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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 Aug 31 2019
Journal Name
Iraqi Journal Of Physics
A Study of the Spectroscopic Performance of Laser Produced CdTe(x):S(1-x) Plasma
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Abstract

In this work, the plasma parameters (electron temperature (Te), electron density( ne), plasma frequency (fp) and Debye length (λD)) have been studied by using the spectrometer that collect the spectrum of Laser produce CdTe(X):S(1-X) plasma at X=0.5 with different energies. The results of electron temperature for CdTe range 0.758-0.768 eV also the electron density 3.648 1018 – 4.560 1018 cm-3  have been measured under vacuum reaching 2.5 10-2 mbar .Optical properties of CdTe:S were determined through the optical transmission method using ultraviolet visible spectrophotometer within the r

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Publication Date
Fri May 15 2026
Journal Name
Iraqi Journal Of Science
Synthesis, Characterization and Quantum Mechanical Study of Some New 2-benzylidenehydrazinecarbothioamide Derivatives as Corrosion Inhibitors for Carbon/mild Steel in Acidic Medium.
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In this work, some of new 2-benzylidenehydrazinecarbothioamide derivatives have been prepared by condensation of thiosemicarbazide and different substituted aromatic benzaldehydes in presence of glacial acetic acid to give compounds (1-6), these compounds have characterized by its physical properties and spectroscopic methods. This work also included theoretical study to prove the ability of these compounds as corrosion inhibitors; The program package of Gaussian 09W with its graphical user interface GaussView 5.0 had used for this purpose; the methods of Density Functional Theory (DFT) with basis set of 6-311G (d,p) / hybrid function of B3LYP and semiempirical method of PM3 have been used, the study included theoretical simulation

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Publication Date
Mon Jan 01 2018
Journal Name
Journal Of The College Of Languages (jcl)
The Word " בַּיִת " (House) in the Book of Joshua A Comparative Semitic Linguistic Study
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In this paper we have dealt with the word "  בַּיִת" in the Book of Joshua because it makes one of those that highly employed the  word    בַּיִת"  " in the Old Testament. The Book of Joshua comes  sixth   in the order of tanakh wich was written by Joshua son of  Noon in Palestine during the fifteenth century  B.C. and it covers a three-decade era extending from the death  of Moses til the death of Joshua son of Noon.

      The word " בַּיִת " in this paper refers to the place, where expressions are made by a noun modified by a noun . The modifier is"" בַּיִת , and the modified is another noun. Herein, we

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Publication Date
Wed Mar 20 2019
Journal Name
Journal Of Legal Sciences
Sale Based on an Open Price – A Comparative Study
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The ultimate goal of any sale contract is to maximize the combined returns of the parties, knowing that these returns are not realized (in long-term contracts) except in the final stages of the contract. Therefore, this requires the parties to the contract to leave some elements open, including the price, because the adoption of a fixed price and inflexible will not be appropriate to meet their desires when contracting, especially with ignorance of matters beyond their will and may affect the market conditions, and the possibility of modifying the fixed price through The elimination is very limited, especially when the parties to the contract are equally in terms of economic strength. Hence, in order to respond to market uncertainties, the

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Publication Date
Fri Jan 01 2021
Journal Name
Annals Of Maxillofacial Surgery
The use of screw retained hybrid arch bar for maxillomandibular fixation in the treatment of mandibular fractures: A comparative study
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Introduction: The use of screw-retained hybrid arch bars (HABs) is a relatively recent development in the treatment of mandibular fractures. The purpose of this study is to compare the clinical outcome between HAB and the conventional Erich arch bar (EAB) in the closed treatment of mandibular fractures. Materials and methods: This study included 18 patients who were treated for mandibular fractures with maxillomandibular fixation (MMF), patients were randomly assigned into a control group (n = 10) in which EAB was used and study group (n = 8) in which HAB was used. The outcome variables were time required for application and removal, gingival inflammation scores, postoperative complications, and incidence of wire-stick injury or gloves perf

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Publication Date
Wed Apr 05 2023
Journal Name
Journal Of Engineering
A Developed Model for Selecting Optimum Locations of Water Harvesting Dams Using GIS Techniques
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An integrated GIS-VBA (Geographical Information System – Visual Basic for Application), model is developed for selecting an optimum water harvesting dam location among an available locations in a watershed. The proposed model allows quick and precise estimation of an adopted weighted objective function for each selected location. In addition to that for each location, a different dam height is used as a nominee for optimum selection. The VBA model includes an optimization model with a weighted objective function that includes beneficiary items (positive) , such as the available storage , the dam height allowed by the site as an indicator for the potential of hydroelectric power generation , the rainfall rate as a source of water . In a

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Publication Date
Wed May 10 2023
Journal Name
Journal Of Planner And Development
The impact of population density in sustainable housing - An applied study in the city of Baghdad (Mahalla 817), Al-Bayaa as a model
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Population density represents an important indicator for determining the growth of the size of urban areas. Population density has a direct impact on the quality of life, and its excessive rise may lead to the deterioration of basic service facilities. The problem of the research is that the increase in the total population densities of the residential neighborhood may reflect negatively on the nature of the services provided to the residents in these shops, and thus the failure to achieve sustainability in the residential locality. The research assumes that the increase in population densities negatively affects the achievement of sustainability in the residential neighborhood.

 

      

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Publication Date
Fri Dec 01 2023
Journal Name
Al-khwarizmi Engineering Journal
Development of an ANN Model for RGB Color Classification using the Dataset Extracted from a Fabricated Colorimeter
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Codes of red, green, and blue data (RGB) extracted from a lab-fabricated colorimeter device were used to build a proposed classifier with the objective of classifying colors of objects based on defined categories of fundamental colors. Primary, secondary, and tertiary colors namely red, green, orange, yellow, pink, purple, blue, brown, grey, white, and black, were employed in machine learning (ML) by applying an artificial neural network (ANN) algorithm using Python. The classifier, which was based on the ANN algorithm, required a definition of the mentioned eleven colors in the form of RGB codes in order to acquire the capability of classification. The software's capacity to forecast the color of the code that belongs to an ob

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Publication Date
Fri Dec 01 2023
Journal Name
Al-khwarizmi Engineering Journal
Development of an ANN Model for RGB Color Classification using the Dataset Extracted from a Fabricated Colorimeter
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Codes of red, green, and blue data (RGB) extracted from a lab-fabricated colorimeter device were used to build a proposed classifier with the objective of classifying colors of objects based on defined categories of fundamental colors. Primary, secondary, and tertiary colors namely red, green, orange, yellow, pink, purple, blue, brown, grey, white, and black, were employed in machine learning (ML) by applying an artificial neural network (ANN) algorithm using Python. The classifier, which was based on the ANN algorithm, required a definition of the mentioned eleven colors in the form of RGB codes in order to acquire the capability of classification. The software's capacity to forecast the color of the code that belongs to an object under de

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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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