Apr 03 2025
Journal Name
Isa Transactions
Optimal hybrid type-3 fuzzy controller for horizontal axis wind turbines: Comparative study
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The blade pitch angle (BPA) controller is key factor to improve the power generation of wind turbine (WT). Due to the aerodynamic structural behavior of the rotor blades, wind turbine system performance is influenced by pitch angle and environmental conditions such as wind speed, which fluctuate throughout the day. Therefore, to overcome the pitch angle control (PAC) problem, high wind speed conditions, and due to type-1 and type-2 fuzzy logic limitations for handling high levels of uncertainty, the newly proposed optimal hybrid type-3 fuzzy logic controller has been applied and compared since type-3 fuzzy controllers utilize three-dimensional membership functions, unlike type-2 and type-1 fuzzy logic controllers. In this paper six differen

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Publication Date
Sun Jun 30 2019
Journal Name
Journal Of The College Of Education For Women
Ready-made clothes for students of the University of Baghdad between reality and ambition ( A field study )
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     تعد الملابس وسيلة هامة لكل مايقوم به الانسان في حياته العامة ، فهي الانطباع والكلمة الخارجية عن ذاته الداخلية فهي تعكس فكرة الفرد عن ذاته وعن شخصيته , كما تعد وسيلة تعبير جمالية وفنية , فهي تساعد على اخفاء عيوب الجسد وابراز محاسنه . ويتوقف اختيار الفرد لملابسه على مجموعة  عوامل منها احتياجه , قدراته المالية , سنه , مركزه الاجتماعي , طبيعة عمله ,الظروف الجوية التي يعيش فيها وعلى مايُؤمن به من قيم و

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Publication Date
Mon May 21 2007
Journal Name
Journal Of Planner And Development
Using the Input - Output Model in building the economic plan using the computer
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The origin of this technique lies in the analysis of François Kenai (1694-1774), the leader of the School of Naturalists, presented in Tableau Economique. This method was developed by Karl Marx in his analysis of the Departmental Relationships and the nature of these relations in the models of " "He said. The current picture of this type of economic analysis is credited to the Russian economist Vasily Leontif. This analytical model is commonly used in developing economic plans in developing countries (p. 1, p. 86). There are several types of input and output models, such as static model, mobile model, regional models, and so on. However, this research will be confined to the open-ended model, which found areas in practical application.

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Publication Date
Thu Feb 01 2024
Journal Name
Baghdad Science Journal
Molecular study of the relationship of gene expression of some genes with the temperature variation of bacterial growth
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Pseudomonas aeruginosa is an opportunistic pathogen responsible for serious infections. At least three different exopolysaccharides, alginate, polysaccharide synthesis locus (Psl), and pellicle exopolysaccharide (Pel) make up the biofilm matrix in P. aeruginosa . The effect of temperature on the biofilm formation and gene expression was examined by microtiter plate and real-time quantitative polymerase chain reaction (qRT-PCR). To be able to determine the effect of temperature on biofilm formation and gene expression of P. aeruginosa, 303 clinical and environmental samples were collected. Pseudomonas aeruginosa was isolated from 61 (20.1%) and 48 (15.8%) of the clinical and e

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Publication Date
Thu Mar 21 2024
Journal Name
International Development Planning Review
THE EFFECT OF USING A DISABLING FORCE TRAINING TOOL ON WALKING PERFORMANCE: AN ANALYTICAL STUDY OF TIME AND STEP LENGTH IN THE 20 KM WALKING RACE EVENT FOR APPLICANTS
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Publication Date
Thu Jan 31 2019
Journal Name
Journal Of Engineering
Biological Structure in Contemporary Architecture Work of Architect Caltrava a Model
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Theoretical trends have appeared Which posed the concept of biological structures in contemporary architecture concept, Spread through the emergence of architectural production that reflect and indicate the nature of the construction structures based on the ideas and principles of biological structures in biological science: Despite the emergence of many architectural proposals that tried to explain the concept in the field of architecture, but it is not dealt with in depth and not given a comprehensive definition: So there was need to search for the concept and its beginning in the biological field as a general framework down to the field of architecture for the purpose of reducing the limits of their search framework T

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Publication Date
Mon May 01 2017
Journal Name
Energy Procedia
A Coupled Model of the Linear Joule Engine with Embedded Tubular Permanent Magnet Linear Alternator
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Publication Date
Mon Jul 01 2019
Journal Name
Journal Of Educational And Psychological Researches
Constructing a Scale for the Nine Types of Students Personality: Constructing a Scale for the Nine Types of Students Personality
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Abstract

The current research aims to construct a scale for the nine types of students’ personality according to Rob Fitzel model. To do this, (162) items were formed that present the nine types of personality with (18) items for each type. To test the validity of the scale, a sample of (584) students of Al-Mustansrya University were chosen. The data of their responses was analyzed by using factor analysis. The findings explored (9) factors as one factor for each type of personality with (12) items for each one. Then, the reliability of the scale was found by using the test-retest method and Alfa Cronbach method.

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Publication Date
Thu Dec 31 2015
Journal Name
مجلة كلية العلوم الاسلامية
The Secret of Marriage in Christianity A Descriptive Study
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Marriage is a holly secret in Christian religion .So it id natural that its ceremonies acquired religious form .In general the marriage is contracted by minister of religion in presence of the two parties or by a proxy or presence of parents if it is necessary . And to make the condition of publicity for the marriage ,its procedures must be made before witnesses .Also the minister of religionhave to confirm the agreement of the two parties before beginning the procedures.The marriage ceremonies are made.These procedures are religious traditions that includes praying and make blessings and putting the rings in fingers by thepriest . The marriage is a holly secret performed by the crown pray according to the church religious traditions

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