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bijps-1604
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 19 2023
Journal Name
Journal Of Ethnic And Cultural Studies
Request Constructions in Classical Arabic versus Modern Arabic: A Corpus-based Study
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The present study aims to investigate the various request constructions used in Classical Arabic and Modern Arabic language by identifying the differences in their usage in these two different genres. Also, the study attempts to trace the cases of felicitous and infelicitous requests in the Arabic language. Methodologically, the current study employs a web-based corpus tool (Sketch Engine) to analyze different corpora: the first one is Classical Arabic, represented by King Saud University Corpus of Classical Arabic, while the second is The Arabic Web Corpus “arTenTen” representing Modern Arabic. To do so, the study relies on felicity conditions to qualitatively interpret the quantitative data, i.e., following a mixed mode method

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Publication Date
Sun Aug 01 2021
Journal Name
Journal Of Mechanical Engineering Research And Developments
Slot Design Procedure for a NACA 4412 at High Angle of Attack
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The main objective of the present work is to find a method increases the efficiency of the airfoil that is used for blade in wind turbine, wing in aircraft, propeller and helicopter (like NACA 4412). By overcoming the separation of flow at high angle of attacks, a slotted airfoil had been used and solved numerically through connecting the pressure side in the bottom surface with the suction side in the top surface of the airfoil to energize the separated flow. Slot exit, width and slope were considered as a parameters of slot configuration to determine the effective design of consideration. Reynolds number was taken as [1.6 x106 ] and the angle of attacks were ranged from (0o - 20o ). The numerical solution with Ansys Fluent commercial prog

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Publication Date
Wed Mar 18 2020
Journal Name
Baghdad Science Journal
A Hybrid Method of Linguistic and Statistical Features for Arabic Sentiment Analysis
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          Sentiment analysis refers to the task of identifying polarity of positive and negative for particular text that yield an opinion. Arabic language has been expanded dramatically in the last decade especially with the emergence of social websites (e.g. Twitter, Facebook, etc.). Several studies addressed sentiment analysis for Arabic language using various techniques. The most efficient techniques according to the literature were the machine learning due to their capabilities to build a training model. Yet, there is still issues facing the Arabic sentiment analysis using machine learning techniques. Such issues are related to employing robust features that have the ability to discrimina

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Publication Date
Fri Jan 01 2021
Journal Name
Computers, Materials & Continua
A Technical Framework for Selection of Autonomous UAV Navigation Technologies and Sensors
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Publication Date
Tue Jul 02 2013
Journal Name
Journal Of Baghdad College Of Dentistry
Local Drug Delivery Systems for Treating Periodontal Diseases: A Review of Literature
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Publication Date
Mon Jun 09 2025
Journal Name
Journal Of Discrete Mathematical Sciences And Cryptography
A novel improvement of skew tent map for generating Pseudo random numbers
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An encryption system needs unpredictability and randomness property to maintain information security during transmission and storage. Although chaotic maps have this property, they have limitations such as low Lyapunov exponents, low sensitivity and limited chaotic regions. The paper presents a new improved skewed tent map to address these problems. The improved skew tent map (ISTM) increases the sensitivity to initial conditions and control parameters. It has uniform distribution of output sequences. The programs for ISTM chaotic behavior were implemented in MATLAB R2023b. The novel ISTM produces a binary sequence, with high degree of complexity and good randomness properties. The performance of the ISTM generator shows effective s

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Publication Date
Thu Sep 30 2004
Journal Name
Iraqi Journal Of Chemical And Petroleum Engineering
A Simple Method for Studying Crushability and Grindability of Rocks and Minerals
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Publication Date
Thu Dec 31 2020
Journal Name
Political Sciences Journal
Islamic feminism is a discussion of paths for establishing an Islamic epistemology
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If feminist philosophy in the context of feminist research focuses on how to produce an alternative knowledge and culture for women and forming anew awareness of their roles in the face of prevailing misconceptions then the topic of Islamic feminism is presented as a philosophical topic in the field of human knowledge to discuss how to produce an alternative knowledge of traditional knowledge prevailing in patriarchal societies to restore the balance of power and authority in the relationship between the sexes to create an effective feminist role in advocating for and defending womenś issues to achieve this Islamic feminism sought to establish an Islamic epistemology .

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Publication Date
Sun Mar 01 2026
Journal Name
Journal Of Baghdad College Of Dentistry
Local drug delivery systems for treating periodontal diseases (A review of literature)
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In this review of literature, the light will be concentrated on the local drugs delivery systems for treating the periodontal diseases. Principles, types, advantages and indications of each type will be discussed in this paper.

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Publication Date
Sat Sep 01 2018
Journal Name
King's College London
A novel sol-gel silica formulation for management of methadone hydrochloride abuse
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Introduction: Methadone hydrochloride (MDN) is an effective pharmacological substitution treatment for opioids dependence, adopted in different countries as methadone maintenance treatment (MMT) programmes. However, MDN can exacerbate the addiction problem if it is abused and injected intravenously, and the frequent visits to the MMT centres can reduce patient compliance. The overall aim of this study is to develop a novel extended-release capsule of MDN using the sol-gel silica (SGS) technique that has the potential to counteract medication-tampering techniques and associated health risks and reduce the frequent visits to MMT centres. Methods: For MDN recrystallisation, a closed container method (CCM) and hot-stage method (HSM) were conduc

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