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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 Nov 19 2024
Journal Name
Review Of Clinical Pharmacology And Pharmacokinetics - International Edition
Clinical use of tumor necrosis factor-alpha inhibitors in Iraq: a review of their documented efficacy, safety, and associated genetics
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This comprehensive review examines the efficacy and safety of tumor necrosis factor-alpha (TNF-α) inhibitors in treating various autoimmune diseases, and focuses on their application in Iraqi patients. Elevated TNF-α levels are linked to autoimmune disorders, leading to the development of anti-TNF-α therapies such as infliximab, etanercept, adalimumab, certolizumab pegol, and golimumab, which have gained FDA approval for conditions like psoriasis, in¬flammatory bowel disease, ankylosing spondylitis, and rheumatoid arthritis. While these therapies demonstrate sig¬nificant therapeutic benefits, including improved quality of life and disease management, they also carry risks, such as increased susceptibility to infections and pote

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Publication Date
Fri Nov 02 2018
Journal Name
Iraqi National Journal Of Nursing Specialties
Inducing the Health Promotion Model for Nursing Practice: Qualitative Study
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Objective: To generate a model that conceptualizes the phenomenon of health promotion and its related factors.
Methodology: A grounded theory methodology is used as qualitative method to explore the health promotion as
phenomenon of interest and its other related factors from the perspectives of specialists in this field. The study is
carried out from January 2002 through September 2004. A sample of (20) specialists in health sciences are
selected and interviewed as experts in the area of health promotion. The investigators conducted intensive and
structured interviews with the specialists to collect the data. These interviews were transcribed verbatim,
analyzed and interpreted.
Results: Findings of the study indicat

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Publication Date
Wed Jan 01 2020
Journal Name
Journal Of Southwest Jiaotong University
A Recognition System for Subjects' Signature Using the Spatial Distribution of Signature Body
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This investigation proposed an identification system of offline signature by utilizing rotation compensation depending on the features that were saved in the database. The proposed system contains five principle stages, they are: (1) data acquisition, (2) signature data file loading, (3) signature preprocessing, (4) feature extraction, and (5) feature matching. The feature extraction includes determination of the center point coordinates, and the angle for rotation compensation (θ), implementation of rotation compensation, determination of discriminating features and statistical condition. During this work seven essential collections of features are utilized to acquire the characteristics: (i) density (D), (ii) average (A), (iii) s

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Publication Date
Tue Aug 15 2023
Journal Name
Journal Of Current Researches On Social Sciences
An Examination of Discourse Investigation of Fallacies in Religious Texts: Islam as a Case Study
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BN RASHİD, 2023

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Publication Date
Fri Feb 10 2023
Journal Name
Journal Of Applied Mathematics
The Dynamics of a Delayed Ecoepidemiological Model with Nonlinear Incidence Rate
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In this paper, the general framework for calculating the stability of equilibria, Hopf bifurcation of a delayed prey-predator system with an SI type of disease in the prey population, is investigated. The impact of the incubation period delay on disease transmission utilizing a nonlinear incidence rate was taken into account. For the purpose of explaining the predation process, a modified Holling type II functional response was used. First, the existence, uniform boundedness, and positivity of the solutions of the considered model system, along with the behavior of equilibria and the existence of Hopf bifurcation, are studied. The critical values of the delay parameter for which stability switches and the nature of the Hopf bifurcat

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Publication Date
Thu Apr 01 2021
Journal Name
Computer Methods And Programs In Biomedicine
A hybrid approach based on multiple Eigenvalues selection (MES) for the automated grading of a brain tumor using MRI
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Publication Date
Wed May 19 2010
Journal Name
Journal Of College Of Science, University Of Babylon
H-Point Standard Addition Method for Simultaneous Determination of Cimetidine and Erythromycin Ethylsuccinate Drugs Using Bromothymol Blue as a Chromogenic Complexing Agent
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The H-Point Standard Addition Method (H-PSAM) has been applied for spectrophotometric simultaneous determination of Cimetidine and Erythromycin ethylsuccinate using Bromothymol Blue (BTB) as a chromogenic complexing agent in a buffer solution at pH 5.5.

Publication Date
Mon Mar 15 2021
Journal Name
Al-academy
Anthropology and Representations of Magic in Arab Theatrical Text Harut and Marut's Play as a Model: وصال خلفة كاظم البكري
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The research (Anthropology and Representations of magic in Arab Theatrical Text, Harut and Marut's play as a Model) is concerned with studying magic and the forms of its presence in the theatrical text in different human cultures where it belongs. The research consists of four chapters.
The first chapter includes the research problem that revolves around the following questions: (what is the mechanism of employing magic anthropology and its representations in the Arab theatrical text Harut and Marut's play as a model?), and the research importance which is attributed to the necessity of studying (magic) in the Arab theatrical text as it is considered the inauguration of one of the social phenomena that many researchers in the field o

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Publication Date
Sun Dec 01 2019
Journal Name
2019 First International Conference Of Computer And Applied Sciences (cas)
A Comparison for Some of the estimation methods of the Parallel Stress-Strength model In the case of Inverse Rayleigh Distribution
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Publication Date
Tue Apr 29 2025
Journal Name
Modern Sport
A Comparative Study on the Results of the Administrative Performance Skills Scale Among Heads of Sports Talent Departments in the Ministry of Youth and Sports
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Sports management is a fundamental pillar that supports sports institutions and plays a pivotal role in achieving advanced levels of success in talent development. The Talent Development Project is one of the key strategic initiatives of the Ministry of Youth and Sports. This study compares department heads with effective managerial competence to those with ineffective competence to highlight differences in performance quality. Through this comparison, the urgent need to assess the administrative performance skills of the heads of sports talent departments becomes evident, particularly their ability to lead and manage the Sports Talent Development Project. The objective is to identify strengths and weaknesses, establish a clear framework fo

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