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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 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
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
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
Thu Dec 01 2022
Journal Name
Baghdad Science Journal
Molecular Characterization of Potential Crop Pathogens Associated with Weeds as Endophytes in Uniilorin Plantations, Nigeria
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Crop diseases are usually caused by inoculum of pathogens which might exist on alternate hosts or weeds as endophytes. These endophytes, cum pathogens, usually confer some beneficial attributes to these weeds or alternate hosts from protection against herbivores, disease resistance, stress tolerance to secondary metabolites production. This study was therefore carried out to isolate potential crop pathogens which exist as endophytes on weed species in the University of Ilorin plantations. Green asymptomatic leaves were collected from 10 weed species across the plantations, and processed for their endophytic fungi isolation. Isolates were purified into pure cultures and used for molecular identification using the internal transcribed spac

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Publication Date
Sat Dec 01 2018
Journal Name
Indian Journal Of Natural Sciences
Determination of the Electron Density Variation for Ionosphere Layer Over Iraqi Zone Using IRI Model
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KA Hadi, AH Asma’a, IJONS, 2018 - Cited by 1

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Publication Date
Tue Aug 01 2017
Journal Name
International Journal Of Innovative Research In Science, Engineering And Technology
Nasal Prosthesis Fabrication using Rapid Prototyping and 3D Printing (A Case Study)
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Abstract: Facial defects resulting from neoplasms, congenital, acquired malformations or trauma can be restored with facial prosthesis using different materials and retention methods to achieve life-like look and function. A nasal prosthesis can re-establish aesthetic form and anatomic contours for mid-facial defects, often more effectively than by surgical reconstruction as the nose is relatively immobile structure. For successful results, lot of factors such as harmony, texture, color matching and blending of tissue interface with the prosthesis are important. The aim of this study is to describe the non-surgical rehabilitation with nasal prosthesis for an Iraqi patient who received rhinectomy as a result of squamous cell carcinoma of the

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Publication Date
Thu Sep 01 2016
Journal Name
Revista Brasileira De Zootecnia
Effect of using insect larvae meal as a complete protein source on quality and productivity characteristics of laying hens
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Publication Date
Tue Jun 01 2010
Journal Name
Journal Of Economics And Administrative Sciences
Bayes Estimator as a Function of Some Classical Estimator
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Maximum likelihood estimation method, uniformly minimum variance unbiased estimation method and minimum mean square error estimation, as classical estimation procedures, are frequently used for parameter estimation in statistics, which assuming the parameter is constant , while Bayes method assuming the parameter is random variable and hence the Bayes estimator is an estimator which minimize the Bayes risk for each value the random observable and for square error lose function the Bayes estimator is the posterior mean. It is well known that the Bayesian estimation is hardly used as a parameter estimation technique due to some difficulties to finding a prior distribution.

The interest of this paper is that

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Publication Date
Sun Mar 01 2015
Journal Name
Baghdad Science Journal
Terrestrial Invertebrates as a Bioindicators of Heavy Metals Pollution
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Bioaccumulation of heavy metals in the terrestrial invertebrates in Al-Jadriyia district Baghdad- Iraq were investigated. Forth terrestrial invertebrates snails, slug, isopods, and diplopods , were selected for this study. The results showed that all invertebrate groups have the ability in accumulate considerable amounts of heavy metals. Higher levels of zinc and copper were observed in the isopods specimens, it's about ( 60.50±0.58 ) and ( 96.00±0.58 ) ppm respectively , while higher levels of lead were observed in the diplopods specimens ,it's about ( 23.00±1.15 ) ppm ,but the higher levels of both iron and cadmium were observed in snail specimens , it's about ( 590.00±1.15 ) and ( 9.50±1.15 ) ppm respectively .but the

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