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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
Sat Jun 30 2018
Journal Name
College Of Islamic Sciences
Narrative narration in the poetry of Mohammed Abdul Muttalib   (Top poem as a model)
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Poets of the age since ancient times to recount the events of their adventures in a fun story style in which the elements of the story of personalities, time and place, and we do not mean this modern art technique (poetic story) as it is now, but was aimed at the pleasures of the other receiving because it is the rule of the quality of literary output, Other times the narrative of events inspired by his broad imagination and this mixing indicates the story's involvement with Arabic poetry to be (poetic story) and this depends entirely on addressing the poet to the recipient, and requires in this narrative to be familiar with the elements of influence and suspense in the other or turned into a monotonous and dull narrative Influential, un

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Publication Date
Sat Feb 01 2014
Journal Name
Journal Of Economics And Administrative Sciences
A comparison of the Semiparametric Estimators model smoothing methods different using
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In this paper, we made comparison among different parametric ,nonparametric and semiparametric estimators for partial linear regression model users parametric represented by ols and nonparametric methods represented by cubic smoothing spline estimator and Nadaraya-Watson estimator, we study three nonparametric regression models and samples sizes  n=40,60,100,variances used σ2=0.5,1,1.5 the results  for the first model show that N.W estimator for partial linear regression model(PLM) is the best followed the cubic smoothing spline estimator for (PLM),and the results of the second and the third model show that the best estimator is C.S.S.followed by N.W estimator for (PLM) ,the

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Publication Date
Thu Dec 21 2023
Journal Name
Mathematical Modelling Of Engineering Problems
Enhancing Spatial Accuracy of OpenStreetMap Data: A Geometric Approach
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OpenStreetMap (OSM), recognised for its current and readily accessible spatial database, frequently serves regions lacking precise data at the necessary granularity. Global collaboration among OSM contributors presents challenges to data quality and uniformity, exacerbated by the sheer volume of input and indistinct data annotation protocols. This study presents a methodological improvement in the spatial accuracy of OSM datasets centred over Baghdad, Iraq, utilising data derived from OSM services and satellite imagery. An analytical focus was placed on two geometric correction methods: a two-dimensional polynomial affine transformation and a two-dimensional polynomial conformal transformation. The former involves twelve coefficients for ad

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Publication Date
Mon Jul 01 2019
Journal Name
Journal Of Engineering
The Characters of the Form in the Vernacular Architecture A comparative study of the form's characters of facades of individual houses and commercial buildings in the City of Baghdad after 2003–Zayoona district as a case study
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The characters of facades' form of the Iraqi building after 2003 have been changed, it has been described by many names. The problem of the research is that what are the features of the characters of the form in the façades of the buildings in Baghdad city after 2003? Are the façade of the individual houses or the commercial buildings is the heaviest in the visual weight? The research aims to answer those questions by choosing the vernacular architecture as a measurement tool. It is the informal image of the architecture, which is built by people informally and spontaneously, without official control and legislation to be organized. This is smellier to what has happened in Baghdad, after 2003 according to previous stud

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Publication Date
Fri Oct 28 2022
Journal Name
Political Sciences Journal
A future view for the political systems of the Arab Gulf states After normalization ... the United Arab Emirates as a case study
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The dangers of (Israel's) integration with Arab countries in the middle east region will threaten the Arab security structure dimension, which the latter makes the Arab regional system vulnerable for distortion due to its nominal and symbolic value which is far from the Arab self and questioning with its effectiveness in comparing with the real capabilities to Arab countries in achieving the common targets. So, how to assess the different problems that began to hit the structure of the Arab regional system? and how to pledge an allegiance after putting forward what is known as the American Deal of the Century for the administration of former US President Donald Trump for making another step toward normalization with (Israel)?. The reveal

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Publication Date
Wed Mar 08 2017
Journal Name
Ibn Al-haitham Journal For Pure And Applied Sciences
Amino Acids as Environmentally-Friendly Corrosion Inhibitors for 2024 Aluminium Alloy in Akaline Medium
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The corrosion behavior of 2024 aluminium alloy was investigated in alkaline medium (pH=13) containing 0.6 . in absence and presence of different concentrations of three amino acids separately [Methionine, Glutamice acid and Lysine] as environmentally friendly corrosion inhibitors over the temperature range (293-308)K. Electrochemical polarization method using potentiostatic technique was employed. The inhibition efficiency increased with an increase of the inhibitor concentration but decreased with increase in temperature . The maximum efficiency value was found with lysine =80.4 of 293 k and 10 . concentration of lysine. The adsorption of the amino acids was found to obey Langmuir adsorption isotherm . Some thermodynamic parameter âˆ

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Publication Date
Tue Jun 15 2021
Journal Name
Al-academy
Visual discourse of statues of symbolic figures Christ as a model (An analytical study): مصطفى ممتاز نوري الياور
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The topic of this research deals with an analytical study of the nature of the visual sent by the sculptural monument of the person of Christ around the world, the nature of this monument, the manner of its embodiment, the mechanism of reception for each of the societies that this monument addressed to them, how it was reflected on them, how it was reflected on them, and whether these works are related to their culture or not, I discussed this study All this, and the researcher has established theoretical research axes for the research according to the desired goal of this study, which is the definition of the mechanism of visual discourse of statues of Christ around the world and were as follows: (The first axis: the discourse and visua

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Publication Date
Sun Jan 01 2012
Journal Name
مجلة واسط للعلوم والطب
Study of nuclear characters to some 164, 166, 168 68 Er isotopes by using the interacting boson model IBM-1
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The aim of this study is to show the concepts of nuclear shape and the geometrical picture to the even-even nuclei of 164,166,168E isotopes in the context of the Interacting boson Model IBM-1. The energy spectra were calculated and the effective charge values (eB) of the electromagnetic transition strength were obtained and used to calculate the B(E2) values of the electromagnetic transitions and the quadrupole moment Q of 2+ -states. The Hamiltonian parameters were calculated by taking in account the properties of these nuclei. Comparison were made with the available experimental data and included in tables. The geometrical picture of these nuclei were looked at by calculating the deformation which were represented by the potentia

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Publication Date
Sat Jun 01 2019
Journal Name
Al-nahrain Journal Of Science
THREE DIMENSIONAL EXPLICIT MODEL FOR COMETARY TAIL IONSINTERACTIONSWITH SOLAR WIND
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The different interactions between cometary tail and solar wind ions are studied in the present paper based on three-dimensional Lax explicit method. The model used in this research is based on the continuity equations describing the cometary tail-solar wind interactions. Three dimensional system was considered in this paper. Simulation of the physical system was achieved using computer code written using Matlab 7.0. The parameters studied here assumed Halley comet type and include the particle density , the particles velocity v, the magnetic field strength B, dynamic pressure p and internal energy E. The results of the present research showed that the interaction near the cometary nucleus is mainly affected by the new ions added to the

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Publication Date
Wed May 10 2017
Journal Name
Ibn Al-haitham Journal For Pure And Applied Sciences
A Comparative Anatomical Study of Petioles to Thirteen Taxa for Scutellaria L. (Labiatae) in Iraq
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   Petioles of nine species and four subspecies for Scutellaria L. which are growing wildly in Iraq were studied anatomically. Systmatic importance for the cross sections of those petioles were found. The winged petioles were seen in all taxa but they were different in their shapes , some of them U – shaped but they were semi ellipsoid in others , also they were different in their numbers of vascular bundles in the wings , and the shapes of central vascular bundles , so those  taxa were divided into groups .

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