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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
Fri Aug 08 2025
Journal Name
Al–bahith Al–a'alami
Foreign Series in the Kurdish Satellite Channels and Their Role in the Development of Awareness among Young People in the Kurdistan Region (Korean Series as a Model) (A Field Study on a Sample of Students of the Institute of Fine Arts in the City of Sulay
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The dubbing process for the Foreign Dramas by the Kurdish language became a serious phenomenon in the Kurdish satellite TV, especially in the past few years. It attracted a wide audience, especially young adolescents. And prepared by some breakthrough hostile to Kurdish culture and value coordinated by others remedy for the structural gaps and lapses have, as a result of climate which is brought into existence globalization and secretions variety dimensional, saturated value and cognitive effects bearing a strong identity of its elements. From here, the problem of this research is the ambiguity of their role in a series of developmental processes Kurdish awareness of young people and the extent of the impact that caused it.

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Publication Date
Wed Mar 18 2020
Journal Name
Baghdad Science Journal
The A Comparative Study of the Adsorption of Crystal Violet Dye from Aqueous Solution on Rice Husk and Charcoal
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            In this work, the adsorption of crystal violet dye from aqueous solution on charcoal and rice husk has been investigated, where the impact of variable factors (contact time; the dosage of adsorbent, pH, temperature, and ionic strength) have been studied. It has been found that charcoal and rice husk have an appropriate adsorption limit with regards to the expulsion of crystal violet dye from fluid arrangements. The harmony adsorption is for all intents and purposes accomplished in 45 min for charcoal and 60 min for rice husk. The amount of crystal violet dye adsorbed (0.4 g of charcoal and 0.5 g of rice husk) increased with an increasing pH and the value of 11 is the best

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Publication Date
Fri Feb 28 2025
Journal Name
Energies
Synergizing Machine Learning and Physical Models for Enhanced Gas Production Forecasting: A Comparative Study of Short- and Long-Term Feasibility
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Advanced strategies for production forecasting, operational optimization, and decision-making enhancement have been employed through reservoir management and machine learning (ML) techniques. A hybrid model is established to predict future gas output in a gas reservoir through historical production data, including reservoir pressure, cumulative gas production, and cumulative water production for 67 months. The procedure starts with data preprocessing and applies seasonal exponential smoothing (SES) to capture seasonality and trends in production data, while an Artificial Neural Network (ANN) captures complicated spatiotemporal connections. The history replication in the models is quantified for accuracy through metric keys such as m

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Publication Date
Wed Feb 12 2020
Journal Name
Journal Of Xi'an University Of Architecture & Technology
A COMPARATIVE STUDY OF DIRECTIVES IN SAMUEL BECKETT’S ‘END GAME’ AND ‘WAITING FOR GODOT’
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DBN Rashid, JOURNAL OF XI'AN UNIVERSITY OF ARCHITECTURE & TECHNOLOGY, 2020

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Publication Date
Mon Feb 04 2019
Journal Name
Journal Of The College Of Education For Women
Effectiveness of Graduality, Escalation and Argumentation in Quranic Politeness Discourse “Surat Ghafir a Model” A Pragmatic Study
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Theauthor addressed politeness discourse in “Surat Ghafir”. Quran texts include many rhetorical utterances which are considered pragmatic mechanismsconcerned with finding polite discourse. examining these texts allow to determine the effectiveness degree in the discourse, and to find the effect level that leads to interaction between the speaker and the listener. Graduation is considered an effect and a mechanism of discourse escalation.
The author reached a common definition of the graduation effectiveness term, due to its importance in finding polite discourse that is constructed by lingual manifestations some of which are escalation and graduation. Escalation is a mechanism to show the level of discourse graduation, it is a mea

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Publication Date
Fri Jan 01 2021
Journal Name
E3s Web Of Conferences 318, 03002 (2021)
A Comparative Study on Behavior of RC Columns Strengthened by CFRP and Steel Jacket
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This paper studies the behavior of axially loaded RC columns which are confined with carbon fiber reinforced polymers’ sheet (CFRP) and steel jackets (SJ). The study is based on twelve axially loaded RC columns tested up to failure. It is divided into three schemes based on its strengthening type; each scheme has four columns. The main parameters in this study were the compressive strength of the concrete and steel reinforcement ratio. Furthermore, the results of the experimental test showed a substantial enhancement in the column's load-carrying capacity. When compared to the original columns, the CFRP sheet had a significant effect on improving the ductility of the column by increasing the axial deformation by about 59.2 to 95.7

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Publication Date
Thu Jul 08 2021
Journal Name
Turkish Online Journal Of Qualitative Inquiry (tojqi)
Civil Protection of Rights contiguous to Author’s Royalty in Iraqi Law A comparative study
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Publication Date
Thu Dec 30 2021
Journal Name
College Of Islamic Sciences
Non-traded Tales in Imami and Hanafi Doctrines (A Comparative Study of Religion Fundamentals)
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The present study is about tales attributed to certain people and are not traded. Such a study has a great importance for religion scholars and conveyors of hadiths since it is considered as one of the important sources of Islamic legislation that represent the Holy Sunna, and the majority of the recent study is concerned with non-traded tales of religion scholars. The research starts with the definition of such type of tales and then its types, conditions, legality, exceptions, and the benefit from studying such matter. It is mainly concerned with the opinions of the Imami and Hanafi region scholars respectively, and with comparing between the two doctrines i.e. Imami and Hanafi at the end of each

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Publication Date
Sun Oct 01 2017
Journal Name
International Journal Of Oral And Maxillofacial Surgery
Characteristics of mandibular injuries caused by bullets and improvised explosive devices: a comparative study
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The purpose of this study was to investigate the difference in mandibular trauma caused by two mechanisms for the delivery of missile injuries: firearms and improvised explosive devices (IEDs). The data investigated included sex, age, mechanism of injury, and other clinical and radiographic manifestations. Seventy consecutive patients, predominantly male, with a mean age of 28.6 ± 14 years (range 2–60 years) were enrolled: 38 patients (54.3%) sustained mandibular fractures caused by bullet injuries and 32 patients (45.7%) had mandibular fractures caused by IED explosion injuries. The study revealed that the differences in most of the investigated variables were not statistically significant; the only significant differences were the inci

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Publication Date
Thu Jan 01 2015
Journal Name
Conference Proceedings Of The Society For Experimental Mechanics Series
A comparative study of mode decomposition to relate next-ERA, PCA, and ICA modes
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This paper discusses a comparative study to relate parametric and non-parametric mode decomposition algorithms for response-only data. Three popular mode decomposition algorithms are included in this study: the Eigensystem Realization Algorithm with the Natural Excitation Technique (NExT-ERA) for the parametric algorithm, as well as the Principal Component Analysis (PCA) and the Independent Component Analysis (ICA) for the non-parametric algorithms. A comprehensive parametric study is provided for (i) different response types, (ii) excitation types, (iii) system damping, and (iv) sensor spatial resolution to compare the mode shapes and modal coordinates of using a 10-DOF building model. The mode decomposition results are also compared using

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