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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 10 2018
Journal Name
In Book: Challenges In Mechanics Of Time-dependent Materials, Volume 2edition: 1stchapter: 11
A Case Study to Evaluate Live Load Distributions for Pre-stressed RC Bridge
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Publication Date
Tue Dec 05 2023
Journal Name
Baghdad Science Journal
Classification of Diseases in Oil Palm Leaves Using the GoogLeNet Model
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The general health of palm trees, encompassing the roots, stems, and leaves, significantly impacts palm oil production, therefore, meticulous attention is needed to achieve optimal yield. One of the challenges encountered in sustaining productive crops is the prevalence of pests and diseases afflicting oil palm plants. These diseases can detrimentally influence growth and development, leading to decreased productivity. Oil palm productivity is closely related to the conditions of its leaves, which play a vital role in photosynthesis. This research employed a comprehensive dataset of 1,230 images, consisting of 410 showing leaves, another 410 depicting bagworm infestations, and an additional 410 displaying caterpillar infestations. Furthe

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Publication Date
Wed Jan 01 2014
Journal Name
Journal Of The College Of Languages (jcl)
Politeness: A Socio- Pragmatic Study
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The most influential theory of ‘Politeness’ was formulated in 1978 and revised in 1987 by Brown and Levinson. ‘Politeness’, which represents the interlocutors’ desire to be pleasant to each other through a positive manner of addressing, was claimed to be a universal phenomenon. The gist of the theory is the intention to mitigate ‘Face’ threats carried by certain ‘Face’ threatening acts towards others.

            ‘Politeness Theory’ is based on the concept that interlocutors have ‘Face’ (i.e., self and public – image) which they consciously project, try to protect and to preserve. The theory holds that various politeness strategies are used to prot

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Publication Date
Tue Feb 09 2016
Journal Name
Advances In Environmental Biology
A study effect Histological changes
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Publication Date
Sun Jul 17 2022
Journal Name
Al–bahith Al–a'alami
(دراسة تحليلية): ( A field study )
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The research aimed to identify the effects of the modern of technology on translating the media term from English language to Arabic. and try to identify the use of the impact of foreign media terminologies on the Arabic media term, and to know the effect of the translation process on Arabic media terminologies.

This research is considered an analytical study by using survey study for 111 items and the results for the study as following:

1.High percentage of the (use of foreign terms work to low the level of production) was (68.13%) and average 3.55

2.The percentage of (The multiplicity of translation of the foreign term into Arabic effects on the opinions and cognitive ideas of the Arab researcher and affects the

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Publication Date
Wed Mar 15 2023
Journal Name
Al-academy
Geometrical Foundations of Shape in Structural Design of Contemporary Ceramic Pots "The artist "IBRAHIM SAEED" is a model"
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Each era has advantages in terms of innovation and development in form, technology, style, and design in ceramic vessels, both at the level of functional and aesthetic performance, so this study aimed to demonstrate the importance of geometrical foundations in the design structure of contemporary ceramic vessels, and also to reveal the constructive skills in The structure of the ceramic figure.
The researchers used the descriptive analytical approach to suit the nature of the study, and they described and analyzed the ceramic works in terms of geometric shape systems, elements and foundations of design in construction, formal diversity in the general design of ceramic vessels, and references and sources of artwork. In addition to th

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Publication Date
Sun Dec 02 2012
Journal Name
Baghdad Science Journal
The Dissolution Study For Sodium Selenite Tablets Using Atomic Absorption Spectrophotometer
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The development of a meaningful dissolution procedure for drug products with limited water solubility has been a challenge to both the pharmaceutical industry and the agencies that regulate them. Natural surfactants aid in the dissolution and subsequent absorption of drugs with limited aqueous solubility. In vitro, various techniques have been used to achieve adequate dissolution of the sparingly water – soluble or water insoluble drug products such as the use of mechanical methods (i.e., increased agitation and the disintegration method) or hydro alcoholic medium or large volumes of medium. The necessity of assuring the quality of drugs , especially those with low aqueous solubility and in vivo absorption , has led to the development and

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Publication Date
Thu Jan 23 2025
Journal Name
Научный форум
PHRASEOLOGISMS RELATED TO THE USE OF COLORS IN SPEECH AS A MEANS OF ENRICHING MODERN RUSSIAN LANGUAGE
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The paper examines key aspects of the use of phraseologi-cal units related to colors in Russian culture and speech. It explores their role in shaping cultural identity, reflecting national characteristics and men-tality. The study analyzes the frequency and contexts of the use of color-related phraseological units in contemporary speech, as well as the influ-ence of media and literature on their popularization. The author highlights the significance of phraseological units in preserving cultural heritage and fostering a deeper understanding of language and culture.

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Publication Date
Thu Oct 01 2020
Journal Name
Biochemical And Cellular Archives
ISOLATION OF SOME PATHOGENIC BACTERIA FROM STUDENTS’ MAKEUP AS A PART OF BIOSAFETY IN THE MEDICAL LABORATORIES
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The bacterial contamination of lipsticks and face cream may become a great important matter in the medical laboratories. The present study was designed to determine the types of bacterial contamination in the face cream and lipsticks of undergraduate students. Also, the study aimed to determine the sensitivity of the isolated bacteria against many antibacterial agents. The study included 190 swabs samples from 190 face cream and lipsticks samples of the females’ students from five departments in the Medical Technology Institute, Almansour, Middle Technical University were collected in February 2018. The swab samples were collected with sterile condition and cultured on enriched Blood agar and MacConkey agar. Serial dilutions were made up

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Publication Date
Mon Jun 14 2021
Journal Name
Turkish Journal Of Physiotherapy And Rehabilitation
A STUDY OF THE DIMENSIONS OF COMPETITION ANXIETY AND ITS RELATIONSHIP TO THE DIMENSIONS OF SPORTING ACHIEVEMENT MOTIVATION FOR YOUNG TENNIS PLAYERS
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One of the most important phenomena facing the athlete is the anxiety of sports competition, as he faces many psychological problems during training and in competitions of psychological tension, fear and anxiety that accompany him sometimes, which leads to affecting his level, and sports competition anxiety is a special type of anxiety that occurs in the athlete It is related to the attitudes of sports competitions and that participation in sports competitions and the associated emotional experiences are among the important factors that motivate the practice of sports activity and try to advance and develop his sports level. It is assumed that when the individual begins to practice any activity, he aims to reach a level or degree of achie

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