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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 Mar 10 2021
Journal Name
Periodicals Of Engineering And Natural Sciences (pen)
A hybrid Grey Wolf optimizer with multi-population differential evolution for global optimization problems
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Publication Date
Sat Mar 01 2025
Journal Name
Acta Marisiensis - Seria Medica
Transcatheter balloon valvuloplasty for children with severe pulmonary valve stenosis: A single-center experience
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Abstract<p> <bold>Objectives</bold>: this study aim to assess the effectiveness of the Transcatheter balloon valvoplasty (BVP) of severe Pulmonary stenosis (PS) and identify possible complications and predictors for the outcome.</p><p> <bold>Methods</bold>: A retrospective study was conducted at the Iraqi Center of Cardiac Diseases for a 2-year duration in the period from 2021 to the end of 2023; the patients with confirmed severe PS of both genders within the age equal to or less than 18 years were included. For every patient included in the present study, the following data were collected: Demographic data, Echoc</p> ... Show More
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Publication Date
Sat Apr 20 2024
Journal Name
Ibn Al-haitham Journal For Pure And Applied Sciences
An Approximate Solution for a Second Order Elliptic Inverse Coefficient Problem with Nonlocal Integral
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This article studies the nonlocal inverse boundary value problem for a rectangular domain, a second-order, elliptic equation and a two-dimensional equation. The main objective of the article is to find the unidentified coefficient and provide a solution to the problem. The two-dimensional second-order, convection equation is solved directly using the finite difference method (FDM). However, the inverse problem was successfully solved the MATLAB subroutine lsqnonlin from the optimization toolbox after reformulating it as a nonlinear regularized least-square optimization problem with a simple bound on the unknown quantity. Considering that the problem under study is often ill-posed and that even a small error in the input data can hav

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Publication Date
Fri Dec 01 2017
Journal Name
Journal Of Economics And Administrative Sciences
The role of Job description and Perceived organizational support to achieving An Excellent Job performance - An Exploratory study of the views of a sample of department heads at Sulaimaniyah University.
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     This research Sought to identify the correlation relationships and the impact of each of the job description and perceived organizational support, Excellent Job performance of the heads of academic departments in the faculties of the University of Sulaymaniyah Iraqi Kurdistan Region, totaling (89) as President, and to achieve this was Default plan includes research variables as well as the formulation of a number of preparation fundamental assumptions, and researchers used a questionnaire for this purpose as a tool head of the collection of data and information, as it was distributed (80) copies, and the number of retrieved them (76) a copy of a valid statistical analysis, as well as conducting personal i

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Publication Date
Sun Dec 04 2011
Journal Name
Baghdad Science Journal
Effect of Gamma Irradiation on Vegetative Growth of three Sugarcane Genotypes (Saccharum officinarum L.) in field
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I n vitro rooting plantlets of three sugarcane genotypes(Co.j.64, Co.j.86 and Missan) were cultured in the field after exposed at different doses of gamma rays (1,2,3,4,) kr. Data of reduction percentage on vegetative growth, roots number, length per plant and their diameter were investigated. Results showed gradual reductions in number of shoots, length and diameter as according to increasing of gamma doses. The reduction percentage in shoot number, length were reached 57.86,70.36 % at 4 kr respectively which have mean number and length per plant reached (9.27 and 55.33 cm) as compared with the control treatment ,While 1 kr caused higher percent in diameter reached 9.69 % with mean of diameter per plant reached 2.57 cm. Mean time , Ge

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Publication Date
Thu Oct 31 2024
Journal Name
Mathematical Modelling Of Engineering Problems
Investigating the Effects of Canard Dihedral Angle on the Wing Span Loading in a Forward-Swept Wing Aircraft at Transonic Speeds at Steady State Conditions Using Computational Fluid Dynamics
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Forward-swept wings were researched and introduced to improve maneuverability, control, and fuel efficiency while reducing drag and they are often used alongside canards, to further enhance their characteristics. In this research, the effects of canard dihedral angles on the wing loading of a forward-swept wing in transonic flow conditions were studied, as the wing loading provides a measure of wing’s efficiency (lift/drag). A generic aircraft model from literatures was selected, simulated, and compared to, using CFD software ANSYS/Fluent where the flow equations were solved to calculate the aerodynamic characteristics. The research was carried at two different Mach numbers, 0.6 and 0.9, for five different canard dihedral angles which tra

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Publication Date
Tue Jan 05 2021
Journal Name
International Journal Of Research In Social Sciences & Humanities
THE SCIENCES OF THE QUR’AN IN THE INTERPRETATION OF A BRIGHTENING OF THE QUR’AN BY AL-TALAQANI
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The paper deals with the study of the sciences of the Qur’an according to the interpreter, Ayatollah Sayyid Mahmoud al-Talaqani, a religious jihadist figure from Iran. He is the author of the exegesis (Ishraq from Al-Quran), which consists of six parts, which he wrote inside the prisons of the Shah and in exile. Mr. Al-Talaqani agreed with some of the commentators in his positions on the sciences of the Qur’an, and some of them disagreed with others.

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Publication Date
Sun Feb 18 2024
Journal Name
Migration Letters
Knee Injuries And Rehabilitation: A Comprehensive Review Of The Psychological Landscape
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MT Suhail, SA Hussein, MN Abdulhussein, WQ Abdaullateef, M khairallah Aid…, Migration Letters, 2024

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Publication Date
Mon Sep 14 2020
Journal Name
British Journal Of Neurosurgery
Head injuries caused by the ritual of ‘Tatbir’: a neurosurgical perspective
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Publication Date
Sun Jun 30 2002
Journal Name
Iraqi Journal Of Chemical And Petroleum Engineering
The Convective Heat Transfer of Fluid Flowing Across a Vertical Plate
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