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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
Sat Dec 31 2022
Journal Name
Al-kindy College Medical Journal
Molecular Microbiology in Clinical Practice: Current and Future Applications: Molecular Microbiology
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Technological advances have yielded new molecular biology-based methods for the diagnosis of infectious diseases.  The newest and most powerful molecular diagnostic tests are available at regional and national reference laboratories, as well as at specialized centers that are certified to conduct metagenomic testing.  Metagenomic assays utilize advances in DNA extraction technology, DNA sequence library construction, high throughput DNA sequencing and automated data analysis to identify millions of individual strands of DNA extracted from clinical samples.  At present, metagenomic assays are only possible at a small number of special research, academic and commercial laboratories.  Continued research in human and path

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Publication Date
Fri Jan 13 2023
Journal Name
World Academy Of Sciences Journal
Potential effects of miR‑146 expression in relation to malondialdehyde as a biomarker for oxidative damage in patients with breast cancer
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Publication Date
Wed Jun 01 2016
Journal Name
Journal Of Economics And Administrative Sciences
Budget Programs and Performance away to enhance the control in government economic units
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     The control function of important functions in the system of government for several reasons , perhaps the most important of the magnitude of spending and spending in one of the tools adopted in the implementation of the control function.                               

        Perhaps the most prominent stages of the development budget in terms of setup and use in the budget programs and performance , as specialized literature  show its importance in strengthening financial and operationl

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Publication Date
Thu Sep 30 2021
Journal Name
Journal Of Economics And Administrative Sciences
The Role of Product Innovation on an Improvement of the Organization's Reputation /A Field Study in State Organization for Marketing of Oil (SOMO)
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 This paper aims to verify the existence of relationships between product innovation and the reputation of the organization. The study problem is that the State Organization for Marketing of Oil (SOMO) system is inflexible in terms of marketing procedures and needs innovative, unconventional methods in innovating its products and improving performance. The reputation of the organization. The importance of the study lies in that it is an attempt to raise the interest of SOMO in its approach to the research variables in order to enhance its competitive position in the future and improve the marketing business environment, which contributes to enhancing the reputation of the organization by product innovation. The study sample

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Publication Date
Thu Jan 09 2020
Journal Name
Plant Archives
Molecular Study of Two Fungi Millerozyma Farinosa and Candida Orthopsilosis by PCR Using Its Gene and Phylogenetic Structuring Tree Isolated from Diabetic Patient in Baghdad
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Diabetic mellitus is one of the main risk factors of fungal infections because poor glycemic control is associated with a high level of glucose in blood and saliva which could be treated as nutrient to fungi. This study aimed to isolate and identification of pathogenic fungi from diabetic patient. 140 samples were taken from different places of human body from the national center of diabetic patients that related to Mustansiriyah University / college of medicine and Al-yarmuk Hospital in Baghdad. 84 sample (60%) tested positive to fungi and 56 sample (40%) tested negative to fungi. The most frequented fungi isolated have been chosen for molecular identification by PCR (Millerozyma farinosa and Candida orthopsilosis) using specific pri

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Publication Date
Fri Nov 21 2025
Journal Name
Al–bahith Al–a'alami
Evaluation in the Kurdish Media Institutions (A Descriptive Study Survey)
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The importance of evaluation depends on many institutions, whether governmental or private, including media institutions, rely on the list to evaluate the weight of things and appreciation, as well as judging things, achievements, and everything related to the institution is concerned. Because through evaluation, institutions can recognize weaknesses and strengths. It is also an effective tool for management review, through which the institution can review everything related to planning and decision-making, leadership, incentives and other administrative matters.

Therefore, this study attempts to shed light on the evaluation process, its basics and its importance in general and in the Kurdish media institutions as a model in part

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Publication Date
Sun May 01 2022
Journal Name
Journal Of Engineering
The Collapsible Soil, Types, Mechanism, and identification: A Review Study
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Collapsible soil has a metastable structure that experiences a large reduction in volume or collapse when wetting. The characteristics of collapsible soil contribute to different problems for infrastructures constructed on its such as cracks and excessive settlement found in buildings, railways channels, bridges, and roads. This paper aims to provide an art review on collapse soil behavior all over the world, type of collapse soil, identification of collapse potential, and factors that affect collapsibility soil. As urban grow in several parts of the world, the collapsible soil will have more get to the water. As a result, there will be an increase in the number of wetting collapse problems, so it's very important to com

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Publication Date
Tue Dec 27 2022
Journal Name
College Of Islamic Sciences
Verbal joint in the Holy Quran A descriptive analytical study
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The research paper talks about one of the topics that deals with one of the high-style styles in the Holy Qur’an that carries with it a high and influential style in directing the Qur’anic context, as the verses are singled out with certain words, each of which came out to other meanings, which is what was called in the past “what the wording agreed and the meaning differed Or the so-called “faces and analogues” and the meaning of analogues in the language and the Qur’an; To mention a word in a place and it means a meaning other than the other, and to interpret each word with a meaning other than the other meant by the faces, and accordingly the goal of the research is in the linguistic significance, in order to reveal the tr

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Publication Date
Sat Dec 30 2023
Journal Name
Journal Of The College Of Education For Women
The Middle East and Contemporary Geostrategic Shifts: A Geopolitical Study
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This research focuses on the contemporary geostrategic transformations that afflicted the countries of the Middle East, with a focus on the countries of the Arab East, after the collapse of the system of international relations, and the emergence of the unipolar system led by the United States of America. After the events of September 11 and the events that followed, especially the occupation of Iraq in 2003, the study area witnessed a group of geopolitical variables and the emergence of dangerous phenomena that threatened the state structure in the countries of the Middle East; the most notably are the phenomenon of terrorism, cross-border armed groups, sectarian polarization, the phenomenon of migration and the internal and the externa

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Publication Date
Wed Jun 01 2022
Journal Name
Political Sciences Journal
The Middle East and its Strategic Dimensions: a theoretical study
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Characterized the Middle East has geographic, economic, and geostrategic peculiarities, but it suffers from many problems, such as disagreement over what it means as a concept, or what it represents of a geographic extension. The question is related to the ambiguity surrounding the concept of the Middle East? The purpose of its launch? As it relates to its geostrategic, economic, and geo-cultural importance? And manifestations of this importance? And to what extent he retained his value in the strategies of the major powers? Research hypotheses:

-The multiplicity of concepts for the Middle East region, with international political and Geostrategic interests.- The geostrategic value of the Middle East has made it a focal point for

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