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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 May 18 2016
Journal Name
Al-academy
The Application of Experimentation in the Iraqi theatre shows "Othello in the Kitchen" As a model: عادل كريم سالم
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The researcher tackles the most outstanding conditions of experimentation, the importance of the study lies in being helpful to the workers in the field of theatre in general and directors in particular which the conditions of experimentation that should be taken.The study aims at knowing the experimental basis which the director (Sami Abdulhamid) followed in the realization of this.The researcher tackles in the First inquiry the concept of experimentation and the second tackles the conditions of experimentation.In the methodology of study the researcher analyzed the show of the "Othello in the Kitchen" and comes up to the following: 1. the dhows has cone with the nature of the previous shows experienced the methods that were not familia

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Publication Date
Fri Oct 10 2025
Journal Name
Journal Of Visualized Experiments
Explainable AI for Visual Inspection: A Comparative Analysis and Review
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Explainable Artificial Intelligence (XAI) techniques enable transparency and trust in automated visual inspection systems by making black-box machine learning models understandable. While XAI has been widely applied, prior reviews have not addressed the specific demands of industrial and medical inspection tasks. This paper reviews studies applying XAI techniques to visual inspection across industrial and medical domains. A systematic search was conducted in IEEE Xplore, Scopus, PubMed, arXiv, and Web of Science for studies published between 2014 and 2025, with inclusion criteria requiring the application of XAI in inspection tasks using public or domain-specific datasets. From an initial pool of studies, 75 were included and categorized in

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Publication Date
Fri Mar 01 2024
Journal Name
الذكوات البيض
The problem of employing political discourse and its role in promoting community peace: Iraq as a model
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After 2003, Iraq witnessed new challenges represented by the predominance of sectarian discourses, hatred and extremism at the expense of moderate political discourse and the predominance of sub-affiliations and external agendas at the expense of national affiliation, which led to the creation of an unsafe or stable environment dominated by the character of violence and terrorism. Moderate discourse would work to fuse sub-affiliations into one melting pot in which it would be the first loyalty to the homeland and not to the tribe, party or sect... Etc., and this in turn will contribute to promoting peaceful coexistence between the various other sub-affiliations within the framework of one community construction

Publication Date
Sat Jul 01 2017
Journal Name
Al–bahith Al–a'alami
A Dubbed Turkish Drama and their Effects of the Behavior of Algerian Women: A Survey Study of a Sample of Women – The City of Mesila is a Model
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The study aims to identify the effects of dubbed Turkish drama on the public through the application of a sample of the views of women. The study also attempts to monitor the causes and motives due to the act of observation and to identify the various effects of this act. In order to achieve these goals, the researcher relies on the descriptive approach in addition to the questionnaire and interviews to collect data. It ends with a number of results such as: The study aims to identify the effects of dubbed Turkish drama on the public through the application of a sample of the views of women. The study also attempts to monitor the causes and motives due to the act of observation and to identify the various effects of this act. In ord

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Publication Date
Fri Nov 05 2021
Journal Name
Review Of International Geographical Education Online
Measuring The Efficiency of The Departments of The College of Administration and Economics / University of Baghdad Using the Method of Data Envelopment Analysis (DEA), A Comparative Study
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Publication Date
Fri Jan 01 2021
Journal Name
Review Of International Geographical Education Online
Measuring The Efficiency of The Departments of The College of Administration and Economics / University of Baghdad Using the Method of Data Envelopment Analysis (DEA), A Comparative Study
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The research aims at the possibility of measuring the technical and scale efficiency (SE) of the departments of the College of Administration and Economics at the University of Baghdad for a period lasting 8 years, from the academic year 2013-2014 to 2018-2019 using the method of Applied Data Analysis with an input and output orientation to maintain the distinguished competitive position and try to identify weaknesses in performance and address them. Nevertheless, the research problem lies in diagnosing the most acceptable specializations in the labor market and determining the reasons for students’ reluctance to enter some departments. Furthermore, the (Win4DEAp) program was used to measure technical and scale efficiency (SE) and rely on

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Scopus
Publication Date
Thu Dec 01 2022
Journal Name
Advances In Cancer Biology - Metastasis
CX3CL1 as potential immunotherapeutic tool for bone metastases in lung cancer: A preclinical study
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Publication Date
Wed Jun 11 2008
Journal Name
Journal Of Al-nahrain University
ANALYSIS OF A MOLECULAR DYNAMICS SIMULATION OF THE ACETYLCHOLINESTERASE ENZYME AND ITS COMPLEX WITH (AXILLARIDINE-A) INHIBITOR
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Molecular dynamics (MD) simulations were carried out in order to investigate the binding mode of axillaridine-A at the active site of human acetylcholinesterase (AChE) enzyme. 2.0 nanosecond of MD simulations was made for the protein and the complex to dynamically explore the active site and the behavior of the ligand at the peripheral AChE binding site. These calculations for the enzyme alone showed that the active site of AChE is located at the bottom of a deep and narrow cavity whose surface is lined with rings of aromatic residues and Tyr72 is almost perpendicular to the Trp286 ring and forms a stable - interaction. The size of the active site of the complex decreases with time due to increase the interaction. Axillaridine-A forms

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Publication Date
Wed Jul 31 2019
Journal Name
Journal Of Engineering
A Comparative Study of Various Intelligent Optimization Algorithms Based on Path Planning and Neural Controller for Mobile Robot
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In this paper, a cognitive system based on a nonlinear neural controller and intelligent algorithm that will guide an autonomous mobile robot during continuous path-tracking and navigate over solid obstacles with avoidance was proposed. The goal of the proposed structure is to plan and track the reference path equation for the autonomous mobile robot in the mining environment to avoid the obstacles and reach to the target position by using intelligent optimization algorithms. Particle Swarm Optimization (PSO) and Artificial Bee Colony (ABC) Algorithms are used to finding the solutions of the mobile robot navigation problems in the mine by searching the optimal paths and finding the reference path equation of the optimal

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Publication Date
Sun Apr 30 2017
Journal Name
Journal Of Engineering
Sustainable Roadway Planning: A Model for a Proposed Rating System in Iraq
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     The goal of the research is to develop a sustainable rating system for roadway projects in Iraq for all of the life cycle stages of the projects which are (planning, design, construction and operation and maintenance). This paper investigates the criteria and its weightings of the suggested roadway rating system depending on sustainable planning activities. The methodology started in suggesting a group of sustainable criteria for planning stage and then suggesting weights from (1-5) points for each one of it. After that data were collected by using a closed questionnaire directed to the roadway experts group in order to verify the criteria weightings based on the relative importance of the roadway related impacts

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