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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
Fri Sep 30 2022
Journal Name
Iraqi Journal Of Science
A Class of Harmonic Multivalent Functions for Higher Derivatives Associated with General Linear Operator
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    The main goal of this paper is to introduce the higher derivatives multivalent harmonic function class, which is defined by the general linear operator. As a result, geometric properties such as coefficient estimation, convex combination, extreme point, distortion theorem and convolution property are obtained. Finally, we show that this class is invariant under the Bernandi-Libera-Livingston integral for harmonic functions.

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Publication Date
Mon Sep 01 2014
Journal Name
19th International Conference On Methods And Models In Automation And Robotics (mmar) 2014
A PSO-optimized type-2 fuzzy logic controller for navigation of multiple mobile robots
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Publication Date
Wed Aug 31 2022
Journal Name
Al-kindy College Medical Journal
A comparison of cross sections for Selenium -73 radioisotopes produced by accelerators and reactors
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Background: Selenium-73 with half- life of 7.15 hour emits β+ in nature and has six stable isotopes which are ( 74Se,76Se,77Se,78Se,80Se and 82Se ). Selenium-73 has many applications in technology and radioselenium compounds of metallic have found various applications in medicine.

Objective:  To make a comparison between different reactions that produced cross sections of Se-73 radioisotopes.

Subjects and methods: The feasibility of the production of Selenium -73 via various nuclear reactions was investigated. Excitation functions of 73Se production by the re

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Publication Date
Fri Dec 01 2023
Journal Name
Case Studies In Chemical And Environmental Engineering
Kinetic modeling of a solar photo-electro-Fenton process for treating petroleum refinery wastewater
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Publication Date
Sun Oct 01 2017
Journal Name
Ieee Transactions On Neural Systems And Rehabilitation Engineering
A Framework of Temporal-Spatial Descriptors-Based Feature Extraction for Improved Myoelectric Pattern Recognition
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Publication Date
Wed May 01 2019
Journal Name
Ieee International Electric Machines & Drives Conference (iemdc)
An Investigation of Short Translator Linear Machines for Use in a Free Piston Engine
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Publication Date
Wed Jun 07 2023
Journal Name
Journal Of Educational And Psychological Researches
The Effectiveness of a Program in Developing Awareness of the Criteria for Judging Electronic Educational Materials Among Students of Teaching Diploma at Dhofar University
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The study aims to develop the awareness of the criteria for judging electronic educational materials among students of educational qualification at Dhofar University over spreading the Corona pandemic through a program based on mini-educational units. The study was applied to (18) students studying Teaching diploma at Dhofar University for the academic year 2020-2021, and their number. They were chosen intentionally. The study resulted in reaching a list of criteria for judging electronic educational materials, roughly (18) criteria in the selection themes and (15) criteria in the use theme. The level of awareness of the sample members with the criteria for selecting and using electronic educational materials and the effectiveness of the

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Publication Date
Mon Feb 18 2019
Journal Name
Journal Of Accounting And Financial Studies ( Jafs )
The Role of Insurance Awareness in marketing Insurance Services: An Explorative Research views of a Sample of Employees in the National Company for Insurance
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This research aims at shedding light on the concept of insurance awareness and clarifying its role on marketing insurance services of a sample of (100) employees in the National Company for Insurance. Questionnaire is used as a main instrument for collecting data and information from the sample. Their answers were analyzed by using arithmetic means, standard deviation, centesimal weight, and the correlation coefficient ( , F, t) tests .The research reached several conclusions of which:1.The sample member's response to insurance awareness and marketing insurance services factors was in the medium level.2.There was a positive relationship of a moral sign between insurance awareness and marketing insurance services, that correlation coeffic

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Publication Date
Sat Dec 28 2024
Journal Name
Journal Of College Of Physical Education
Design and standardization of a progressively difficult educational test for football passing skills for first-year students in the College of Physical Education and Sports Sciences
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Standards play a vital role in documenting the values ​​of new test results in the form of tables. They are one of the basic requirements that the standardization process aims for as a complement to standardizing test procedures, and contribute to knowing the current reality of the student. The degree of readiness and level as a result of practicing different exercises for sports activities, in addition to the possibility of adopting it for comparison with his group or similar groups, classification, prediction and selection. Developing the skill of handling the football in the educational field is an important matter for achieving distinguished performance among students. This skill requires a level of accuracy, speed and control, and

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Publication Date
Wed Jun 30 2004
Journal Name
Iraqi Journal Of Chemical And Petroleum Engineering
Factors Affecting the Operation of a Fire Tube Boiler
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