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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
Fri Jun 30 2023
Journal Name
حوليات اداب عين شمس
Names of Day of Resurrection in the Hebrew translation of the meanings of the Holy Quran An analytical study Uri Rubin translation as a model
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The present study discusses the names of the Day of Resurrection in Uri Rubin’s translations of the Holy Qur’an. To identify the translation difficulties and complications and to find out the Hebrew equivalence, the study, through the application of a comparative analytical approach, aims at analyzing the linguistic structures of Day of Resurrection names cited in the Holy Qur’an. Heavenly religions are rich with distinct and unique terms that distinguish and reflect their specificity of other religions; something requires a great accuracy in the translation of such terminology. By investigating selected examples of the names of the Day of Resurrection in Arabic and Hebrew, the present study sheds light on the morphological and semant

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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
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
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
Sat May 16 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
Wed Jun 01 2022
Journal Name
Journal Of Sport Science Technology And Physical Activities
The effect of using Daniel's model and Driver’s model in learning a kinetic chain on the uneven bars in the artistic gymnastics for female students
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The aim of this study to identity using Daniel's model and Driver’s model in learning a kinetic chain on the uneven bars in the artistic gymnastics for female students. The researchers used the experimental method to design equivalent groups with a preand post-test, and the research community was identified with the students of the third stage in the college for the academic year 2020-2021 .The subject was, (3) class were randomly selected, so (30) students distributed into (3) groups). has been conducted pretesting after implementation of the curriculum for (4) weeks and used the statistical bag of social sciences(SPSS)to process the results of the research and a set of conclusions was reached, the most important of which is t

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Publication Date
Tue Jul 01 2025
Journal Name
Minerva Dental And Oral Science
Evaluation of the microleakage of new bioactive restorative materials: a comparative in-vitro study
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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
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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