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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 28 2021
Journal Name
Journal Of The College Of Education For Women
A Pragmatic Analysis of Personal Deixes in Lyrical Poetry: Ezra Pound's Lyrics "Girl" and "A Virginal": رماح محي مجيد
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Deixes belong to the field of both semantics and  pragmatics as they lie in the edge of these two fields. Pragmatically, they are concerned with the relationship between the structure of a language and the contexts. The present work aims at analyzing the use of deixes using Levinson’s (1983) and Yule's (1996) concept of deixes, where the latter maintained that the referents of the deixes cannot be realized apart from the context where they are used. He added that the contextual information of certain utterances involves information about the participants (the speaker and the addressee), the time and the place. Consequently, a qualitative- descriptive approach has been adopted to meet the objective of the study which reads, “exam

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Publication Date
Wed Apr 06 2022
Journal Name
Neuroquantology
Theoretical Study of Photons Spectra around High Energy of Quark-antiquark Using QCD Theory
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In this paper, we study and investigate the quark anti-quark interaction mechanism through the annihilation process. The production of photons in association with interaction quark and gluon in the annihilation process. We investigate the effect of critical temperature, strength coupling and photons energy in terms of the quantum chromodynamics model theory framework. We find that the use of large critical temperature Tc =134 allows us to dramatically increase the strength coupling of quarks interaction. Its sensitivity to decreasing in photons rate with respect to strength coupling estimates. We also discuss the effect of photons energy on the rate of the photon , such as energies in range (1.5 to 5 GeV).The photons rate increases

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Publication Date
Sun Jan 01 2023
Journal Name
Journal Of Population Therapeutics And Clinical Pharmacology
Kinetic and thermodynamic study of adsorption of an industrial food dye using Iraqi clay
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Publication Date
Sat May 23 2026
Journal Name
Journal Of Baghdad College Of Dentistry
Enhancement of tooth eruption by using amniotic stem cells (Immunohistochemical study of VEGF marker)
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Background: Tooth eruption is a localized process in the jaws which exhibits precise timing and bilateral symmetry. Develop within the jaws and their eruption is a complex infancy process during which they move through bone to their functional positions within the oral cavity. For species with more than one set of teeth, eruption of the second set also accomplishes. The key to the successful clinical management of tooth eruption consists of understanding that this process consists largely of the local regulation of alveolar bone metabolism to produce bone resorption in the direction of eruption and shift and formation of bone at the opposite side.The amniotic sac contains a considerable quantity of stem cells. These amniotic stem cells are

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Publication Date
Wed Mar 30 2022
Journal Name
Journal Of Economics And Administrative Sciences
Using Quadratic Form Ratio Multiple Test to Estimate Linear Regression Model Parameters in Big Data with Application: Child Labor in Iraq
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              The current paper proposes a new estimator for the linear regression model parameters under Big Data circumstances.  From the diversity of Big Data variables comes many challenges that  can be interesting to the  researchers who try their best to find new and novel methods to estimate the parameters of linear regression model. Data has been collected by Central Statistical Organization IRAQ, and the child labor in Iraq has been chosen as data. Child labor is the most vital phenomena that both society and education are suffering from and it affects the future of our next generation. Two methods have been selected to estimate the parameter

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Publication Date
Mon Sep 23 2019
Journal Name
Baghdad Science Journal
A Semi-Supervised Machine Learning Approach Using K-Means Algorithm to Prevent Burst Header Packet Flooding Attack in Optical Burst Switching Network
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Optical burst switching (OBS) network is a new generation optical communication technology. In an OBS network, an edge node first sends a control packet, called burst header packet (BHP) which reserves the necessary resources for the upcoming data burst (DB). Once the reservation is complete, the DB starts travelling to its destination through the reserved path. A notable attack on OBS network is BHP flooding attack where an edge node sends BHPs to reserve resources, but never actually sends the associated DB. As a result the reserved resources are wasted and when this happen in sufficiently large scale, a denial of service (DoS) may take place. In this study, we propose a semi-supervised machine learning approach using k-means algorithm

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Publication Date
Mon Oct 01 2018
Journal Name
Al–bahith Al–a'alami
The role of social networking sites of Iraqi satellite channels in prioritizing the public “Field study for the public of Dhi Qar governorate
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The study titled “The role of the social media sites of Iraqi satellite channels in prioritizing the public” is a field study for the public of Dhi Qar.
The emergence of the social networking sites we are currently experiencing has undergone radical and important changes in the role of the mass media in light of the growth and rapid spread of modern technologies Or the so-called new media، which led the media organizations to create satellite channels on the social networks، which led to bypass the traditional lines between the public and media institutions with the public gain the possibility of The purpose of the research is to determine the habits and patterns of public use of the social media sites of the Iraqi satellite cha

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Publication Date
Sat May 23 2026
Journal Name
Journal Of Baghdad College Of Dentistry
Comparative study of retention of fiber-reinforced post at middle and cervical one thirds of root canal cemented by polycarboxylate and zinc phosphate cements measured at different storage times
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Background: The purpose of this study was to compare regional bond strength at middle and cervical thirds of the root canal among glass fiber-reinforced composite (FRC) endodontic posts cemented with different cements, using the push-out test to compare the performance (retention) of two types of luting cements; polycarboxylate cement and Zinc phosphate cement used to cement translucent fiber post and to compare the result of the push-out test at different storage times;1 week ,1month and 2 months. Materials and methods: Ninety caries-free, recently extracted single-rooted human teeth with straight root canals was used in this study, The root canals were endodontically instrumented at a working length of 0.5 mm from the apex by m

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Publication Date
Sun Apr 15 2001
Journal Name
University Of Baghdad, College Of Veterinary Medicine
A Study of Antimicrobial Effect of Oil Extracts of Black Seed (Nigella sativa L.) on some Pathogenic Microorganism that is isolated from Clinical Pathogenic Cases.
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Publication Date
Tue Mar 03 2020
Journal Name
Aip Conference Proceedings
Correlation study of (IL-17, IL-17RA) and some biochemical parameters with patients of Iraq colorectal cancer after and before taking a dose of chemotherapy
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Colorectal cancer CRC is the third most commonly diagnosed cancer in males and the second in female, so it is a common and life-threatening disease serum of 48 males and 40 females suffering from CRC disease as group one (G1) without taking a chemotherapy dose, the same patients group tow (G2) after taking the first chemotherapy dose, while group three (G3) whose patients in (G1) and (G2) after second taking a chemotherapy dose. and group four (G4) consist of (30 males and 30 females) healthy Iraqi control. Results showed a significant increase in IL-17, IL-17RA and CEA in G1, while there was a significant decrease in vitamin D concentration in G1 than other groups, also there was positive (+ ve) significant correlation between IL-17 and CE

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