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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
Sun Oct 01 2017
Journal Name
Journal Of Economics And Administrative Sciences
The Possibility of Applying Quality Management System ISO9001: 2008 in Station Project Al Rustumiya - A Case Study
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The research study of the possibility of the application of the quality management system under the international standard ISO ISO9001: 2008 in the station project Rustumiya wastewater treatment of the Department of SEWER BAGHDAD - Baghdad MOREALITY as the first step in the right direction towards the implementation of total quality management (TQM), and the research Find the gap between the international standard and the quality system used in the organization surveyed through the use of checklists to analyze the gap, the checklist have included (191) items distributed on five basic requirements, according to the appearance in the international standard, namely, (quality management system, management responsibility, resource man

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Publication Date
Fri Apr 25 2025
Journal Name
Saudi Endodontic Journal
Insights into periapical inflammatory lesions of the jaws over 30 years in Iraq: A cross-sectional study
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Publication Date
Sun Feb 15 2026
Journal Name
Retos: Nuevas Tendencias En Educación Física, Deporte Y Recreación, Issn-e 1988-2041, Issn 1579-1726, Nº. 68, 2025, Págs. 1048-1062
The impact of knowledge management on cognitive achievement in sports science: A case study in boxing education
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Introduction: Knowledge management plays a crucial role in students’ ability to acquire, organize, retrieve, and apply information, impacting academic performance. In sports sciences, especially in combat sports like boxing, effective knowledge management supports both theoretical understanding and practical skill application. Despite exposure to boxing through training and media, students’ academic performance remains inconsistent. Objective: This study examines the relationship between knowledge management and cognitive achievement among second-year students in the College of Physical Education and Sport Sciences at the University of Basrah. It evaluates how students manage knowledge and its impact on their retention and application

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Publication Date
Fri Jul 01 2022
Journal Name
Iop Conference Series: Earth And Environmental Science
A study Some Technical Indicators Under Impact Tillage Depth and Disk harrow Angle of the Compound Machine
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Abstract<p>The research included studying the effect of different plowing depths (10,20and30) cm and three angles of the disc harrows (18,20and25) when they were combined in one compound machine consisting of a triple plow and disc harrows tied within one structure. Draft force, fuel consumption, practical productivity, and resistance to soil penetration. The results indicated that the plowing depth and disc angle had a significant effect on all studied parameters. The results showed that when the plowing depth increased and the disc angle increased, leads to increased pull force ratio, fuel consumption, resistance to soil penetration, and reduce the machine practical productivity.</p>
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Publication Date
Sat Nov 09 2019
Journal Name
Acta Medica Iranica
The Prevalence of a Clinically Silent Nephrolithiasis in Baghdad Population: An Initial Ultrasound Screening Study From Iraq
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Abstract- Asymptomatic or clinically silent kidney stones are possibly serious because, in their expected passage, they may cause infection, obstruction and renal impairment. The purpose of this study was to determine the prevalence of silent kidney stones in a sample of Baghdad population and consider how this value could affect the justification for a screening system. To our best knowledge, this is the first study of its kind conducted in Iraq. We investigated 714 consecutive patients who sustained an abdominal ultrasound at our hospital with further kidney screening. All these patients did not have clinical signs and symptoms of nephrolithiasis. Age, sex, the indication for ultrasound, the size, side, and the number of the disco

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Publication Date
Sat Jul 01 2023
Journal Name
Journal Of Accounting And Financial Studies ( Jafs )
A proposed audit program for a comprehensive electronic banking system based on business risks : applied research
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The research seeks to identify the comprehensive electronic banking system and the role of the auditor in light of the customer's application of electronic systems that depend on the Internet in providing its services, as a proposed audit program has been prepared in accordance with international auditing controls and standards based on the study of the customer's environment and the analysis of external and internal risks in the light of financial and non-financial indicators, the research reached a set of conclusions, most notably, increasing the dependence of banks on the comprehensive banking system for its ability to provide new and diverse banking services, The researcher suggested several recommendations, the most important of whi

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Publication Date
Sun Sep 22 2024
Journal Name
Journal Of Petroleum Research And Studies
Optimizing Gas Lift for Improved Oil Recovery in a Middle East Field: A Genetic Algorithm Approach
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This paper presents a study of the application of gas lift (GL) to improve oil production in a Middle East field. The field has been experiencing a rapid decline in production due to a drop in reservoir pressure. GL is a widely used artificial lift technique that can be used to increase oil production by reducing the hydrostatic pressure in the wellbore. The study used a full field model to simulate the effects of GL on production. The model was run under different production scenarios, including different water cut and reservoir pressure values. The results showed that GL can significantly increase oil production under all scenarios. The study also found that most wells in the field will soon be closed due to high water cuts. Howev

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Publication Date
Thu Mar 01 2012
Journal Name
Journal Of Accounting And Financial Studies ( Jafs )
The role of Cost awareness of activation of strategic cost management techniques of industrial units: A prospective study at the General Company for the manufacture of medicines and medical supplies in the province of Mosul
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The last ten years observed a shift enormous scientific in the method and way that it deals professional with the cost accounting and reflected the result those shift enormous scientific of increase the competitive environmental that accompanied the emergence of a modern manufacturing environmental on surface the long roductive life and emergence advanced information technology that give a central focus of his important on client with growing global markets growth on a large scale.

        The research aim to define the concept of cost awareness, the concept and methods of  strategic cost management and the role of cost awareness for managers of industrial units in strategic of cost managem

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Publication Date
Fri Mar 12 2021
Journal Name
Sensors
A Robust Handwritten Numeral Recognition Using Hybrid Orthogonal Polynomials and Moments
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Numeral recognition is considered an essential preliminary step for optical character recognition, document understanding, and others. Although several handwritten numeral recognition algorithms have been proposed so far, achieving adequate recognition accuracy and execution time remain challenging to date. In particular, recognition accuracy depends on the features extraction mechanism. As such, a fast and robust numeral recognition method is essential, which meets the desired accuracy by extracting the features efficiently while maintaining fast implementation time. Furthermore, to date most of the existing studies are focused on evaluating their methods based on clean environments, thus limiting understanding of their potential a

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Publication Date
Fri Jan 01 2016
Journal Name
Journal Of Computer And Communications
Pathfinding in Strategy Games and Maze Solving Using A* Search Algorithm
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