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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
Wed Nov 26 2025
Journal Name
Journal Of Baghdad College Of Dentistry
Photogrammetric analysis of facial soft tissue profile of Iraqi adults sample with Class I normal occlusion: (A cross sectional study)
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Background: The purposes of this study were to determine the photogrammetric soft tissue facial profile measurements for Iraqi adults sample with class I normal occlusion using Standardized photographic techniques and to verify the existence of possible gender differences. Materials and methods: Eighty Iraqi adult subjects (40 males and 40 females) with an age ranged between 18-25 years having class I normal occlusion were chosen for this study. Each individual was subjected to clinical examination and digital standardized right side photographic records were taken in the natural head position which is mirror position which the patient looking straight into his eyes into the mirror mounted on the stand. The photographs were analyzed using A

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Publication Date
Mon Mar 13 2017
Journal Name
Journal Of Baghdad College Of Dentistry
Testing Different Properties of A Light-Cured Denture Base Material After Addition of Silicon Oxide Nanofiller (An in Vitro Study)
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ABSTRACT Background: Improving the properties of heat- cured and self-cured acrylic resin have been studied by many researchers. However, little studies concerned with visible light cured resin (VLCR) improved through addition of nanofiller are available. The purpose of this study was to evaluate some properties of (VLCR) after addition of SiO2 nanofiller. Materials and Methods: SiO2 nanofiller were added to (VLCR) tray material after being dissolved in tetrahydrofuran (THF) solvent. According to the pilot study 2% SiO2 nanofiller addition exhibited better properties than the other percentages (1%, 3%). The main study conducted involved (100) specimens divided into 5 groups according to the test included. (20) Specimens were selecte

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Publication Date
Tue Nov 18 2014
Journal Name
Conference: First International Engineering Conference (iec2014)at: Ishik University, Erbil, Krg, Iraq
Visualization of People Attraction from Mobile Phone Trace Database: A Case study on Armada 2008 in French City of Rouen
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The mobile phone is widespread all over the world. This technology is one of the most widespread with more than five billion subscriptions making people describe this interaction system as Wireless Intelligence. Mobile phone networks become the focus of attention of researchers, organizations and governments due to its penetration in all life fields. Analyzing mobile phone traces allows describing human mobility with accuracy as never done before. The main objective in this contribution is to represent the people density in specific regions at specific duration of time according to raw data (mobile phone traces). This type of spatio-temporal data named CDR (Call Data Records), which have properties of the time and spatial indications for th

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Publication Date
Wed Apr 28 2021
Journal Name
Journal Of Engineering
Post-occupancy evaluation Correlated with Medical Staffs' Satisfaction: A Case Study of Indoor Environments of General Hospitals in Sulaimani City
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This study aims at identifying the notion of Post-Occupancy Evaluation (POE) pertinent to the performance of three general hospitals constructed inside the Sulaimani City, tracing the relationship between the quality of the indoor environments and medical staff (doctors and nurses) satisfaction level. Using some indoor environment elements in the right way will positively influence the mood, stress level of the medical staff, and patient recovery as a result. The POE toolkits (AEDET and ASPECT) have been implemented on targeted wards at the selected hospitals. AEDET and ASPECT questionnaires were distributed among 152 medical staff to obtain their perspectives. In total, 112 valid questionnaires were received. The medica

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Publication Date
Wed Jun 01 2022
Journal Name
Canadian Journal Of Chemistry
Hydrogenation of pyridine and hydrogenolysis of piperidine over <i>γ-</i>Mo<sub>2</sub>N catalyst: a DFT study
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Increasing demands on producing environmentally friendly products are becoming a driving force for designing highly active catalysts. Thus, surfaces that efficiently catalyse the nitrogen reduction reactions are greatly sought in moderating air-pollutant emissions. This contribution aims to computationally investigate the hydrodenitrogenation (HDN) networks of pyridine over the γ-Mo2N(111) surface using a density functional theory (DFT) approach. Various adsorption configurations have been considered for the molecularly adsorbed pyridine. Findings indicate that pyridine can be adsorbed via side-on and end-on modes in six geometries in which one adsorption site is revealed to have the lowest adsorption energy (

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Publication Date
Sat Dec 01 2012
Journal Name
Journal Of Economics And Administrative Sciences
An analytical study of the reality of chemical industries in Iraq for the period (1995-2007)
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Is the chemical industries of great importance for the economy of any country, through what is borne by these industries is an important part of the changes contained in the industrial output of transfer and, moreover, that these industries are overlaps and intricacies of sector-wide with the rest of the manufacturing sectors, with agriculture and services , through the offering of these industries produce Production requirements intervention such as chemical fertilizer used in the production of agricultural crops, in addition to the various areas for the use of phosphorus in the food industry, to the extent that it is difficult to find material Food preparation is not included i

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Publication Date
Fri Jun 01 2012
Journal Name
Journal Of Economics And Administrative Sciences
“Using the Statistical Analysis for deduction the childhood status in Iraq during 2006-2010”
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   To deduct the childhood status in Iraq, it was important manner to use statistical tools and approaches concerned with interpreting the causal relationships and their attitudes and use classification method for the important effects (variables) to draw an obvious picture of the phenomena under study in order to make it useful through investing, updating and improving it in by demographic studies in the future. Two statistical methods had been used in the field of analyzing data of multivariate analysis namely, Cluster Analysis and Factor Analysis.  

The present study focuses on four fundamental axes .The nutrition axis, health axis, Educational axis, and the social axis. The study has ca

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Publication Date
Tue Jul 19 2022
Journal Name
Journal Of Economics And Administrative Sciences
Using Game Theory to Determine the Optimal Strategy for the Transportation Sector in Iraq
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In this paper, game theory was used and applied to the transport sector in Iraq, as this sector includes two axes, the public transport axis and the second axis the private transport axis, as each of these axes includes several types of transport, namely (sea transport, air transport, land transport, transport by rail, port transport) and the travel and tourism sector, as public transport lacks this sector, as the competitive advantage matrix for the transport sector was formed and after applying the MinMax-MaxMin principle to the matrix in all its stages, it was found that there was an equilibrium point except for the last stage where the equilibrium point was not available Therefore, the use of the linear programming method was

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Publication Date
Mon Dec 28 2020
Journal Name
International Journal Of Psychosocial Rehabilitation
Predicting the Sporting Achievement in the Pole Vault for Men Using Artificial Neural Networks
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The physical sports sector in Iraq suffers from the problem of achieving sports achievements in individual and team games in various Asian and international competitions, for many reasons, including the lack of exploitation of modern, accurate and flexible technologies and means, especially in the field of information technology, especially the technology of artificial neural networks. The main goal of this study is to build an intelligent mathematical model to predict sport achievement in pole vaulting for men, the methodology of the research included the use of five variables as inputs to the neural network, which are Avarage of Speed (m/sec in Before distance 05 meters latest and Distance 05 meters latest, The maximum speed achieved in t

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Publication Date
Wed Jun 03 2020
Journal Name
Political Sciences Journal
Using the general budget for the year 2019 to achieve sustainable development in Iraq
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The public budget is on the same time an art and a science .As an accountable science it seeks balance between public income and public expenditure for an accountable year. And as an accountable art it seeks to achieve economic balance by distributing equitable income in order to reach sustainable development .This is the optimal use of all natural and human resources to address scarcity of natural resources facing the increase need of human resources by spending on education, health, environment, housing, agriculture and industry to achieve social justice for the current generation and future generations. Since the first budget in Iraq on 1921 an accounting budget, is balancing the sections and items has been adopted and since the publi

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