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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
Sun Jan 01 2023
Journal Name
Journal Of Engineering
Optimization of Locations for Bioswales Stormwater Management Using BMP Siting Tool - Case Study of Sulaymaniyah City-KRG-Iraq
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Today, urban Stormwater management is one of the main concerns of municipalities and stakeholders. Drought and water scarcity made rainwater harvesting one of the main steps toward climate change adaptation. Due to the deterioration of the quality of urban runoff and the increase of impermeable urban land use, the treatment of urban runoff is essential. Best Management Practice (BMP) and Low Impact Development (LID) approaches are necessary to combat climate change consequences by improving the quantity and quality of water resources. The application of Bioswales along urban streets and roadways can reduce the stress on water resources, recharge groundwater and prevent groundwater pollution. While Sulaymaniyah City has a

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Publication Date
Tue Dec 01 2020
Journal Name
Journal Of Economics And Administrative Sciences
The Impact Of Knowledge Innovation On Strategic Empowerment (Comparative Field Research)
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The Innovation Of Knowledge Is An Important And A Key Element In The Progress And Business Excellence Organizations, Therefore Requires Several Elements To Help Create And Implement And Move The Innovation Process Of Knowledge, Including The Strategic Empowerment Associated With The Element Of The Process Of Strategic Momentum Engine Driven Wheel Continuous Dynamic Innovation, And Focused Research Problem By Measuring The Availability Of Strategic Empowerment When Individuals From By Senior Departments And Ways To Help Organizations To Provide Empowerment Commensurate With The Requirements Of Achieving The Goals Of Time And Place Appropriate For The Individual, And The Importance Of Research Stems From The Importance Of The Varia

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Publication Date
Wed Oct 11 2023
Journal Name
Journal Of Educational And Psychological Researches
Motivations of Volunteers in Jordan: An Exploratory Study Based on a Sample of University Students within the Context of their Social Relations
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Volunteerism is an element included in many human cultures. It represents a positive cooperative act between individuals and groups. It expresses the social value systems. As a social phenomenon, it develops in societies according to innumerous circumstances and conditions. This study uses a functional approach that assumes that volunteering performs six functions for volunteers. Namely, we assume that volunteering (1) creates a sense of protection (2) meets significant cultural values (3) improves professional status of volunteers, (4) strengthens their social relationships, (5) helps them achieve a better understanding of life, and finally, (6) enhances their outlook and self-esteem. The central aim of the study is to discuss these fun

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Publication Date
Sun Jan 01 2017
Journal Name
Journal Of Engineering
Two – Dimensional Mathematical Model to Study Erosion Problem of Tigris River Banks at Nu’maniyah
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The high and low water levels in Tigris River threaten the banks of the river. The study area is located on the main stream of Tigris River at Nu’maniyah City and the length of the considered reach is 5.4 km, especially the region from 400 m upstream Nu’maniyah Bridge and downstream of the bridge up to 1250 mwhich increased the risk ofthe problemthat itheading towardsthe streetand causingdanger tonearbyareas.

The aim of this research is to identify the reason of slope collapse and find proper treatments for erosion problem in the river banks with the least cost. The modeling approach consisted of several steps, the first of which  is by using “mini” JET (Jet Erosion Test) d

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Publication Date
Thu Nov 01 2007
Journal Name
University Of Baghdad
The Psychic Experience and its Effects on the Creative Process: A Study in Selected Poems By Allen Ginsberg and David Gascoyne
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Evidences indicate that human beings were preoccupied with extreme forms of mental and psychic experiences long before they were recorded in literature. Greek myths and legends appear to include symbolizations of delusions, mania, and other bizarre forms of thought and behaviuor. The figure of the mad man or woman is analogous to the wild man, or the imaginary being who appears in various forms throughout western literature and art. Various studies refer to the notion of the wild man as a response to a persistent psychological urge. This urge gives an external expression and a valid form to the impulses of reckless physical self-assertion which is believed to be hidden in all of us, but is normally kept under control. Such impulses were exp

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Publication Date
Sun Mar 15 2020
Journal Name
Journal Of The College Of Education For Women
General Conditions of Women in Ibn al-Jawzi’s Book Safwat Al-Safwa: A Historical Study
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The research aims at the scholars’attention to the importance and role of Arab Muslim women through books and historical studies that historians and scholars have taken up like Ibn Al-Jawzi (597 AH) and his book Safwat Al-Safwa,  where he presented the conduct of worship and their words and deeds, and explained to women worshipers other aspects of their lives, such as the scientific aspect Crafts and works as well as their prominent role in preaching and religious guidance, and the impact of this on their morals and qualities. This study showed the strength of the personality of women and their high interest in worship. The importance of the study lies in knowledge.The research followed the role of Muslim women to carry t

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Publication Date
Wed May 01 2024
Journal Name
Clinical Epidemiology And Global Health
Systemic and cutaneous side effects of COVID-19 vaccines in Iraq, A cross-sectional study
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Publication Date
Fri Nov 22 2019
Journal Name
Chalcogenide Letters
CONCENTRATION EFFECTS ON ELECTRONIC AND SPECTROSCOPIC PROPERTIES OF ZnCdS WURTZOIDS: A DENSITY FUNCTIONAL THEORY STUDY
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Publication Date
Mon Mar 11 2019
Journal Name
Baghdad Science Journal
A Spectral, Optical, Microscopic Study, Synthesis and Characterization of PVC Films Containing Schiff Base Complexes
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In this work, synthesis of conducting polymeric films namely, PVC thin films was carried out containing Schiff base (L) with Cu2+, Cr3+, Ni2+, Co2+, in addition to inspecting the possibilities of measuring energy gap values of PVC-L-M with variety metal ions. These new polymeric films (PVC-L-M) were characterized by FTIR spectrophotometry, energy gap and surface morphology. The optical data recorded that the band gap values are influenced by the type of metals. All modified films have a red shift in optical properties in the ultraviolet region. The PVC-L-Co(II) was the lowest value of the optical band gap, 3.1 eV.

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Publication Date
Wed Jun 01 2011
Journal Name
Journal Of Economics And Administrative Sciences
Competitiveness of an enterprise under a flexible manufacturing system. Manufacturing strategy and flexibility - Case study
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The research has designed for studying the relationship between manufacturing strategy and its flexibility under the flexible manufacturing system with their reflection on the competitive environmental performance of the firm. To interpret and tackle the problem, a hypothesis has formulated stating that “ the competitive performance of a firm is interpreted by the manufacturing strategy and flexibility which are derived from the firm and its business  strategies under the flexible manufacturing system”. Related literatures with their theoretical dissertations, which enhanced the thoughtful content, have analyzed. An illustrative case study on the flexible manufacturing system at Toyota Motors Corporation working at the g

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