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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
Mon Nov 24 2025
Journal Name
Journal Of Baghdad College Of Dentistry
An Assessment of Alpha-Amylase as Salivary Psychological Stress Marker in Relation to Temporomandibular Disorders among a Sample of Dental Students
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Background: University dental students perceived a higher level of stress prior to the final exam associated with raised salivary alpha-amylase levels which could be considered as a useful noninvasive biomarker for measuring acute stress. Using a Helkimo anamnestic and clinical dysfunction scoring for temporomandibular disorders can give a better insight about the association of this marker and temporomandibular disorders. The aim of this study was to evaluation level of salivary alpha-amylase in stressor students with temporomandibular disorders and the relation between the marker in relation to temporomandibular disorders severity. This might give a better understanding to the role of psychological stress as an etiological factor for deve

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Publication Date
Tue Jun 15 2021
Journal Name
Iraqi Journal Of Pharmaceutical Sciences ( P-issn 1683 - 3597 E-issn 2521 - 3512)
Comparative Study of Liver Function and Rh Blood Group between both Physiological and Pathological Neonatal Jaundice
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Abstract

Backgrounds: Jaundice occurs in most newborn due to increased bilirubin concentration. Jaundice is observed during the first week after birth in approximately 60% of term neonates. A high level of bilirubin is neurotoxic and may cause neonatal kernicterus, auditory neuropathy or death.

Objectives: to compare the Rh group compatibility, serum bilirubin (total and direct), serum albumin and several liver enzymes between physiological and pathological neonatal jaundice

Materials and Methods: A cross sectional study for one hundred neonates with jaundice divided into group 1: 50 newborns with physiological jaundice, Group 2: 50 newborns with

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Publication Date
Sun Jan 04 2015
Journal Name
Journal Of Educational And Psychological Researches
The Relationship between Social Anxiety and Mindfulness In Iraqi Women Living In Iraq And The UK; A Comparison Study
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The continuous pressure of work and daily life and the increasing financial and social stress that Iraqi women are experiencing (both inside and outside Iraq) is one of the main causes of anxiety, particularly in those of working class women. This group of women carry the burden of carrying out multiple roles and responsibilities at the same time. All this collectively make them more prone to developing anxiety compared to men. In addition, the physiological and psychological nature of women, as females, on top of the other roles in life, like being a wife or mother or daughter or sister, all add extra pressure on women especially for those who are considered as productive working individuals in the society. In order to study the relatio

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Publication Date
Wed Dec 25 2019
Journal Name
Journal Of Accounting And Financial Studies ( Jafs )
A Vision to development the Islamic banks that operating under the financial system based on interest: (Iraq Case Study)
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This paper aims to build a modern vision for Islamic banks to ensure sustainability and growth, as well it aims to highlight the positive Iraqi steps in the Islamic banking sector. In order to build this vision, several scientific research approaches were adopted (quantitative, descriptive analytical, descriptive). As for the research community, it was for all the Iraqi private commercial banks, including Islamic banks. The research samples varied according to a diversity of the methods and the data availability. A questionnaire was constructed and conducted, measuring internal and external honesty. 50 questionnaires were distributed to Iraqi academic specialized in Islamic banking. All distributed forms were subject to a thorough analys

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Publication Date
Wed Feb 01 2017
Journal Name
Journal Of Economics And Administrative Sciences
Star model –model of organization design and reflections of its variables and dimensions of health performance on-filed study in medical city hospital
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Abstract

      The goal of current research to describe and diagnose the level of attention of doctors to design and regulatory dimensions, (strategic vision, organizational structure, organizational processes, business systems, personnel), and the performance of hospitals and dimensions, in six hospitals in medicine and selected a sample for research, as well as identify organizational design effect in the performance of hospitals and dimensions (efficiency, the development of human resources, patient satisfaction, achieve financial results, quality of health care).

 Research has focused in part theoretical on key variables to look organizational des

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Publication Date
Sat Oct 01 2022
Journal Name
Civil Engineering Journal
Using CRF Tool for Analyzing the Resilience of Cities
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The new sustainable development goals set by the UN include a goal of making cities inclusive, safe, sustainable, and resilient. Cities are growing at huge rates, and conditions of deteriorating QOL̛s are increasing in the form of poor access to services, and slums are remarkable, especially in the cities of the Middle East; hence, the research problem can arise from a lack of knowledge regarding the in determination of a way to assess the resilience of cities to develop mechanisms that will improve the quality of urban life. In this study, a tool called CRF has been applied for the assessment of the city's resilience principles of health and quality of life, economics and social, infrastructure and environmental systems, and the principle

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Publication Date
Tue Oct 18 2022
Journal Name
Arab World English Journal For Translation & Literary Studiesissn: 2550-1542 |www.awej-tls.org17awej For Translation & Literary Studies,
The impact of landscape on the emotional shift in Tayo’s Character: A Study of memory and displacement in Leslie Marmon Silko’s Ceremony
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This paper examines the decolonizing methods used by Leslie Marmon Silko in her novel Ceremony (1977) to heal the indigenous people from the patriarchal traditions of the white hegemony. This study aims to emphasize the vulnerable responses of the Pueblo people to the memories of the clan and to highlight Silko’s methods to sustain the history and lifestyle of the indigenous people. Therefore, Silko’s novel can be situated historically and culturally within memory-studies. To analyze the contrasting behaviors of characters, this paper projects the relationship between the collective patriarchal doctrines and that of the individual within the framework of memory studies. Theories of Jan and Aleida Assmann are used here to explore the

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Publication Date
Sun Jan 01 2023
Journal Name
International Journal Of Research In Social Sciences & Humanities
The Impact of Strategic Improvisation on Organizational Health: An Analytical Study of the Opinions of a Sample of the Leaders of the Dhi Qar Health Department
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The current research aims to identify the level of impact of strategic improvisation as an independent variable on organizational health. The dependent variable in the Department of Health of Dhi Qar to reach appropriate mechanisms in order to reach appropriate mechanisms and recommendations proposed to contribute to the achievement of organizational health in the Department of Health of Dhi Qar (the research department) and based on the importance of the subject of research in government institutions and the important and service role of the Department of Health of Dhi Qar in the Iraqi society. The descriptive analytical approach was adopted in the completion of the research based on the opinions of the leaders in the surveyed depa

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Publication Date
Sun Jan 05 2020
Journal Name
Annals Of Tropical Medicine And Public Health
THE EFFECT OF THE TRAINING CURRICULUM ON DEVELOPING KINETIC AND TRANSITIONAL RESPONSE SPEED, ACCURACY OF THE STOPPING WALL PERFORMANCE, AND DEFENDING THE STADIUM IN VOLLEYBALL
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Publication Date
Sat Jun 01 2024
Journal Name
Results In Engineering
Stability analysis for the phytoplankton-zooplankton model with depletion of dissolved oxygen and strong Allee effects
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