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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 Jul 09 2023
Journal Name
Journal Of Engineering
Phenol Removal Using Granular Dead Anaerobic Sludge Permeable Reactive Barrier in a Simulated Groundwater Pilot Plant
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This study investigates the performance of granular dead anaerobic sludge (GDAS) bio-sorbent as permeable reactive barrier in removing phenol from a simulated contaminated shallow groundwater. Batch tests have been performed to characterize the equilibrium sorption properties of the GDAS and sandy soil in phenol-containing aqueous solutions. The results of GDAS tests proved that the best values of operating parameters, which achieve the maximum removal efficiency of phenol (=85%), at equilibrium contact time (=3 hr), initial pH of the solution (=5), initial phenol concentration (=50 mg/l), GDAS dosage (=0.5 g/100 ml), and agitation speed (=250 rpm). Fourier transform infrared (FTIR) analysis proved that the carboxylic acid, aromatic, alk

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Publication Date
Mon May 01 2017
Journal Name
Energy
Solidification enhancement in a triplex-tube latent heat energy storage system using nanoparticles-metal foam combination
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Publication Date
Sun Jan 01 2023
Journal Name
Organization, Technology And Management In Construction: An International Journal
Using the ordinal priority approach for selecting the contractor in construction projects
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Abstract<p>Effective decision-making process is the basis for successfully solving any engineering problem. Many decisions taken in the construction projects differ in their nature due to the complex nature of the construction projects. One of the most crucial decisions that might result in numerous issues over the course of a construction project is the selection of the contractor. This study aims to use the ordinal priority approach (OPA) for the contractor selection process in the construction industry. The proposed model involves two computer programs; the first of these will be used to evaluate the decision-makers/experts in the construction projects, while the second will be used to formul</p> ... Show More
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Publication Date
Wed Feb 01 2017
Journal Name
Journal Of Economics And Administrative Sciences
The development of ethics management system to enhance the social responsibility of government institutions in Iraqi society An analytical study on a sample of top leadership and the presidency of
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Abstract

The objective of this research is to identify the analysis of the ethics of the administration in the development of the social responsibility of one government organizations, and to achieve the objectives of the research was the use of a questionnaire developed for the purpose of data collection and distribution to the research sample, was chosen as a total sample population (50) individuals were relying on statistical package to do a statistical analysis for this research, user, ANSI (SPSS) simple regression analysis, standard deviation, Pearson correlation coefficient.

Research findings show the role of social responsibility in achieving the university's strategy,

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Publication Date
Mon Aug 01 2022
Journal Name
مجلة الرافدين للعلوم الرياضية
Fartlek exercises and their effect on molecular biology (vascular endothelial growth factor-basic fibroblast growth factor) and some physical variables for players 800m arena and field for youth
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The study aimed to : - To determine whether there are significant differences between Fartlek training and the increase in the molecular biology (VEGF - basal fibroblast growth factor) for arena and field players in an (800m) youth event. - Determine whether there are statistically significant differences between Fartlek training and the increase in molecular biology and some physical variables for the players (800m) in the arena and field for youth. - Determine whether the Fartlek training method is the most appropriate to achieve statistically significant differences in the research variables for the players (800m) in the arena and field for youth. The researchers used the experimental method for its suitability and the nature of the rese

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Publication Date
Thu Nov 19 2020
Journal Name
Iop Conference Series: Materials Science And Engineering
CFD Simulation of Velocity Distribution in a River with a Bend Cross Section and a Cubic Bed Roughness Shape
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Publication Date
Sat Dec 24 2022
Journal Name
Iraqi Journal Of Pharmaceutical Sciences ( P-issn 1683 - 3597 E-issn 2521 - 3512)
The Effect of TNF-Alpha Gene Polymorphisms At -376 G/A, -806 C/T, and -1031 T/C on The Likelihood of Becoming a Non-Responder to Etanercept in A Sample of Iraqi Rheumatoid Arthritis Patients
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Tumor necrosis factor-alpha (TNF-α) antagonists’ therapy are expensive and has a non-responsive rate between 30% to 40% in rheumatoid arthritis patients. Genetic variation plays a vital role in the responsiveness to this type of therapy.The aim of this study is to investigate if the presence of genetic polymorphism in the TNF-α gene promoter region at locations -376 G/A (rs1800750), -806 C/T (rs4248158), and -1031 T/C (rs1799964) affects rheumatoid arthritis patient's tendency to be a non-responder to etanercept.

Eighty RA patients on etanercept (ETN) for at least six months were recruited from the Rheumatology Unit at Baghdad Teaching Hospital. Based on The European League Against Rheumatism response (EULAR) criteria, patient

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Publication Date
Sun Oct 01 2023
Journal Name
Bulletin Of Electrical Engineering And Informatics
A novel data offloading scheme for QoS optimization in 5G based internet of medical things
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The internet of medical things (IoMT), which is expected the lead to the biggest technology in worldwide distribution. Using 5th generation (5G) transmission, market possibilities and hazards related to IoMT are improved and detected. This framework describes a strategy for proactively addressing worries and offering a forum to promote development, alter attitudes and maintain people's confidence in the broader healthcare system without compromising security. It is combined with a data offloading system to speed up the transmission of medical data and improved the quality of service (QoS). As a result of this development, we suggested the enriched energy efficient fuzzy (EEEF) data offloading technique to enhance the delivery of dat

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Publication Date
Sat Jan 01 2022
Journal Name
Iranian Journal Of Earth Sciences
Resistivity surveys application for detection of shallow caves in a case example from Western Iraq
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Publication Date
Fri Jan 01 2021
Journal Name
International Journal Of Agricultural And Statistical Sciences
A noval SVR estimation of figarch modal and forecasting for white oil data in Iraq
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The purpose of this paper is to model and forecast the white oil during the period (2012-2019) using volatility GARCH-class. After showing that squared returns of white oil have a significant long memory in the volatility, the return series based on fractional GARCH models are estimated and forecasted for the mean and volatility by quasi maximum likelihood QML as a traditional method. While the competition includes machine learning approaches using Support Vector Regression (SVR). Results showed that the best appropriate model among many other models to forecast the volatility, depending on the lowest value of Akaike information criterion and Schwartz information criterion, also the parameters must be significant. In addition, the residuals

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