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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
Sat Dec 01 2018
Journal Name
Al-khwarizmi Engineering Journal
Enhancement of Hybrid Solar Air Conditioning System using a New Control Strategy
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Enhancement of the performance for hybrid solar air conditioning system was presented in this paper. The refrigerant temperature leaving the condenser was controlled using three-way valve, this valve was installed after the compressor to regulate refrigerant flow rate towards the solar system. A control system using data logger, sensors and computer was proposed to set the opening valve ratio. The function of control program using LabVIEW software is to obtain a minimum refrigerant temperature from the condenser outlet to enhance the overall COP of the unit by increasing the degree of subcooled refrigerant. A variable load electrical heater with coiled pipe was used instead of the solar collector and the storage tank to simulate the sola

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Publication Date
Wed Dec 31 2014
Journal Name
Al-khwarizmi Engineering Journal
Energy Saving of Heat Gain by Using Buried Pipe Inside a Roof
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Abstract

    This work deals with a numerical investigation to evaluate the utilization of a water pipe buried inside a roof to reduce the heat gain and minimize the transmission of heat energy inside the conditioning space in summer season.     The numerical results of this paper showed that the reduction in heat gain and energy saving could be occurred with specific values of parameters, like the number of pipes per square meter, the ratio of pipe diameter to the roof thickness, and the pipe inlet water temperature. Comparing with a normal roof (without pipes), the results indicated a significant reduction in energy heat gain which is about 37.8% when the number of pipes per m

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Publication Date
Thu Jan 01 2015
Journal Name
Energy Sources, Part A: Recovery, Utilization, And Environmental Effects
Ultra Deep Hydrotreatment of Iraqi Vacuum Gas Oil Using a Modified Catalyst
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A set of hydro treating experiments are carried out on vacuum gas oil in a trickle bed reactor to study the hydrodesulfurization and hydrodenitrogenation based on two model compounds, carbazole (non-basic nitrogen compound) and acridine (basic nitrogen compound), which are added at 0–200 ppm to the tested oil, and dibenzotiophene is used as a sulfur model compound at 3,000 ppm over commercial CoMo/ Al2O3 and prepared PtMo/Al2O3. The impregnation method is used to prepare (0.5% Pt) PtMo/Al2O3. The basic sites are found to be very small, and the two catalysts exhibit good metal support interaction. In the absence of nitrogen compounds over the tested catalysts in the trickle bed reactor at temperatures of 523 to 573 K, liquid hourly space v

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Publication Date
Tue Dec 01 2015
Journal Name
Solar Energy
A review of studies on using nanofluids in flat-plate solar collectors
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Continuous escalation of the cost of generating energy is preceded by the fact of scary depletion of the energy reserve of the fossil fuels and pollution of the environment as developed and developing countries burn these fuels. To meet the challenge of the impending energy crisis, renewable energy has been growing rapidly in the last decade. Among the renewable energy sources, solar energy is the most extensively available energy, has the least effect on the environment, and is very efficient in terms of energy conversion. Thus, solar energy has become one of the preferred sources of renewable energy. Flat-plate solar collectors are one of the extensively-used and well-known types of solar collectors. However, the effectiveness of the coll

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Publication Date
Fri Oct 30 2020
Journal Name
Journal Of Economics And Administrative Sciences
The effect of the marketing channel of the service on marine insurance losses: a case study in the Iraqi insurance company
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All businesses seek to improve their levels of profits through various means, most notably their marketing channels, which ensure the delivery of their products to their customers in a safe manner in a timely manner. It considers losses to a minimum and that insurance companies place great interest in marine insurance losses because they often constitute huge amounts compared to other losses, hence the problem of research, which is centred on the type and size of the impact owned by the channel The Iraqi insurance company was chosen to be applied according to the intentional sample method because this company is closely related to the subject matter. The research has reached a set of conclusions, most notably that the choice of i

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Publication Date
Tue Mar 01 2022
Journal Name
Journal Of Osseointegration & Oral Rehablitation
Evaluation of marginal bone loss around SLActive implants by CBCT using different implant dimensions and surgical approaches: A clinical and radiological prospective study
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Aim: The reduction in the amount of marginal bone is the most important demand for the long term success of dental implants. This prospective clinical study was aimed to investigate the marginal bone loss of early loaded SLActive implants with different dimensions and surgical approaches. Materials and methods Fifteen patients aged from 18 to 60 years were divided into 2 groups (flapped and flapless approach) that underwent delayed implant placement protocol with SLActive implants. The marginal bone level was estimated by cone-beam computed tomography during three different periods: preoperatively, 8 weeks after surgery and 24 weeks after loading of the prosthesis. Results: The mean value of marginal bone level was not significantly chan

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Publication Date
Fri Aug 01 2014
Journal Name
Journal Of Economics And Administrative Sciences
Using Bayesian method to estimate the parameters of Exponential Growth Model with Autocorrelation problem and different values of parameter of correlation-using simulation
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We have studied Bayesian method in this paper by using the modified exponential growth model, where this model is more using to represent the growth phenomena. We focus on three of prior functions (Informative, Natural Conjugate, and the function that depends on previous experiments) to use it in the Bayesian method. Where almost of observations for the growth phenomena are depended on one another, which in turn leads to a correlation between those observations, which calls to treat such this problem, called Autocorrelation, and to verified this has been used Bayesian method.

The goal of this study is to knowledge the effect of Autocorrelation on the estimation by using Bayesian method. F

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Publication Date
Sun Nov 23 2025
Journal Name
Journal Of Baghdad College Of Dentistry
The Effects of Different Investment Materials on Dimensional Accuracy and Surface Roughness of Thermosens Maxillary Complete Dentures
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Background: Limited data are available on the dimensional stability and surface roughness of ThermoSens, which is a material used in denture processing. This study aimed to measure the vertical teeth changes and surface roughness of ThermoSens dentures prepared using three different investment materials. Materials and methods: For the dimensional changes test, 30 complete maxillary dentures were prepared using different investment methods: group I, dental stone; group II, silicone putty; and group III, a mixture of dental stone and plaster (ratio, 1:1; n = 10 for each group). Four screws were attached to the dentures: two were attached to the buccal surface of the canine and first molar, and the other two were attached in the flange areas o

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Publication Date
Mon Aug 01 2011
Journal Name
Journal Of Engineering
PROPERTIES OF HARDENED CONCRETE USING CRUSHED CLAY BRICK AS AGGREGATES
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This paper provides the result of an investigation to use of crushed clay brick as
aggregates in producing concrete. Eight different crushed clay brick aggregate concretes were
used in this investigation. Compressive strength, splitting tensile strength and pulse velocity of
crushed clay brick aggregates concrete were determined and compare to natural aggregate
concrete. The compressive strength of crushed clay brick aggregates concretes were always
lower than the compressive strength of natural aggregates concrete regardless the age of
concrete, but the crushed clay brick aggregates concrete showed better performance as the age of
concrete increases and average reduction in compressive strength were 33.5% at the age

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Publication Date
Sun Jun 01 2014
Journal Name
Baghdad Science Journal
Preparation of polymer thin film using as NH3 gas Sensor
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Polyaniline organic Semiconductor polymer thin films have been prepared by oxidative polymerization at room temperature, this polymer was deposited on glass substrate with thickness 900nm, FTIR spectra was tested , the structural,optical and electrical properties were studied through XRD ,UV-Vis ,IR measurements ,the results was appeared that polymer thin film sensing to NH3 gas.

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