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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 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
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
Wed Jan 01 2020
Journal Name
Karbala Journal Of Physical Education Sciences
The effect of using a designed device to develop the technical performance of the descending landing skill facing with half a cycle on the parallel device of the technical men's
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The research included five sections containing the first section on the introduction of the research and its importance and was addressed to the importance of the game of gymnastic and skilled parallel effectiveness and the importance of learning, but the problem of research that there is a difference in learning this skill and difficulty in learning may be one of the most important reasons are fear and fear of falling and injury, And a lack of sense of the movement of the movement is one of the obstacles in the completion of the skill and the goal of research to design a device that helps in learning the skill of descending Almtor facing with half a cycle according to the typical locomotor track on the parallel device of the technical men'

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Publication Date
Sun Nov 26 2017
Journal Name
Journal Of Engineering
Numerical Study of Heat Transfer Enhancement for a Flat Plate Solar Collector by Adding Metal Foam Blocks
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Numerical study has been conducted to investigate the thermal performance enhancement of flat plate solar water collector by integrating the solar collector with metal foam blocks.The flow is assumed to be steady, incompressible and two dimensional in an inclined channel. The channel is provided with eight foam blocks manufactured form copper. The Brinkman-Forchheimer extended Darcy model is utilized to simulate the flow in the porous medium and the Navier-Stokes equation in the fluid region. The energy equation is used with local thermal equilibrium (LTE) assumption to simulate the thermofield inside the porous medium. The current investigation covers a range of solar radiation intensity at 09:00 AM, 12:00 PM, and 04:00

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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
Thu Feb 01 2024
Journal Name
Baghdad Science Journal
Traditional and molecular methods for diagnosing bacterial meningitis in Erbil city, Iraq
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Bacterial meningitis is a leading cause of illness and death worldwide. It is crucial for clinical and public health care, as well as disease control, to identify the meningitis-causing agent promptly. Between June 2021-February 2022, a total of 100 cerebrospinal fluid (CSF) and blood samples were collected from suspected cases of meningitis admitted to Raparin Paediatric Teaching Hospital, Erbil city-Iraq. Cytochemical, cultural, and biochemical tests were conducted, and confirmed by molecular techniques. Bacterial culture findings were positive in 7% of CSF samples and just one positive among blood samples. The most common pathogens found by cultural characteristics and VITEK 2 Compact System were Staphylococcus sciuri in two

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Publication Date
Tue Jun 30 2020
Journal Name
Journal Of Economics And Administrative Sciences
Intellectual Capital and Role in Achieving of Management of Customer Experience : A field study of the views of a sample of the leaders of Iraqi banks
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The issue of intellectual capital is a critical issue in the success and excellence of organizations, especially if it is linked to the management of customer experience, and because of the characteristic of the Iraqi environment, which affected all sectors, including the banking sector, it was important to discuss the types of intellectual capital and its relationship to the management of customer experience, especially when managers private banks, the importance of research lies in the linking of its variables to build the strategic capabilities of banks to achieve excellence and sustainability, it aims to diagnose the extent of interest in the types of intellectual capital and management of customer experience in the Iraqi ban

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