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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
Fri Dec 01 2017
Journal Name
Journal Of Baghdad College Of Dentistry
In Vitro Comparative Assessment of the Effect of Gutta-Fusion Obturation on the Push Out Bond Strength of Three Types of Sealers
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Background: The bond strength of the root canal sealers to dentin is very important property for maintaining the integrity and the seal of root canal filling. The aim of this study was to evaluate and compare the push-out bond strength of root filled with total fill Bioceramic, AH Plus and Gutta-flow®2 sealers using GuttaFusion®obturation system versus single cone obturation technique. Materials and method: sixty of mandibular premolars teeth with straight roots were used in this study, these roots were instrumented using Reciproc system, instrumentation were done with copious irrigation of 3 mL 5.25% sodium hypochlorite solution (NaOCl) during all the steps of preparation, and smear layer will be removed with 1 ml of 17% EDTA kept in

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Publication Date
Wed Jul 01 2015
Journal Name
Al–bahith Al–a'alami
Iraqi Press and its Role in Shaping Electoral Awareness (Iraqi Parliamentary Elections on 30 April, 2014 as a Model)
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The parliamentary election is one of the features of democratic systems that give individuals the right to participate in government and political election-making. Typically, the process of parliamentary elections received wide attention from media, as well as attention from large segments of the public because they understand the vast importance to assume political positions and associated fates of people and their destinies. Its importance comes from the fact that it allows citizens the right to participate in managing the public affairs by granting their confidence and voices to the elected president or his representatives in the parliamentary.
Media task is to emerge democratic societies, in particular, in the mission of urging p

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Publication Date
Thu Jun 01 2023
Journal Name
Journal Of Engineering
Proposing a General Formula for Evaluating the Parametric Cost Using MLR Method
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This research takes up address the practical side by taking case studies for construction projects that include the various Iraqi governorates, as it includes conducting a field survey to identify the impact of parametric costs on construction projects and compare them with what was reached during the analysis and the extent of their validity and accuracy, as well as adopting the approach of personal interviews to know the reality of the state of construction projects. The results showed, after comparing field data and its measurement in construction projects for the sectors (public and private), the correlation between the expected and actual cost change was (97.8%), and this means that the data can be adopted in the re

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Publication Date
Fri May 01 2020
Journal Name
Journal Of Physics: Conference Series
New Approach for Solving (1+1)-Dimensional Differential Equation
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Publication Date
Sat Mar 31 2018
Journal Name
Iraqi Journal Of Chemical And Petroleum Engineering
Study of the Performance of Paraffin Wax as a Phase Change Material in Packed Bed Thermal Energy Storage System
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The present work deals with an experimental investigation of charging and discharging processes in thermal storage system using a phase change material PCM. Paraffin wax was used as the PCM which is formed in spherical capsules and packed in a cylindrical packed column which acted as an energy storage system. Air was used as the heat transfer fluid HTF in thermal storage unit. The effect of flow rate and inlet temperature of HTF on the time of charging and discharging process were studied. The results showed that the faster storage of thermal energy can be made by high flow rate of heat transfer fluid HTF and high inlet temperature of heat transfer fluid. It was found that at 65°C HTF inlet temperature, the melting and solidification pr

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Publication Date
Mon Mar 08 2021
Journal Name
Baghdad Science Journal
A study of fermi hole for some atomic systems
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the electron correlation effect for inter-shell can be described by evaluating the fermi hole and partial fermi hole for Li atom comparing with Be+ and B+2 ions

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Publication Date
Wed Sep 14 2016
Journal Name
Journal Of Baghdad College Of Dentistry
A Comparative Evaluation of Apical Seal Associated with Ultrasonic Retrograde Cavities Filled with Bioactive Material (In Vitro Study)
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Background: The aim of this study was to evaluate and compare the apical microleakage around retrograde cavities prepared with ultrasonic technique and filled with (Biodentineâ„¢) Materials and methods: 40 extracted single rooted human permanent maxillary teeth with mature apices were selected. The roots were prepared chemo-mechanically using k-files with crown-down technique and then obturated with lateral condensation gutta-percha technique. Teeth were divided into four main groups according to the cavity preparation method either manual or ultrasonic technique: Group A (n=10): A class I retrograde cavity at root end was prepared with traditional handpeice equipped and placement of Biodentine with manual condensation. Group B (n=10):

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Publication Date
Sun Jan 01 2012
Journal Name
Tikrit Journal For Dental Sciences
Microleakage Evaluation of a Silorane-Based and Methacrylate-Based Packable and Nanofill Posterior Composites (in vitro comparative study)
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This study compared in vitro the microleakage of a new low shrink silorane-based posterior composite (Filtek™ P90) and two methacrylate-based composites: a packable posterior composite (Filtek™ P60) and a nanofill composite (Filtek™ Supreme XT) through dye penetration test. Thirty sound human upper premolars were used in this study. Standardized class V cavities were prepared at the buccal surface of each tooth. The teeth were then divided into three groups of ten teeth each: (Group 1: restored with Filtek™ P90, Group 2: restored with Filtek™ P60, and Group 3: restored with Filtek™ Supreme XT). Each composite system was used according to the manufacturer's instructions with their corresponding adhesive systems. The teeth were th

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Publication Date
Tue Aug 12 2025
Journal Name
Mustansiria Dental Journal
Soft tissue measurements of Iraqi individuals with Cl I and Cl III skeletal pattern: a comparative cephalometric study
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Publication Date
Thu Apr 18 2019
Journal Name
Al-kindy College Medical Journal
Comparative study of anterior knee pain after patelloplasty with and without circumferential denervation in a total knee arthroplasty
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Background: The anterior knee pain is an important chief complaint of the patients with knee osteoarthritis due to patellofemoral pathology. The pain receptors denervation can be achieved by circumferential denervation of the patellar area by a process of electrocautery.

Objectives: The aim of current study is to assess the pain after total knee arthroplasty (TKA) by patelloplastywith and without circumferential denervation via electrocautery at a minimum follow up with 1 year separately for each patient.

Type of the study:Cross- sectional study.

Methods: Thirty five patients,with mean age of about (62.8) years, were enrolled in this pros

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