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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
Tue Dec 01 2020
Journal Name
Iraqi Journal Of Physics
Comparative study of the linear and nonlinear optical properties for different Iraqi heavy and light crude oils
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Iraqi oil crudes have some of the physical and chemical characteristics that distinguish it from other types of oil crudes in the world. Some of these features such us molecular composition, rheological, viscosity and emulsions are studied carefully by researchers. In this work, a comparative study of the linear and the non-linear optical properties for typical heavy and light crude oils of Iraqi origin was studied utilizing Z-scan technique. The He -Ne laser of wavelength 632.8 nm had been used for this purpose. These samples were collected from Basra and Kut oil fields. The values of the non-linear refractive index (n2), non-linear absorption coefficient (β), and third-order electrical susceptibility (χ3) were e

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Publication Date
Sat Apr 01 2017
Journal Name
Journal Of Engineering
Comparative Study between Nanofiltration and Reverse Osmosis Membranes for the Removal of Heavy Metals from Electroplating Wastewater
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The present work aimed to study the efficiency of nanofiltration (NF) and reverse osmosis (RO) process for water recovery from electroplating wastewater and study the factors affecting the performance of two membrane processes. Nanofiltration and reverse osmosis membranes are made from polyamide as spiral wound module. The inorganic materials ZnCl2, CuCl2.2H2O, NiCl2.6H2O and CrCl3.6H2O were used as feed solutions. The operating parameters studied were: operating time, feed concentrations for heavy metal ions, operating pressure, feed flow rate, feed temperature and feed pH. The experimental results showed, the permeate concentration increased and water flux decreased with increase in time from 0 to 70 min. The permeate concentrations incre

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Publication Date
Fri Mar 31 2017
Journal Name
Journal Of Engineering
Comparative Study between Nanofiltration and Reverse Osmosis Membranes for the Removal of Heavy Metals from Electroplating Wastewater
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The present work aimed to study the efficiency of nanofiltration (NF) and reverseosmosis (RO) process for water recovery from electroplating wastewater and study the factors affecting the performance of two membrane processes. Nanofiltration and reverse osmosismembranes are made from polyamide as spiral wound module. The inorganic materials ZnCl 2 CuCl2 .2H2O, NiCl.2.6H2O and CrCl3.6H2O were used as feed solutions. The operating parametersstudied were: operating time, feed concentrations for heavy metal ions, operating pressure, feed flow rate, feed temperature and feed pH. The experimental results showed, the permeateconcentration increased and water flux decreased with increase in time from 0 to 70 min. Thepermeate concentrations incre

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Publication Date
Thu Nov 21 2019
Journal Name
Journal Of Engineering
A Neural Networks based Predictive Voltage-Tracking Controller Design for Proton Exchange Membrane Fuel Cell Model
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In this work, a new development of predictive voltage-tracking control algorithm for Proton Exchange Membrane Fuel Cell (PEMFCs) model, using a neural network technique based on-line auto-tuning intelligent algorithm was proposed. The aim of proposed robust feedback nonlinear neural predictive voltage controller is to find precisely and quickly the optimal hydrogen partial pressure action to control the stack terminal voltage of the (PEMFC) model for N-step ahead prediction. The Chaotic Particle Swarm Optimization (CPSO) implemented as a stable and robust on-line auto-tune algorithm to find the optimal weights for the proposed predictive neural network controller to improve system performance in terms of fast-tracking de

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Publication Date
Fri Apr 01 2016
Journal Name
Journal Of Economics And Administrative Sciences
A Comparison Between Classic Local Least Estimatop And Bayesian Methoid For Estimating Semiparametric Logistic Regression Model
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Semi-parametric models analysis is one of the most interesting subjects in recent studies due to give an efficient model estimation. The problem when the response variable has one of two values either 0 ( no response) or one – with response which is called the logistic regression model.

We compare two methods Bayesian and . Then the results were compared using MSe criteria.

A simulation had been used to study the empirical behavior for the Logistic model , with  different sample sizes and variances. The results using represent that the Bayesian method is better than the   at small samples sizes.

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Publication Date
Thu Jun 01 2017
Journal Name
Nuclear Physics A
Alpha-cluster preformation factor within cluster-formation model for odd-A and odd–odd heavy nuclei
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Publication Date
Thu Mar 11 2021
Journal Name
Annals Of Tropical Medicine & Public Health
Morphological and Molecular Study of Biofilm Formation by Enterobacter cloacae
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Publication Date
Fri Jan 01 2021
Journal Name
Annals Of Tropical Medicine And Public Health
Morphological and Molecular Study of Biofilm Formation by Enterobacter cloacae
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Publication Date
Wed Mar 30 2016
Journal Name
College Of Islamic Sciences
The provisions of taking the mother's fare breastfeeding comparative jurisprudential study
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This study aimed to clarify the provisions of taking the mother for breastfeeding in Islamic jurisprudence, a comparative study between doctrines of jurisprudence. The ruling on forcing the mother to breastfeed, and the ruling on taking the mother for breastfeeding while she is in the infallibility of her husband, as well as in several reactionary divorces, and the ruling on breastfeeding in several divorced divorces. On breastfeeding in infallibility Face, as well as a several divorce reactionary, and worth the fare which is in several final divorces, and after the end of the marital relationship, has been proposed a number of recommendations, including it, is recommended to teach the provisions of the mother taking the taxi on breastfe

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Publication Date
Fri Dec 31 2021
Journal Name
Political Sciences Journal
Populism in the Palestinian political discourse The Fatah and Hamas movements are a model
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Receipt Date:10/11/2021 Acceptance Date:29/12/2021 Publication Date:31/12/2021

Creative Commons LicenseThis work is licensed under a Creative Commons Attribution 4.0 International License.

The study aimed to clarify the conceptual explanations and the theoretical rooting of the concept of the populist phenomenon. And explore the political and cultural implications and connotations contained in populist political discourse. And to stand on the foundations and meanings on w

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