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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
Thu Oct 31 2024
Journal Name
Sabrao Journal Of Breeding And Genetics
THE ROLE OF NANOTECHNOLOGY IN CROP IMPROVEMENT – A REVIEW
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Publication Date
Sun Jul 01 2001
Journal Name
Bulletin Of The Iraq Natural History Museum (p-issn: 1017-8678 , E-issn: 2311-9799)
HAEMATOZO`A OF THE AVIAN FAMILY PHASIANIDAE IN IRAQ
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A collection of 118 specimens of Iraqi phasianid birds belong to four species was examined
for haematozoa. Results show that 21.2% of them were infected with one or more of four
species of blood parasites; Haemoproteus danilewskyi, H. santosdiasi, Plasmodium sp. and
microfilaria. Haemoproteus danilewskyi is reported here for the first time in Iraq.

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Publication Date
Wed Aug 26 2020
Journal Name
International Journal Of Research In Social Sciences And Humanities
THE ROLE OF A PROTEAN CAREER IN HIGH PERFORMANCE
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Publication Date
Thu Jun 29 2023
Journal Name
Iraqi Journal Of Chemical And Petroleum Engineering
A Review of the Electrical Submersible Pump Development Chronology
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The electric submersible pump, also known as ESP, is a highly effective artificial lift method widely used in the oil industry due to its ability to deliver higher production rates compared to other artificial lift methods. In principle, ESP is a multistage centrifugal pump that converts kinetic energy into dynamic hydraulic pressure necessary to lift fluids at a higher rate with lower bottomhole pressure, especially in oil wells under certain bottomhole condition fluid, and reservoir characteristics. However, several factors and challenges can complicate the completion and optimum development of ESP deployed wells, which need to be addressed to optimize its performance by maximizing efficiency and minimizing costs and uncertainties. To

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Publication Date
Tue Nov 01 2022
Journal Name
Journal Of Engineering
The Use of Lightweight Aggregate in Concrete: A Review
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One of the artificial lightweight aggregates with a wide range of applications is Lightweight Expanded Clay Aggregate. Clay is utilized in the production of light aggregates. Using leftover clay from significant infrastructure development projects to manufacture lightweight aggregates has a favorable environmental impact. This research examines the expanded clay aggregate production process and the impact of processing parameters on its physical and mechanical qualities. It also looks at secondary components that can be used to improve the qualities of concrete with expanded clay aggregates. The effect of the quantity of expanded clay aggregate on the fresh, hardened, and durability qualities of concrete is also studied.

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Publication Date
Mon Nov 24 2025
Journal Name
Al–bahith Al–a'alami
"THE COMMUNICATOR AND THE FACTORS INFLUENCING HIS JOB IN UNIVERSITY PRESS": " A survey study of the managers of administrative departments of public relations and media at Iraqi Universities. "
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The research problem lies in the lack of accurate scientific perceptions concerning the reality of the communicator and the factors influencing his job. The research is aimed at introducing the communicator in the university press, clarifying the obstacles facing him, and uncovering the level of his job satisfaction and his visions of developing his work.

The researcher adopted the survey method in the collection, analysis, and interpretation of the data using a questionnaire.

 A set of results and conclusions has been reached, most importantly are:

 

*The communicator performs multiple missions including writing, editing, and collecting info

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Publication Date
Wed Aug 03 2022
Journal Name
Journal Of Accounting And Financial Studies ( Jafs )
The pioneering trend in managing health institutions and its impact on improving the quality of services : A case study in some institutions of the Iraqi Ministry of Health
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This study seeks to identify the role that the leadership trend plays in the management of health institutions in Iraq and its impact on improving the quality of the health service provided by analyzing some opinions of affiliates working in the Iraqi health sector where a survey list was used as a main tool for collecting primary data, as it was subjected to this analysis ( 60) of the medical staff, of whom (40) are doctors and (20) are affiliated with the rank of assistant physician, and (60) members of the administrative cadre have undergone their various job ranks and administrative specializations (department manager, auditor, observer, accountant, statistician, secretary). Reliance on statistical software (spss) in data ana

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Publication Date
Thu Sep 01 2016
Journal Name
Physica Medica
Quantitative analysis of sentinel lymph node detection using a novel small field of view hybrid gamma camera (HGC)
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Introduction The Hybrid Gamma Camera (HGC) is being developed to enhance the localisation of radiopharmaceutical uptake in targeted tissues during surgical procedures such as sentinel lymph node (SLN) biopsy. Purpose To assess the capability of the HGC, a lymph-node-contrast (LNC) phantom was constructed for an evaluative study simulating medical scenarios of varying radioactivity concentration and SLN size. Materials and methods The phantom was constructed using two methyl methacrylate PMMA plates (8 mm thick). The SLNs were simulated by drilling circular wells of diameters ranging between 10 mm and 2.5 mm (16 wells in total) in one plate. These simulated SLNs were placed underneath scattering material with thicknesses ranging between 5 mm

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Publication Date
Sun Feb 03 2019
Journal Name
Iraqi Journal Of Physics
Investigation of density and form factor of some F isotopes using Hartree-Fock and shell model calculations
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Structure of unstable 21,23,25,26F nuclei have been investigated
using Hartree – Fock (HF) and shell model calculations. The ground
state proton, neutron and matter density distributions, root mean
square (rms) radii and neutron skin thickness of these isotopes are
studied. Shell model calculations are performed using SDBA
interaction. In HF method the selected effective nuclear interactions,
namely the Skyrme parameterizations SLy4, Skeσ, SkBsk9 and
Skxs25 are used. Also, the elastic electron scattering form factors of
these isotopes are studied. The calculated form factors in HF
calculations show many diffraction minima in contrary to shell
model, which predicts less diffraction minima. The long tail

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Publication Date
Mon Oct 01 2018
Journal Name
Iraqi Journal Of Science
Theoretical Study of The Electromagnetic Structure of Boron Isotopes Using Local Scale Transformation Technique
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