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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
Sun Apr 01 2018
Journal Name
Journal Of Economics And Administrative Sciences
Designing and Application of Mathematical Model A Multi – Objectives for Assessment The Quality Of The Project : A Case Study at Saad Public Construction Company
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Abstract

This research aims to design a multi-objective mathematical model to assess the project quality based on three criteria: time, cost and performance. This model has been applied in one of the major projects formations of the Saad Public Company which enables to completion the project on time at an additional cost that would be within the estimated budget with a satisfactory level of the performance which match with consumer requirements. The problem of research is to ensure that the project is completed with the required quality Is subject to constraints, such as time, cost and performance, so this requires prioritizing multiple goals. The project

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Publication Date
Thu Dec 31 2020
Journal Name
Political Sciences Journal
Russian-American competition in the Middle East:Power and roles conflict: Syria as a model
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Because of its importance in the world, Middle East area is one of the competition areas between the major and great powers. Among those powers are Russia and United states of America. The competition between these two powers to control Syria is greatly clear since 2011. It is also one of the most important subject in the international politics. This importance comes from the importance of Russia and the United States of America besides importance of the Middle East. At the end of the cold war, United States of America maintained its role in the international system and became the only pole that dominated the international affairs while Russia tried to overcome the challenges inherited from the former Soviet Union, and it succeeded in th

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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
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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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
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
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
Sat Feb 14 2026
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
Sun Sep 07 2014
Journal Name
Baghdad Science Journal
A comparative taxonomic study of nutlets of Stachys L. in Iraq
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Nutlets of 22 taxa of Stachys (13 species and seven subspecies and two varieties), representing seven of the currently recognized sections distributed in northern Iraq were examined by light microscope. The basic shape of nutlets in most taxa studied is Obovoid, but Oblong also found in S.megalodanta Hausskn.& Bornm. ex P.H.Davis, S.setirefa C.A.Mey. subsp daenensis (Gandog.) Rech.f.and S. kurdica Boiss.& Hohen. var.kurdica, while the Subgloboid shape found in S. iberica M.Bieb. and S. inflata Benth., more over the Broad triangular shape was found in S. nephrophylla Rech.f. and S.lanigera (Bornm.) Rech.f.., the biggest size of nutlets was found in S.inflata L. and the smallest was in S.melampyroides Hand.-Mzt. Regarding sculpturing pa

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Publication Date
Sat Feb 14 2026
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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