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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
Mon Jan 02 2017
Journal Name
Al-academy
How to build a virtual personal imagined in the picture, directed by James Cameron (Avatar) movie as a model
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The personal drama in particular, and one of the key elements underlying the dramatic structure to convey ideas and visions presented by the author when writing the text of the dramatic fall after that on the way out the submission form that suits the proposals of the text and processors directorial would push the wheel of dramatic structure to the front. So take the maker of the artwork (writer) undertook the transfer of those events and personalities in art presumed sometimes real and sometimes, in order to enrich the art inspired by the human reality through the ages, and full of its themes and ideas that led to the development experiences of peoples experiences of living. Therefore, we find it important to research in the characters

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Publication Date
Mon May 30 2022
Journal Name
Egyptian Journal Of Chemistry
Design ,Synthesis, Insilco Study and Biological Evaluation of New Coumarin-Oxadiazole Derivatives as Potent Histone Deacetylase Inhibitors
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Publication Date
Tue Oct 01 2019
Journal Name
2019 12th International Conference On Developments In Esystems Engineering (dese)
Roadway Deterioration Prediction Using Markov Chain Modeling (Wasit Governorate/ Iraq as a Case Study)
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Publication Date
Mon Sep 20 2021
Journal Name
Journal Of Craniofacial Surgery
Presurgical Assessment of Anatomical Landmark Position Using Two Views of Cone Beam Computed Tomography: A Comparative Radiological Study
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Publication Date
Wed Sep 30 2015
Journal Name
College Of Islamic Sciences
The other day in the Holy Quran and the four Gospels: A comparative study
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The other day in the Holy Quran and the four Gospels

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Publication Date
Sun Sep 28 2025
Journal Name
Journal Of Baghdad College Of Dentistry
An Evaluation of Olive Oil as a Separating Medium and Its Effect on Some Mechanical Properties of Processed Acrylic Resin Denture Base (A Comparative Study). Part Two
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Background: During acrylic resin processing, the mold must be separated from the surface of the gypsum to prevent liquid resin from penetrating into the gypsum, and water from the gypsum seeping into the acrylic resin. For many years, tin foil was the most acceptable separating medium, and because it's difficult to apply, a tin-foil substitute is used. In this study, olive oil is used as an alternative to tin foil separating medium for first time, and evaluating its effect as a separating medium on some mechanical properties such as (indentation hardness and transverse strength) of acrylic resins denture base comparing it with those processed using tin-foil and tin foil substitute such as (cold mold seal) separating medium. Materials and M

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Publication Date
Fri Jul 01 2016
Journal Name
Al–bahith Al–a'alami
Manufacturing the Functions and Responsibilities of the Press Photo: The Photo of the Child Elian as a Model
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The theory of the psychologist’s Piaget states that man passes through four stages; other says that mankind passes through five. At each stage, human learn new characteristics, values, skills, and cultures from different environment that differ from one society to another. Therefore, the cultures of societies vary according to the diversity of the environments. These environments also vary depending on the circumstances surrounding them, e.g., in war environment, the individual learns what he does not learn from living in safe environment. As the environment changes, the communicative message also changes. This message is subject to person, groups, organizations and parties and directed to a diverse audience in its orientations and bel

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Publication Date
Wed May 31 2023
Journal Name
International Journal Of Sustainable Development And Planning
Prediction of Formal Transformations in City Structure (Kufa as a Model) Based on the Cellular Automation Model and Markov Chains
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The research utilizes data produced by the Local Urban Management Directorate in Najaf and the imagery data from the Landsat 9 satellite, after being processed by the GIS tool. The research follows a descriptive and analytical approach; we integrated the Markov chain analysis and the cellular automation approach to predict transformations in city structure as a result of changes in land utilization. The research also aims to identify approaches to detect post-classification transformations in order to determine changes in land utilization. To predict the future land utilization in the city of Kufa, and to evaluate data accuracy, we used the Kappa Indicator to determine the potential applicability of the probability matrix that resulted from

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Publication Date
Sun Sep 28 2025
Journal Name
Iraqi Journal Of Science
Synthesis and characterization of some 2-sulphanyl benzimidazole derivatives and study of effect as corrosion inhibitors for carbon steel in sulfuric acid solution
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This research involves the synthesis of some sulphanyl benzimidazole derivatives (Ia-c), which were prepared from reaction of 2-mercaptobenzimidazole substituted benzyl halide, and structures were identified by spectral methods[FTIR, 1H-NMR and 13C-NMR].These compounds were investigated as corrosion inhibitors for carbon steel in 1M H2SO4 solution using weight loss, potentiostatic polarization methods; obtained results showed that the sulphanyl benzimidazole derivatives retard both cathodic and anodic reactions in acidic media, by virtue of adsorption on the carbon steel surface. This adsorption obeyed Langmuir’s adsorption isotherm. The inhibition efficiency of (Ia-c) ranging between (65-92) %. By using different Ib derivative conc

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Publication Date
Wed Jun 30 2021
Journal Name
Iraqi Journal Of Market Research And Consumer Protection
A COMPARATIVE STUDY OF THE CONSUMERS ATTITUDE ON THE MEAT HYGIENE SLAUGHTERED IN AND OUTSIDETHE SLAUGHTER HOUSEES: A COMPARATIVE STUDY OF THE CONSUMERS ATTITUDE ON THE MEAT HYGIENE SLAUGHTERED IN AND OUTSIDETHE SLAUGHTER HOUSEES
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The study was conducted to assess the attitude and awareness of a sample of people regarding the indiscriminate slaughter and its effects on health and the environment compared with slaughtering  in a slaughterhouse. The sample consisted of 120 persons from six equal professional groups contacted with the butchery labour (livestock keeper, truck driver, butcher, veterinarian, shopkeeper and consumer). The age ranged 22-76 years old, mean 52±10  years, lived ≥ 5 years in the Baghdad city. The results showed that there is a preference for slaughtering inside the slaughterhouse due to the presence of veterinary examination, slaughtering and preparing meat in a healthy, easy-to-clean places, unlike the indiscriminate sla

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