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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 Dec 30 2014
Journal Name
College Of Islamic Sciences
Approaches to the formation of a contemporary explanatory mindset: Critical inductive study
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The issue of the development of Qur'anic studies for the tasks, and the first thought of minds and multiple understandings, and the most precious ideas, and the alternatives were floated, and varied visions, especially as we live in an era exploding knowledge, and complicate secretions, and scramble his ideas, and to devise intellectual approaches To achieve the witnesses of civilization in the words of the Almighty (to be martyrs on the people) Surat Al - Baqarah / 143 attendance and participation in the achievement and a positive interaction with the participants of humanity and civilization in the light of the meaning (to know) rooms / 13.
Therefore, we must emerge from the one-dimensional view of the Koran to the complex mindset t

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Publication Date
Wed May 24 2023
Journal Name
College Of Islamic Sciences
Manifestation, implicitness, and the interaction of Quranic discourse systems - a stylistic study
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Stylistics represents a modern approach in understanding the literary text through the linguistic patterns that form it. The distinctive phenomena that the text includes constitute special features in it. As well as exploring its aesthetic aspects through description and analysis at the same time. The close link between stylistics and linguistics made stylistics occupy a prominent place in modern literary criticism.
In this regard, we do not want to dwell on the different directions of stylistics. Rather, we will prolong the discussion in the study of the style as a (deviation. Aversion) from the original. Because this trend plays on the chord of the paradox between the surface structure and the deep structure, especially when the sur

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Publication Date
Tue Dec 01 2015
Journal Name
Journal Of Engineering
Study the Dynamic Behavior of Rotor Supported on a Worn Journal Bearings
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In this paper, the effect of wear in the fluid film journal bearings on the dynamic behavior of rotor bearing system has been studied depending on the analytical driven of dynamic stiffness and damping coefficients of worn journal bearing. The finite element method was used to modeling rotor bearing system. The unbalance response, critical speed and natural frequency of rotor bearing system have been studied to determine the changes in these parameters due to wear. MATLAB software was used to find the analytical values of dynamic coefficients of journal bearing. The results of rotor mounted on fluid film journal bearings showed that the wear in journal bearing increases the amplitude of unbalance response and decrease critical speed, sta

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Publication Date
Sun Mar 31 2024
Journal Name
Iraqi Geological Journal
Exploring the Impact of Petrophysical Uncertainties on Recoverable Reserves: A Case Study
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Reliable estimation of critical parameters such as hydrocarbon pore volume, water saturation, and recovery factor are essential for accurate reserve assessment. The inherent uncertainties associated with these parameters encompass a reasonable range of estimated recoverable volumes for single accumulations or projects. Incorporating this uncertainty range allows for a comprehensive understanding of potential outcomes and associated risks. In this study, we focus on the oil field located in the northern part of Iraq and employ a Monte Carlo based petrophysical uncertainty modeling approach. This method systematically considers various sources of error and utilizes effective interpretation techniques. Leveraging the current state of a

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Publication Date
Wed Jan 01 2014
Journal Name
Journal Of The College Of Languages (jcl)
The stylistics of expressive structure in Al-Sayyab's attempt- A textual study
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Our research tends to study the poetic attempt of  Badr Shakir Al-Sayyab and examine it stylistically, and we suggested his mature collection '' Rain song'' as a pattern for our textual analysis of the poet's attempt.

   In the beginning , we confirm that branches of applied structures meet to produce poetry such as narration , drama , cinema , mythology , allegory , various religious and historical texts , previous events , and special cumentary events related to work production. If all above-mentioned was complicated and disregarded throughout a single text , the text writer would not secure positive results that might keep open continuity between him and his readers.

   Therefore , this issue w

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Publication Date
Sun Sep 30 2012
Journal Name
College Of Islamic Sciences
Surat Al-Qaria: a linguistic study
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Praise be to God, Lord of the worlds, and the best of prayers, and extradition was made to our master Muhammad and his whole family and companions:
And after:
Surat Al-Qariah is from the royal fence, which is in the thirtieth part of the Noble Qur’an. The commentators differed on the number of verses, and the reason for its naming. This surah talked about the conditions of people on the Day of Resurrection, and about how people were removed from their graves, all of which I spoke about in the preamble.
The research is divided into six topics: the first topic dealt with strange terms, while the second topic dealt with the most important audio issues mentioned in the surah, namely (slurring, advertising, substitution, and silenc

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Publication Date
Fri Jun 03 2022
Journal Name
Military Medical Science Letters
COVID-19 AMONG A SAMPLE OF IRAQI PATIENTS WITH RHEUMATIC DISEASES: A MULTICENTER STUDY
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Publication Date
Sun Mar 06 2016
Journal Name
Baghdad Science Journal
A study of Soil Invertebrates community in a Date - Palm plantation in Baghdad, Iraq
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Soil invertebrates community an important role as part of essential food chain and responsible for the decomposition in the soil, helps soil aeration , nutrients recycling and increase agricultural production by providing the essential elements necessary for photosynthesis and energy flow in ecosystems.The aim of the present study was to investigate the soil invertebrates community in one of the date palms plantation in Aljaderia district South of Baghdad, , and their relationships with some physical and chemical properties of the soil , as Five randomly distributed replicates of soil samples were collected monthly. Invertebrates samples were sorted from the soil with two methods, direct method to isolate large invertebrates and indirec

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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
Sat Feb 01 2020
Journal Name
Journal Of Economics And Administrative Sciences
Evaluation of banking performance according to the CAMELS model An applied study of Al-Mansour Investment Bank for the period 2014-2018.
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The banking sector has a significant impact on the economic growth of the country, and the importance of this sector must assess its financial performance from time to time, to measure the situation related to money for each bank and how to put the supervision of the efficiency of the full. The research aims at evaluating the financial performance according to the elements of the CAMELS model, which including capital adequacy, asset quality, management efficiency, profitability, liquidity, and market risk sensitivity. The research included the study of Al-Mansour Investment Bank during the period from 2014 to 2018. The base capital ratio was used to total assets to measure capital adequacy The proportion of investments to total a

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