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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
Wed Aug 01 2018
Journal Name
Journal Of Zankoy Sulaimani - Part A
A Comparison Study on the Formation of Administrative and Leadership Policies for the Team and Individual Olympic Games in the Iraqi National Olympic Committee
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The planning for the formation of administrative policies and guidance through leadership are important things for managing administrative processes and sporting activities. As both contribute in the stability of the administrative conditions, and their development in the sport federations, whether they both were attentive about team and individual Olympic Games. The two researchers observe that, there is a variation in the correct way of application. Particularly in the formulation of administrative policies and leadership describing it as, modern management standards for both team and individual Olympic Games in the Iraqi National Olympic Committee. That led to cause a misconception and lack of clarity for some administrators of those uni

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Publication Date
Thu May 14 2020
Journal Name
Journal Of Planner And Development
“The role of parametric approach in design highest climatic performance buildings: local housing design patterns as a sample”
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In light of increasing demand for energy consumption due to life complexity and its requirements, which reflected on architecture in type and size, Environmental challenges have emerged in the need to reduce emissions and power consumption within the construction sector. Which urged designers to improve the environmental performance of buildings by adopting new design approaches, Invest digital technology to facilitate design decision-making, in short time, effort and cost. Which doesn’t stop at the limits of acceptable efficiency, but extends to the level of (the highest performance), which doesn’t provide by traditional approaches that adopted by researchers and local institutions in their studies and architectural practices, limit

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Publication Date
Sun Apr 01 2018
Journal Name
Journal Of Educational And Psychological Researches
The obstacles that encounter a program of rehabilitating released prisoners as perceived by prisoners themselves in tubas' province
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The study intends to explore the obstacles that encounter a program of rehabilitating released prisoners as perceived by prisoners themselves in tubas' province. To this end, the researcher used a questionnaire as an instrument which was applied on (150) prisoner had chosen randomly to collect the study data. The findings revealed no significant differences among obstacles the encounter program regarding to the following variables: age, detention period, and number of detention, additionally, the findings found that there is a variance of obstacles mean according to the prisoners themselves, rehabilitation program, and the facility of that program.

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Publication Date
Mon Jun 30 2014
Journal Name
Iraqi Journal Of Chemical And Petroleum Engineering
Research Octane Number Improvement of Iraqi Gasoline by Adsorption of n-Paraffins Using Zeolite Molecular Sieves
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This study focused on the improvement of the quality of gasoline and enhancing its octane number by the reduction of n-paraffins using zeolite 5A. This study was made using batch and continuous mode. The parameters which affected the n-paraffin removal efficiency for each mode were studied. Temperature (30 and 40 ˚C) and mixing time up to 120 min for different amounts of zeolite ranging (10-60 g) were investigated in a batch mode. A maximum removal efficiency of 64% was obtained using 60 g of zeolite at 30 ˚C after a mixing time 120 min. The effect of feed flow rate (0.3-0.8 l/hr) and bed height (10-20 cm) were also studied in a continuous mode. The equilibrium isotherm study was made using different amounts of zeolite (2-20 g) and the

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Publication Date
Mon Sep 03 2018
Journal Name
Al-academy
The Interchange of Sign Transformation between Locality and Universality in the Iraqi Theatre, "Romeo and Juliet in Baghdad Show" - A Model
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The research deals with the interchange of the sign transformed from the universal to the local in the theatrical show through the direction processing in the production of a communicative artistic discourse and message, thus making the process of reading the speech and recognizing it by taking into account the cultural differences, customs and local rituals of each country, region, or area. The problem of the research was focused on answering the following question: What are the requirements for the sign in terms of its transformation between the universality and locality in the read-out?

               The importance of research is to determine the requiremen

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Publication Date
Wed Sep 14 2016
Journal Name
Journal Of Baghdad College Of Dentistry
Comparison of Shear Bond Strength of Three Different Brackets Bonded on Zirconium Surfaces (In Vitro Study)
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Background: With the increased in the demands of adult orthodontics, the challenge of direct bonding to non-enamel surface (zirconium) had been increased. The present study was carried out to compare the shear bond strength of three different brackets (stainless steel, sapphire and composite) bonded to zirconium surface and study the mode of bond failure. Materials and methods: The sample was comprised of 30 models (8mm *6mm*1.5mm) of full contour zirconium veneers. They were divided into three groups according to the brackets type; all samples were treated first by sandblast with aluminum oxide particle 50 µm then coated by z-prime plus primer. A central incisor bracket of each group was bonded to the prepared zirconium surface with lig

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Publication Date
Wed Oct 24 2018
Journal Name
Journal Of Economics And Administrative Sciences
Training Programs And Their Impact On The Quality Of municipal Services /Field Research In The Municipality Of Baghdad
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     The objective of this research is to measure the training programs and identify the nature and then measure how it reflected on the quality of municipal services provided by the municipal departments investigated by measuring the quality of services based on quality standards, the researcher chose four municipal departments in the Rusafa / Baghdad (164 people) representing the directors and their assistants, officials of the municipal departments, the people and the engineering staff in charge of the task forces as well, including the survey of the views of the concerned persons in the management of the Vocational Training Institute in the Secretariat of the Republic, The quality of the municipal services

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Publication Date
Fri Nov 01 2019
Journal Name
Journal Of Global Pharma Technology
Synthesis and Phase Transition Study of New Mesogence Derived from 1, 4-Phenylenediamine
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This work include synthesized and characterization the compound [I] by reaction 1,4-phenylenediamine with chloro acetic acid then this compound reaction with methanol in present sulfuric acid to synthesized ester compound [II] after that reaction with hydrazine hydrate to synthesized acide hydrazide [III] and the later compound reaction with substituted acetophenone[IV]n to synthesized substituted acetophenone hydrazones[V-XI]. In addition synthesized4-formylpyrazole derivatives [XIIXVIII] via cyclisation substituted acetophenone hydrazones [V-XI] with Vilsmeier-Haack reagent DMF/POCl3. The compounds characterized by melting points, FTIR, 1HNMR and mass spectroscopy. The mesomorphic behavior studied by using polarized optical microscopy and

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Scopus
Publication Date
Fri Jun 15 2018
Journal Name
Journal Of Baghdad College Of Dentistry
Periodontal health status of patients with Maxillary Chronic Rhinosinusitis (Part 1: Clinical study)
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Background: Periodontal diseases (PD) are inflammatory conditions of the tissues supporting the teeth, most often gingivitis and periodontitis. Maxillary chronic rhinosinusitis (MCRS) is the inflammation of the maxillary sinuses which is last for at least 12 consecutive weeks duration. Aims of study: Distribution of periodontal diseases among patients with Maxillary chronic rhinosinusitis according to gender and age. Materials and methods: Males and females subjects (25-45 years), divided into two groups; 150 patients suffer from MCRS and 130 subjects without MCRS. Clinical periodontal parameters; Plaque Index (PL.I), Gingival Index (G.I), Probing Pocket Depth (PPD), Clinical Attachment Level (CAL) and Bleeding On Probing (BOP) recorded f

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Publication Date
Wed Jan 30 2013
Journal Name
Al-kindy College Medical Journal
Paraphilia in Iraq, a general sketch A study in the sex clinic, at Al-Rashad teaching mental hospital
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Background; paraphilias were studied in the sex
clinic, at Al-Rashad teaching mental hospital, in the
years 2009-2010, a subject never touched before in the
field of psychiatry in Iraq.
Aims of the study :
1-to identify the prevalence of types and number of
paraphilias in those patients.
2-to study the relationship of paraphilias with
sociodemographic factors of the patients.
Patients and methods; using the diagnostic criteria of
DSM IV TR, 52 patients from the outpatient sex clinic
at Al-Rashad mental hospital, collected and studied (41
males and 11 females).
Results; the ratio of men to women was 3.7 : 1, the
majority of our sample was in the age range of 21-30
years (36.35%), with a limited

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