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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
Thu Apr 10 2025
Journal Name
University Of Baghdad
Decolonizing Trauma and Cocooning Identity: A Study in Selected Postcolonial Plays
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The concept of decolonization of trauma has intrigued researchers for years due to its prolonged effect on personal and cultural levels. The process of intellectual decolonization involves defensive survival mechanisms, such as cultural rituals using traditional practices, nostalgic dialogues that idealize memories and recollections, and conversations about identity to navigate postcolonial trauma displacement. Symbolic connections evoke strong emotional responses, bridging the gap between the characters‘ physical dislocation and their imaginary homeland. Cocooning identity represents a space where a multidimensional self emerges—one that holds the victim of trauma, the survivor who endures, and the narrator, who constructs an idealized

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Publication Date
Sat Nov 05 2022
Journal Name
Resmilitaris
Job Burnout Among Social Workers in Iraqi society: A Social Study
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There are a number of obstacles in the field of work of social workers that prevent them from performing their full role. Their tasks may sometimes be easy and manageable and at other times they may be difficult and complex, however professional roles are mostly the latter, contribute to the feeling of the inability to provide the work required at the level expected by others. In such cases, the relationship binding specialists to their work is affected negatively and this has devastating effects on the professional process as a whole, including their professional practice. This feeling of helplessness and depletion of energy and effort leads to a state of fatigue and emotional exhaustion that can be defined as job burnout, our study aims t

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Publication Date
Sun Jan 01 2023
Journal Name
Medical Journal Of Babylon
Platelet-rich Fibrin Potential Role in Periodontal Regeneration: A Review Study
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Periodontitis is a persistent bacterial-causing disease which damages the supporting periodontium of the teeth. The complexity of supporting tissue structure makes the regeneration a challenge for periodontists. Early investigations were focused on discovering therapeutic substitutes that are biocompatible, simple to prepare and economic. This might cause a local release of growth factors that accelerate the healing process of the soft and hard tissue. Recently, platelet-rich fibrin (PRF) has received a wide attention as a biocompatible regenerative material in both dental and medical fields. PRF is a natural fibrin-derived biomaterial, and it is easy to obtain. It can be gotten from individual blood without the use of any external anticoag

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Publication Date
Tue Nov 01 2022
Journal Name
Alustath
Metrical Phonology in Classical English and Arabic Poetry: A Contrastive Study
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One of the prominent goals of Metrical Phonology Theory is providing stress of poetry on the syllable-, the foot-, and the phonological word- levels. Analysing poetry is one of the most prominent and controversial issues for the involved number and types of syllables, feet, and meters are stable in poetry compared to other literary texts. The prosodic seeds of the theory have been planted by Firth (1948) in English, while in Arabic يديهارفلا in the second half of the eighth century (A.D.) has done so. Investigating the metrical structure of poetry has been conducted in various languages, whereas scrutinising the metrical structure of English and Arabic poetry has received little attention. This study aims at capturing the

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Publication Date
Sun Jan 20 2002
Journal Name
Journal Of The College Of Languages (jcl)
Domestic Animals in English and Iraqi Rural Proverbs: A Pragmastylistic Study
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Proverbs gain their importance not only from the fact that they represent a cultural record of the people of every nation, but they reveal the way they use language and how they exploit their environments as a good source of inspiration to enrich that language.  Domestic animals, as part of every environment, play a major role in composing proverbs in every nation.

       This study is an attempt to pragmastylistically analyse some selected English and Iraqi rural proverbs using domestic animals in their texts. It limits itself to investigate certain stylistic and pragmatic devices such as: the type of sentences, their lengths, their content and grammatical words, the part of speech used, metaph

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Publication Date
Fri Mar 15 2019
Journal Name
Journal Of The College Of Education For Women
Eyes Drugs and Treatment at Ibn al –Haytham: A Historical Study
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            Ibn al-Haytham is the pioneer of optics, which is a science that had described optics circumstances. Optics or landscape science as it was known by the Arab and Muslim scientists at the time when  is a science known as the conditions of sighters in their quantity and quality as the proximity and distance from the beholder , the different forms , conditions and what mediate between the beholder and the microscopes , to explain useful knowledge of what obscures the sight of the conditions of sighters and is used to measure the space Distant criminality and  mirrors.

Ibn al-Haitham wrote his famous book The Book of Mirrors and studied mistakes adopted the m

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Publication Date
Sat Jan 01 2022
Journal Name
Materials Research Express
Thermochromic and opacity behaviors in vanadium dioxide nanofilms: a theoretical study
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Abstract<p>Vanadium dioxide nanofilms are one of the most essential materials in electronic applications like smart windows. Therefore, studying and understanding the optical properties of such films is crucial to modify the parameters that control these properties. To this end, this work focuses on investigating the opacity as a function of the energy directed at the nanofilms with different thicknesses (1–100) nm. Effective mediator theories (EMTs), which are considered as the application of Bruggeman’s formalism and the Looyenga mixing rule, have been used to estimate the dielectric constant of VO<sub>2</sub> nanofilms. The results show different opacity behaviors at different w</p> ... Show More
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Publication Date
Wed Jun 01 2022
Journal Name
Journal Of Nursing Education
Compassion Competence Among Nursing Students From Different Cultures: A Multinational Study
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Background:

Compassion competence is a nurse's ability to provide patient-centered care and communicate with patients in a sensitive and insightful manner. This descriptive cross-sectional survey study aimed to assess the compassion competence of a multinational group of nursing students.

Method:

A total of 1,158 undergraduate nursing students participated in this study, and stratified random sampling method was used to select participants from the 100 study level to the 400 or 500 level. Data were collected using the Compassion Competence Scale.

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Publication Date
Sat Jan 01 2022
Journal Name
Materials Research Express
Thermochromic and opacity behaviors in vanadium dioxide nanofilms: a theoretical study
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Abstract<p>Vanadium dioxide nanofilms are one of the most essential materials in electronic applications like smart windows. Therefore, studying and understanding the optical properties of such films is crucial to modify the parameters that control these properties. To this end, this work focuses on investigating the opacity as a function of the energy directed at the nanofilms with different thicknesses (1–100) nm. Effective mediator theories (EMTs), which are considered as the application of Bruggeman’s formalism and the Looyenga mixing rule, have been used to estimate the dielectric constant of VO<sub>2</sub> nanofilms. The results show different opacity behaviors at different w</p> ... Show More
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Publication Date
Sun Jun 23 2019
Journal Name
Arma
Safe Mud Weight Window Determination: A Case Study from Southern Iraq
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ABSTRACT:. The Lower Cretaceous Zubair formation is comprised of sandstones intercalated with shale sequences. The main challenges that were encountered while drilling into this formation included severe wellbore instability-related issues across the weaker formations overlaying the reservoir section (pay zone). These issues have a significant impact on well costs and timeline. In this paper, a comprehensive geomechanical study was carried out to understand the causes of the wellbore failure and to improve drilling design and drilling performance on further development wells in the field. Failure criteria known as Mogi-Coulomb was used to determine an operating mud weight window required for safe drilling. The accuracy of the geomechanical

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