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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 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 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
Thu Oct 18 2018
Journal Name
International Journal Of Research In Social Sciences And Humanities
A Linguistic study of Presupposition in Rattigan’s play ‘while the sun shines’
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As a kind of linguistic study, the study of presupposition in drama is one of captivating topic to explore, because of the capability of this topic to make people perceive the presupposition differently. Presupposition is one of the most important concepts in linguistics. It refers to the implicit inferences made in communication between people. These inferences are necessary to understand the utterances correctly. The research particularly endeavors to focus on the linguistic constructions that activate presupposition.

Publication Date
Sat Sep 30 2023
Journal Name
Journal Of The College Of Education For Women
A Pragmatic Study of Narcissism in the American Movie Big Eyes (2014)
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Narcissism is a complicated phenomenon that can be reflected in the narcissist’s language. Investigating narcissism in terms of linguistics, and pragmatics in particular, does not seem to have been given its due attention, as this study reveals. Thus, this study is an endeavor to discover how narcissism is reflected in the American movie Big Eyes (2014). It is known for introducing narcissistic behaviors. This paper aims to identify the types, motivations, and pragmatic manifestations of narcissism in the selected movie. Three pragmatic theories are chosen to scrutinize narcissism in the data: Searle’s speech acts (1969), Grice’s maxims breaching (1975), and Culppeper’s impoliteness (1996). To cope with the nature of the

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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 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 Jan 01 2023
Journal Name
Corporate And Business Strategy Review
The role of learning organizations in crisis management strategy: A case study
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The problem of the paper focused on the role of the learning organization in the crisis management strategy, and the extent of the actual interest in both the learning organization and the crisis management and aimed at diagnosing and analyzing that and surrounding questions. The Statistical Package for the Social Sciences (SPSS) program was used to calculate the results and the correlation coefficient between the two main variables. The methodology was descriptive and analytical. The case study was followed by a questionnaire that was distributed to a sample of 31 teachers. The paper adopted a seven-dimensional model of systemic thinking that encourages questioning, empowerment, provision of advanced technologies, and strategic lea

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Publication Date
Wed Jan 01 2020
Journal Name
Solid State Technology
Image Fusion Using A Convolutional Neural Network
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Image Fusion Using A Convolutional Neural Network

Publication Date
Sun Sep 24 2023
Journal Name
Journal Of Al-qadisiyah For Computer Science And Mathematics
Human Recognition Using Ear Features: A Review
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Over the past few years, ear biometrics has attracted a lot of attention. It is a trusted biometric for the identification and recognition of humans due to its consistent shape and rich texture variation. The ear presents an attractive solution since it is visible, ear images are easily captured, and the ear structure remains relatively stable over time.  In this paper, a comprehensive review of prior research was conducted to establish the efficacy of utilizing ear features for individual identification through the employment of both manually-crafted features and deep-learning approaches. The objective of this model is to present the accuracy rate of person identification systems based on either manually-crafted features such as D

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Publication Date
Thu Jul 01 2021
Journal Name
International Journal Of Nonlinear Analysis And Application
Forecasting enhancement using a hodrick-prescott filter
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: Sound forecasts are essential elements of planning, especially for dealing with seasonality, sudden changes in demand levels, strikes, large fluctuations in the economy, and price-cutting manoeuvres for competition. Forecasting can help decision maker to manage these problems by identifying which technologies are appropriate for their needs. The proposal forecasting model is utilized to extract the trend and cyclical component individually through developing the Hodrick–Prescott filter technique. Then, the fit models of these two real components are estimated to predict the future behaviour of electricity peak load. Accordingly, the optimal model obtained to fit the periodic component is estimated using spectrum analysis and Fourier mod

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