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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
Fri Dec 29 2017
Journal Name
Al-khwarizmi Engineering Journal
Design and Implementation of a Proposal Network Firewall
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In today's world, most business, regardless of size, believe that access to Internet is imperative if they are going to complete effectively. Yet connecting a private computer (or a network) to the Internet can expose critical or confidential data to malicious attack from anywhere in the world since unprotected connections to the Internet (or any network topology) leaves the user computer vulnerable to hacker attacks and other Internet threats. Therefore, to provide high degree of protection to the network and network's user, Firewall need to be used.

Firewall provides a barrier between the user computer and the Internet (i.e. it prevents unauthor

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Publication Date
Sat Jun 30 2007
Journal Name
Al-kindy College Medical Journal
Lung Cancer in a Sample of Iraqi Patients
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Background: Lung cancer is responsible for the most
cancer deaths in both men and women throughout the
world. Deaths from lung cancer (160,440 in 2004,
according to the National Cancer Institute) exceed the
number of deaths from four other major cancers combined
(breast, colon, pancreatic and prostate).
Objective: To assess the behavior and the approaches of
lung cancer in a sample of Iraqi patients.
Methods: This descriptive retrospective study was
performed using the records of 390 patients proved to have
lung cancer that had attending the Thoracic Surgery
Department of Surgical Specialties Hospital-Medical City
\Baghdad for the period from January, 1st
, 2001 to
December, 31st
,2002.
Res

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Publication Date
Sun Dec 01 2019
Journal Name
Al-khwarizmi Engineering Journal
Investigation of Effecting Parameters in a Turning Operation
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        In this study multi objective optimization is utilized to optimize a turning operation to reveal the appropriate level of process features. The goal of this work is to evaluate the optimal combination of cutting parameters like feed, spindle speed, inclination angle and workpiece material to have a best surface quality Taguchi technique L9 mixed orthogonal array, has been adopted to optimize the roughness of surface. Three rods of length around (200 mm) for the three metals are used for this work. Each rod is divided into three parts with 50 mm length. For brass the optimum parametric mix for minimum Ra is A1, B1 and C3, i.e., at tool inclination angle (5), feedrate of 0.01, spindle speed of 120

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Publication Date
Tue Aug 01 2023
Journal Name
Journal Of Engineering
Geomechanics Analysis of Well Drilling Instability: A Review
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Wellbore instability is a significant problem faced during drilling operations and causes loss of circulation, caving, stuck pipe, and well kick or blowout. These problems take extra time to treat and increase the Nonproductive Time (NPT). This paper aims to review the factors that influence the stability of wellbores and know the methods that have been reached to reduce them. Based on a current survey, the factors that affect the stability of the wellbore are far-field stress, rock mechanical properties, natural fractures, pore pressure, wellbore trajectory, drilling fluid chemicals, mobile formations, naturally over-pressured shale collapse, mud weight, temperature, and time. Also, the most suitable ways to reduce well

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Publication Date
Thu Jun 08 2023
Journal Name
Open Engineering
A review of rutting in asphalt concrete pavement
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Undoubtedly, rutting in asphalt concrete pavement is considered a major dilemma in terms of pavement performance and safety faced by road users as well as the road authorities. Rutting is a bowl-shaped depression in the wheel paths that develop gradually with the increasing number of load applications. Heavy axle loadings besides the high pavement summer temperature enhance the problem of rutting. According to the AASHTO design equation for flexible pavements, a 1.1 in rut depth will reduce the present serviceability index of relatively new pavement, having no other distress, from 4.2 to 2.5. With this amount of drop in serviceability, the entire life of the pavement in effect has been lost. Therefore, it is crucial to look at the mechani

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Publication Date
Wed Nov 30 2022
Journal Name
مجلة الجامعة العراقية
The competencies of lecturers and their roles in managing E-training workshops, a Pedagogical Pointview
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The aim of the research is to shed light on identifying the extent of the university professor's competencies and their roles in managing and training participants in e-training workshops as a pedagogical point view. The research sample consisted of a group of (30) university professors (lecturers) in the training workshops, in scientific,humanitarian and social disciplines, including (12) a university professor (holding a trainer certificate), , the research methodology is descriptive, and the community is a group of trained participants. (115) participated in (40) e-training workshops organized by the Center for Continuing Education at the University of Baghdad (and the selection of workshops within the researcher's specialization in the

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Publication Date
Fri Nov 01 2019
Journal Name
International Journal On Interactive Design And Manufacturing (ijidem)
A real-time automated sorting of robotic vision system based on the interactive design approach
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Publication Date
Thu Sep 30 2021
Journal Name
Journal Of Economics And Administrative Sciences
HRA and its Impact on Employees Performance: A Field Research in the Ministry of Education
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          The research aims to determine the impact of Human Resources Accounting (HRA) on employee’s performance. The research’s problem was embodied in the lack of interest in HRA, which was reflected on the performance of employees in the Ministry of Education; the research adopted the descriptive-analytical approach, and the research community included the directors of departments and people at the headquarters of the Ministry of Education. The sample size was (224) individuals from the total community of 533. The questionnaire was adopted as the main tool for collecting data and information, as well as the interviews that were conducted by the researcher. In order to analyze t

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Publication Date
Sat Feb 19 2022
Journal Name
Advances In Continuous And Discrete Models
Geometric properties of the meromorphic functions class through special functions associated with a linear operator
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Abstract<p>According to the theory of regular geometric functions, the relevance of geometry to analysis is a critical feature. One of the significant tools to study operators is to utilize the convolution product. The dynamic techniques of convolution have attracted numerous complex analyses in current research. In this effort, an attempt is made by utilizing the said techniques to study a new linear complex operator connecting an incomplete beta function and a Hurwitz–Lerch zeta function of certain meromorphic functions. Furthermore, we employ a method based on the first-order differential subordination to derive new and better differential complex inequalities, namely differential subordinations.</p>
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Publication Date
Sun Jul 07 2013
Journal Name
Journal Of Educational And Psychological Researches
knowledge management and managers have a primary school principals from the standpoint of their assistants
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knowledge management and managers have a primary school principals from the standpoint of their assistants M . Dr. Suad Vegetables Abbas Research problem: The administration school require a leader administratively The efficiency and skills of management and knowledge to make it effective in the administration follows the scientific method and knowledge of those who through administrative methods emanating from the trends of modern management in the management of educational , as well as the presence of the leaders of effective management has the knowledge and know-how administrative work and how to deal with others and investment optimized for all of the resources available through the future capable of Orientalism to the extent that ou

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