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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 Sep 05 2023
Journal Name
Iraqi Post Graduate Medical Journal.
Immunohistochemical Expression of Carbonic Anhydrase IX and PAX8 in Renal Cell Carcinoma: A Clinicopathological Correlation Study.
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Publication Date
Tue May 12 2020
Journal Name
The Fourth Annual International Conference On Languages, Linguistics, Translation And Literature (www.llld.ir), 1-2 February 2020, Iran-ahwaz, Book Of Articles, Volume Two
A Study of Susan Glaspell's Regionalism and Ideal Feminism with Special Reference to Her Play Trifles
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Abstract The main purpose of the research is to clarify and investigate in details about Susan Glaspell’s role in shedding light on the predicament of women in American society in the early twentieth century showing how sense of the place played an important role in limiting the opportunities of female protagonists who try to escape the roles imposed upon them by society. Glaspell lived in the early twentieth century in the Midwest and tackled the important issues like: women's suffrage, birth control, socialism, union organizing when women were not able to vote or sit as a member on juries. Her Feminist cause is quite obvious through her works from her first one act play Suppressed Desire to the final three act play, Alison’s House. Th

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Publication Date
Tue May 15 2012
Journal Name
Alustath Journal For Human And Social Sciences
A Syntactico-Semantic Study of English Phrasal Verbs دراسة نحوية دلالية للأفعال المركبة في اللغة الانكليزية
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This paper is an attempt to investigate the syntactic and semantic features of the English phrasal verbs. In this paper, phrasal verbs were classified into subgroups according to their syntactic and semantic characteristics. After giving a survey of literature written on the meaning and definition of phrasal verbs, two sections have been devoted to tackle the most important issues in this category of English verbs. Section one sheds light on the basic definitions of the term ‘phrasal verb’ which are, according to the researcher’s point of view, sufficient to cover the area of the study. In addition, it studies the number and the importance of phrasal verbs in English. Section two deals with the syntactic and semantic features of Engli

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Publication Date
Mon Jan 08 2024
Journal Name
Al-rafidain Journal Of Medical Sciences ( Issn 2789-3219 )
Recurrence Rate of Pleomorphic Adenoma in Minor Salivary Glands After Surgical Excision: A Retrospective Clinical Study
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Background: Pleomorphic adenoma of the minor salivary gland is a rare benign tumor. It commonly occurs in the hard and soft palates. Treatment by surgical excision achieved success in improving the patient’s health. Objective: To evaluate the recurrence rate after surgical treatment of pleomorphic adenoma in minor salivary glands. Methods: This retrospective study included patients who attended the Maxillofacial Surgery Unit in Ghazi Al-Hariri Hospital, Baghdad, from 2019 to 2021, complaining of soft tissue lumps involving the soft and hard palate, buccal mucosa, and upper lip. After the provisional diagnosis of these lesions, a total surgical excision of the tumor with a safe margin of 1 mm was performed, and the biopsy was sent for hist

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Publication Date
Tue Dec 01 2020
Journal Name
Cureus
Clinical Descriptive Study of Masturbatory Behavior Among Infants and Preschool Children: A Recent Observation From Iraq
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Publication Date
Wed Aug 01 2018
Journal Name
Journal Of Economics And Administrative Sciences
A Study on Transportation Models in Their Minimum and Maximum Values with Applications of Real Data
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The purpose of this paper is to apply different transportation models in their minimum and maximum values by finding starting basic feasible solution and finding the optimal solution. The requirements of transportation models were presented with one of their applications in the case of minimizing the objective function, which was conducted by the researcher as real data, which took place one month in 2015, in one of the poultry farms for the production of eggs

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Publication Date
Mon Jan 16 2023
Journal Name
Iraqi National Journal Of Nursing Specialties
Dependence Severity, Locus of Control, and Readiness to Change in Male Alcoholic Clients: A Correlational Study
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Objectives: To assess the level of dependence severity, locus of control, and readiness to change in male alcohol clients and measure the correlation between dependence with a locus of control and readiness to change.

Methodology: A descriptive correlational design was conducted in the substance use rehabilitation centers at psychiatric teaching hospitals in Baghdad city from November /2021 to May 2022. The instrument of the study was designed by using sociodemographic, the clinical characteristics of the client, the Short-form Alcohol Dependence Data Questionnaire (SADD), Drinking Related Internal-External Locus of Control Scale: (DRIE), and the Stages of Change Readiness and Treatment Eagerness Scale (SOCRATES). The data was co

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Publication Date
Sat Dec 11 2021
Journal Name
Engineering, Technology & Applied Science Research
Behavior of RC Beams Strengthened with NSM-CFRP Strips Subjected to Fire Exposure: A Numerical Study
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The use of Near-Surface Mounted (NSM) Carbon-Fiber-Reinforced Polymer (CFRP) strips is an efficient technology for increasing flexural and shear strength or for repairing damaged Reinforced Concrete (RC) members. This strengthening method is a promising technology. However, the thin layer of concrete covering the NSM-CFRP strips is not adequate to resist heat effect when directly exposed to a fire or at a high temperature. There is clear evidence that the strength and stiffness of CFRPs severely deteriorate at high temperatures. Therefore, in terms of fire resistance, the NSM technique has a significant defect. Thus, it is very important to develop a set of efficient fire protection systems to overcome these disadvantages. This pape

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Publication Date
Fri Dec 15 2023
Journal Name
Journal Of Baghdad College Of Dentistry
Local application of Opuntia ficus-indica / Punica granatum oils on cutaneous wound healing: a histochemical study
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Background: The healing process involves the restoration of the body’s structural integrity. The extracellular matrix, blood cells, cytokines, and growth factors are all involved in this dynamic, intricate, multicellular process. Hemostasis, the inflammatory phase, the proliferative phase, and the maturation phase are all included. Opuntia ficus-indica oil (OFI) and Punica grantum (PGS) oil are extensively used natural treatments that are regarded as advantageous for their sedative, spasmolytic, and anti-inflammatory properties, as well as for angiogenesis promotion, fibroblast increase, collagen production and deposition, and extracellular-matrix remodeling. Materials and methods: Twenty-four New Zealand rab

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Publication Date
Sun Mar 15 2020
Journal Name
Journal Of Baghdad College Of Dentistry
Effect of sulcular green tea extract irrigation on experimental rabbit’s gingivitis (A histopathological study)
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Background: Considering the antioxidant, anti-inflammatory, and antimicrobial properties of green tea, this study aimed to evaluate the histopathological effect of the sulcular irrigation of green tea extract in the treatment of experimental gingivitis in rabbit.

Materials and methods: For this experimental study, 45 male rabbits, separated in two groups, control non- irrigated group (5rabbits) and study group (40 rabbits), gingivitis induced by ligatures was packed subgingivally in the lower right central incisors of the experimental group for seven days. Then, the animals were randomly designated to two irrigated groups (20 rabbits

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