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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
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
Thu Sep 01 2022
Journal Name
Civil Engineering And Architecture
Strengthening AL-Kadhimin Tilted Minaret by Using a System of Micro-piles
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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
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 May 10 2023
Journal Name
Journal Of Engineering
Vibration Control Analysis of a Smart Flexible Cantilever Beam Using Smart Material
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This paper features the modeling and design of a pole placement and output Feedback control technique for the Active Vibration Control (AVC) of a smart flexible cantilever beam for a Single Input Single Output (SISO) case. Measurements and actuation actions done by using patches of piezoelectric layer, it is bonded to the master structure as sensor/actuator at a certain position of the cantilever beam.
The smart structure is modeled based on the concept of piezoelectric theory, Bernoulli -Euler beam theory, using Finite Element Method (FEM) and the state space techniques. The number of modes is reduced using the controllability and observability grammians retaining the first three
dominant vibratory modes, and for the reduced syste

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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
Tue Feb 01 2022
Journal Name
Methods And Objects Of Chemical Analysis
Spectrophotometric Analysis of Quaternary Drug Mixtures using Artificial Neural network model
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Novel artificial neural network (ANN) model was constructed for calibration of a multivariate model for simultaneously quantitative analysis of the quaternary mixture composed of carbamazepine, carvedilol, diazepam, and furosemide. An eighty-four mixing formula where prepared and analyzed spectrophotometrically. Each analyte was formulated in six samples at different concentrations thus twentyfour samples for the four analytes were tested. A neural network of 10 hidden neurons was capable to fit data 100%. The suggested model can be applied for the quantitative chemical analysis for the proposed quaternary mixture.

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Publication Date
Tue Sep 06 2022
Journal Name
Methods And Objects Of Chemical Analysis
Spectrophotometric Analysis of Quaternary Drug Mixtures using Artificial Neural network model
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A Novel artificial neural network (ANN) model was constructed for calibration of a multivariate model for simultaneously quantitative analysis of the quaternary mixture composed of carbamazepine, carvedilol, diazepam, and furosemide. An eighty-four mixing formula where prepared and analyzed spectrophotometrically. Each analyte was formulated in six samples at different concentrations thus twenty four samples for the four analytes were tested. A neural network of 10 hidden neurons was capable to fit data 100%. The suggested model can be applied for the quantitative chemical analysis for the proposed quaternary mixture.

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Publication Date
Sun Jan 01 2023
Journal Name
International Conference Of Computational Methods In Sciences And Engineering Iccmse 2021
Penetration of charged particles in ZnO using energy loss function model
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In this paper, we propose an approach to estimate the induced potential, which is generated by swift heavy ions traversing a ZnO thin film, via an energy loss function (ELF). This induced potential is related to the projectile charge density, ρq(k) and is described by the extended Drude dielectric function. At zero momentum transfer, the resulting ELF exhibits good agreement with the previously reported results. The ELF, obtained by the extended Drude model, displays a realistic behavior over the Bethe ridge. It is observed that the induced potential relies on the heavy ion velocity and charge state q. Further, the numerical results show that the induced potential for neutral H, as projectile, dominates when the heavy ion velocity is less

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Publication Date
Sat Jan 01 2022
Journal Name
Methods And Objects Of Chemical Analysis
Spectrophotometric Analysis of Quaternary Drug Mixtures using Artificial Neural network model
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A Novel artificial neural network (ANN) model was constructed for calibration of a multivariate model for simultaneously quantitative analysis of the quaternary mixture composed of carbamazepine, carvedilol, diazepam, and furosemide. An eighty-four mixing formula where prepared and analyzed spectrophotometrically. Each analyte was formulated in six samples at different concentrations thus twentyfour samples for the four analytes were tested. A neural network of 10 hidden neurons was capable to fit data 100%. The suggested model can be applied for the quantitative chemical analysis for the proposed quaternary mixture.

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Scopus (2)
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