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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
Mon Mar 31 2025
Journal Name
The Iraqi Geological Journal
Evaluation of Machine Learning Techniques for Missing Well Log Data in Buzurgan Oil Field: A Case Study
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The investigation of machine learning techniques for addressing missing well-log data has garnered considerable interest recently, especially as the oil and gas sector pursues novel approaches to improve data interpretation and reservoir characterization. Conversely, for wells that have been in operation for several years, conventional measurement techniques frequently encounter challenges related to availability, including the lack of well-log data, cost considerations, and precision issues. This study's objective is to enhance reservoir characterization by automating well-log creation using machine-learning techniques. Among the methods are multi-resolution graph-based clustering and the similarity threshold method. By using cutti

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Publication Date
Sat Oct 16 2021
Journal Name
Journal Of Advance Research In Chemical Sciences
Study of Schiff Bases Complexes of Trimethoprim: A Review
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Publication Date
Thu Sep 16 2021
Journal Name
Journal Of Advance Research In Chemical Sciences
Study of Schiff Bases Complexes of Trimethoprim: A Review
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Trimethoprim derivative Schiff bases are versatile ligands synthesized with carbonyl groups from the condensation of primary amines (amino acids). Because of their broad range of biological activity, these compounds are very important in the medical and pharmaceutical fields. Biological activities such as antibacterial, antifungal and antitumor activity are often seen. Transition metal complexes derived from biological activity Schiff base ligands have been commonly used

Publication Date
Wed Sep 30 2020
Journal Name
College Of Islamic Sciences
Saba is a semantic study of examples of pronouns
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which is much useful in the Arabic Language generally in the Holly Quran especially. It is the pronoun  I have taken in the semantic aspect from it and I have done on the surra sabba which varities  the semantical pronoun in it among the pronoun of the speaker the conscience of the addressee the absent  such the the siprat pronoun that comes in it with the explanation for its importance and its work and this is the subject of the first unit which I advanced it from the concept of the pronoun Linguistically and convention. After that I have lighten in some meanings which I have done in the surrat as a semantic , magnification , proud, reprimand and others which I ended my research I have reached the results from it

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Publication Date
Mon Apr 02 2018
Journal Name
University Of Baghdad, College Of Education For Pure Sciences / Ibn Al-haitham, Department Of Mathematics
A Study of Some Generalizations of Fibrewise Bitopological Spaces
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In this research, we introduce and study the concept of fibrewise bitopological spaces. We generalize some fundamental results from fibrewise topology into fibrewise bitopological space. We also introduce the concepts of fibrewise closed bitopological spaces,(resp., open, locally sliceable and locally sectionable). We state and prove several propositions concerning with these concepts. On the other hand, we extend separation axioms of ordinary bitopology into fibrewise setting. The separation axioms we extend are called fibrewise pairwise T_0 spaces, fibrewise pairwise T_1 spaces, fibrewise pairwise R_0 spaces, fibrewise pairwise Hausdorff spaces, fibrewise pairwise functionally Hausdorff spaces, fibrewise pairwise regular spaces, fibrewise

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Publication Date
Thu Dec 16 2021
Journal Name
Journal Of Advance Research In Chemical Sciences
Study of Schiff Bases Complexes of Trimethoprim: A Review
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Trimethoprim derivative Schiff bases are versatile ligands synthesized with carbonyl groups from the condensation of primary amines (amino acids). Because of their broad range of biological activity, these compounds are very important in the medical and pharmaceutical fields. Biological activities such as antibacterial, antifungal and antitumor activity are often seen. Transition metal complexes derived from biological activity Schiff base ligands have been commonly used.

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Publication Date
Sun Mar 15 2020
Journal Name
Journal Of Baghdad College Of Dentistry
Comparative study of the antioxidant effects of lavender and flax oils in recurrent aphthous ulceration treatment
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Background: Recurrent aphthous ulceration (RAU) is an inflammatory condition of unknown etiology characterized by painful recurrent (single or multiple) ulcerations of the oral mucosa. It is one of the most common and poorly understood mucosal disorders. It occurs more frequently in times of stress. Local and systemic conditions, genetic, immunologic, microbial factors, and oxidative stress may play a role in the pathogenesis of RAU. The objective of this study was to evaluate the free radical metabolism and antioxidant activity of RAU patients treated by lavender or flax oil paint.

Materials and Methods: Sixty-six RAU patients were enroll

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Publication Date
Tue Dec 30 2008
Journal Name
Al-kindy College Medical Journal
Use of Ascetic Fluid Cholesterol as a Marker to Differentiate between Types of Ascetic Fluid
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Background:- Cholesterol is high in ascetic fluid due
to malignancy and other causes of exudates.
Objective:-To use cholesterol as a marker to
differentiate between exudative and transudative
ascetic fluid and to compare that with other routine
parameters.
Methods:-Twenty eight patients were included in this
study 17 females with mean age of 41.9 years, 11
males with mean age of 48.2 years. The patients were
divided in group I suspected transudate, and group II
suspected exudate according to history and clinical
examination.
Ascetic fluid samples were sent for total protein,
albumin, and cholesterol measurement blood samples
were sent for serum protein and albumin measurement.
Results:-In this

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Publication Date
Sun Nov 01 2020
Journal Name
Iop Conference Series: Materials Science And Engineering
Assessment of some mechanical properties of PMMA/silica/zirconia nanocomposite as a denture base material
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Abstract<p>In this research, nanocomposites of poly(methyl methacrylate) (PMMA) and a mixture of nano silica (SiO<sub>2</sub>) and nano zirconia (ZrO<sub>2</sub>) were prepared in different weight percentages of the nano fillers to improve some of the properties of PMMA resin to be used as a denture base material. The nano filles were surface modified with a coupling agent and added to the PMMA in different amounts. Impact strength, transverse strength, hardness and roughness were tested for both control and experimental groups. The results indicate that PMMA/silica/zirconia nanocomposites, prepared with 5% by weight of both types of fillers, had a slight increase in impact s</p> ... Show More
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Publication Date
Fri Jan 30 2026
Journal Name
Journal Of Baghdad College Of Dentistry
Effect of sodium fluoride addition as a disinfectant on some properties of alginate impression material
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Background: Impression materials, impression trays, and poured stone cast have been said to be the main source of cross infection between patients and dentists. However, it was observed that disinfection of the impression is not performed systematically in routine dental practice. Disinfection of alginates either by immersion or spray technique was found to cause dimensional inaccuracies, although with proper disinfection of alginates there were small dimensional changes. A variety of fluoride releasing products designed for topical use is currently available. Following their use, varied amount of fluoride is systemically absorbed depending on the fluoride concentration and the manner of its use. The objective of this study was to evaluate

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