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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
Wed May 01 2024
Journal Name
Journal Of Madenat Alelem College
Study 1,4- Naphthoquinone Derivative and Biological Activity: A Review
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In this work, we focused on studying 1,4-naphthoquinones and their derivatives, and knowing the methods of preparing them using different auxiliary agents and forming derivatives containing heterocyclic rings, active groups and saturated rings containing heterogeneous elements . In addition, due to their strong antibacterial, antifungal and anticancer activity, 1,4-naphthoquinone compounds biological importance and are considered a source of various pharmaceutical compounds.

Publication Date
Sun Jun 20 2021
Journal Name
Baghdad Science Journal
A Scoping Study on Lightweight Cryptography Reviews in IoT
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The efforts in designing and developing lightweight cryptography (LWC) started a decade ago. Many scholarly studies in literature report the enhancement of conventional cryptographic algorithms and the development of new algorithms. This significant number of studies resulted in the rise of many review studies on LWC in IoT. Due to the vast number of review studies on LWC in IoT, it is not known what the studies cover and how extensive the review studies are. Therefore, this article aimed to bridge the gap in the review studies by conducting a systematic scoping study. It analyzed the existing review articles on LWC in IoT to discover the extensiveness of the reviews and the topics covered. The results of the study suggested that many re

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Publication Date
Fri Jun 01 2012
Journal Name
Journal Of The College Of Languages (jcl)
Sound Assimilation in English and Arabic: a Contrastive Study
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      This piece of research deals with assimilation as one of the phonological processes in the language. It is a trial to give more attention to this important process in English language with deep explanation to its counterpart in Arabic. in addition, this study sheds light on the points of similarities and differences concerning this process in the two languages. Assimilation in English means two sounds are involved, and one becomes more like the other.

     The assimilating phoneme picks up one or more of the features of another nearby phoneme. The English phoneme /n/ has t

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Publication Date
Sun Dec 22 2024
Journal Name
Journal Of Petroleum Research And Studies
Optimizing Well Placement with Genetic Algorithms: A Case Study
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Maximizing the net present value (NPV) of oil field development is heavily dependent on optimizing well placement. The traditional approach entails the use of expert intuition to design well configurations and locations, followed by economic analysis and reservoir simulation to determine the most effective plan. However, this approach often proves inadequate due to the complexity and nonlinearity of reservoirs. In recent years, computational techniques have been developed to optimize well placement by defining decision variables (such as well coordinates), objective functions (such as NPV or cumulative oil production), and constraints. This paper presents a study on the use of genetic algorithms for well placement optimization, a ty

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Publication Date
Mon Jan 01 2024
Journal Name
Aip Conference Proceedings
Negative skin friction evaluation and mitigation: A review study
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Publication Date
Mon Sep 01 2025
Journal Name
Iranian Journal Of Nursing And Midwifery Research
Girls’ Experiences Regarding Obesity: A Qualitative Study in Iraq
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Abstract<sec> <title>Background:

Obesity among girls can cause physical, psychological, or social problems. Different cultures have different lifestyle and dietary habits which affect people’s experience about obesity. This study aimed to assess girls’ experience toward obesity.

Materials and Methods:

In 2023, a qualitative conventional content analysis method was used in this study to meet the study’s objective in Baghdad and Babylon, Iraq. A probability purposive sampling method was used to gather the sample from three high schools in t

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Publication Date
Wed Jan 01 2020
Journal Name
Desalination And Water Treatment
Stabilization of phenol trapped by agricultural waste: a study of the influence of ambient temperature on the adsorbed phenol
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Stabilization of phenol trapped by agricultural waste: a study of the influence of ambient temperature on the adsorbed phenol

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Publication Date
Fri Nov 11 2022
Journal Name
Ibn Al-haitham Journal For Pure And Applied Sciences
Analytical Methods for Determination of Ketoprofen Drug: A review
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Ketoprofen has recently been proven to offer therapeutic potential in preventing cancers such as colorectal and lung tumors, as well as in treating neurological illnesses. The goal of this review is to show the methods that have been used for determining ketoprofen in pharmaceutical formulations. Precision product quality control is crucial to confirm the composition of the drugs in pharmaceutical use. Several analytical techniques, including chromatographic and spectroscopic methods, have been used for determining ketoprofen in different sample forms such as a tablet, capsule, ampoule, gel, and human plasma. The limit of detection of ketoprofen was 0.1 ng/ ml using liquid chromatography with tandem mass spectrometry, while it was 0

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Publication Date
Thu Dec 01 2016
Journal Name
Bulletin Of The Iraq Natural History Museum (p-issn: 1017-8678 , E-issn: 2311-9799)
A NEW RECORD OF ZIZIPHORA SPECIES (LAMIACEAE) FOR IRAQ
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    Ziziphora persica Bunge is recorded as a new Study in Iraq. This species has been collected from Jabal Sinjar in Nineveh province in the north western part of Iraq. The morphological characters, habitat and geographical distribution of the species with a key to Ziziphora L. species in Iraq have been provided.

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Publication Date
Sun Feb 10 2019
Journal Name
Journal Of The College Of Education For Women
Toward a stereotype specification for measurement of university women
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A- The research problem: the research problem which is the garments industry, as a
whole it does not rely on a single system in the sizes of the clothing and the working
companies, see that it is not plausible that the sizes be unificd and consistent in all companies.
The current sizes in the domestic Iraqi markets are not suitable for some females ,on the other
hand the Iraqi industry suffers the lack of a modern standard for some Iraqis female bodies.
B- The Signifiance of the research: lies in the study of the diversity of the human body
sizes and naming them to reflect the desires and requirements of the consumer and try to find
a method to meet their expectations as well as to raise the level of garments industr

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