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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 Apr 02 2019
Journal Name
Artificial Intelligence Research
A three-stage learning algorithm for deep multilayer perceptron with effective weight initialisation based on sparse auto-encoder
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A three-stage learning algorithm for deep multilayer perceptron (DMLP) with effective weight initialisation based on sparse auto-encoder is proposed in this paper, which aims to overcome difficulties in training deep neural networks with limited training data in high-dimensional feature space. At the first stage, unsupervised learning is adopted using sparse auto-encoder to obtain the initial weights of the feature extraction layers of the DMLP. At the second stage, error back-propagation is used to train the DMLP by fixing the weights obtained at the first stage for its feature extraction layers. At the third stage, all the weights of the DMLP obtained at the second stage are refined by error back-propagation. Network structures an

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Publication Date
Tue Feb 05 2019
Journal Name
Journal Of The College Of Education For Women
A comparative study in disruptive behavior at the Deprived and non-Deprived students from their parents at the Secondary stage
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The current research aims to :
•know the level of the chaotic behavior of the sample as a whole .
•Know the differences with statistical significance in disorderly behavior between the
disadvantaged and non-disadvantaged peers .
To achieve these objectives, the selected sample of Talbhalmrahlh medium and specifically
students of the second grade average, were chosen randomly stratified's (360) students
included sex (male, female) and (deprived of the Father and the non-deprived) for the
academic year (2013-2014) to the province Baghdad on both sides (Rusafa-Karkh (
As applied to them measurements of disorderly behavior, which is prepared by the researcher,
having achieved _khasaúsma of psychometric (valid

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Publication Date
Wed Mar 29 2023
Journal Name
Iraqi Journal Of Chemical And Petroleum Engineering
Effect of Heterogeneity on Capillary Pressure and Relative Permeability Curves in Carbonate Reservoirs. A Case Study for Mishrif Formation in West Qurna/1 Oilfield, Iraq
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The special core analysis tests were accomplished on a set of core plugs for Mishrif Formation (mA, mB1, and mB2cde/mC units) in West Qurna/1 oilfield, southern Iraq. Oil relative permeability (Kro) data and the Corey-type fit of the data as functions of the brine saturation at the core outlet face for individual samples in the water-oil imbibition process to estimate relative permeability measurements by the centrifuge method were utilized. Identical correlations for oil and water relative permeabilities were extracted by steady-state and unsteady-state methods. For the mA samples, the gas-water capillary pressure curves were within a narrow range (almost identical) indicating that mA is a homogeneous unit. Kro curves for three mB2

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Publication Date
Wed Mar 29 2023
Journal Name
Iraqi Journal Of Chemical And Petroleum Engineering
Effect of Heterogeneity on Capillary Pressure and Relative Permeability Curves in Carbonate Reservoirs. A Case Study for Mishrif Formation in West Qurna/1 Oilfield, Iraq
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The special core analysis tests were accomplished on a set of core plugs for Mishrif Formation (mA, mB1, and mB2cde/mC units) in West Qurna/1 oilfield, southern Iraq. Oil relative permeability (Kro) data and the Corey-type fit of the data as functions of the brine saturation at the core outlet face for individual samples in the water-oil imbibition process to estimate relative permeability measurements by the centrifuge method were utilized. Identical correlations for oil and water relative permeabilities were extracted by steady-state and unsteady-state methods. For the mA samples, the gas-water capillary pressure curves were within a narrow range (almost identical) indicating that mA is a homogeneous unit. Kro curves for thr

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Publication Date
Sun Apr 01 2018
Journal Name
Al–bahith Al–a'alami
Effectiveness of sports television programs in the development of sports culture among youth: field study
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The aim of the research is to determine the extent to which young people watch television sports programs and the impact of viewing on the level of sports culture among young people and the impact of demographic variables on youth over the viewing of sports programs, The study was conducted on a sample of (200) male and female students from the faculties of the University of Baghdad, where a questionnaire form composed of several axes and questions was prepared to measure the effectiveness of sports programs in youth culture, The statistical program used spss to empty data and extract results by frequency, percentages, correlations, The research reached several results, the most important of which is that there is a strong influence of s

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Publication Date
Sun Sep 04 2016
Journal Name
Baghdad Science Journal
Degradation of Brilliant Green by Using a bentonite Clay- Based Fe Nano Composite Film as a Heterogeneous Photo- Fenton Catalyst.
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This paper aims to study the chemical degradation of Brilliant Green in water via photo-Fenton (H2O2/Fe2+/UV) and Fenton (H2O2/Fe2+) reaction. Fe- B nano particles are applied as incrustation in the inner wall surface of reactor. The data form X- Ray diffraction (XRD) analysis that Fe- B nanocomposite catalyst consist mainly of SiO2 (quartz) and Fe2O3 (hematite) crystallites. B.G dye degradation is estimated to discover the catalytic action of Fe- B synthesized surface in the presence of UVC light and hydrogen peroxide. B.G dye solution with 10 ppm primary concentration is reduced by 99.9% under the later parameter 2ml H2O2, pH= 7, temperature =25°C within 10 min. It is clear that pH of the solution affects the photo- catalytic degradation

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Publication Date
Sun Jan 01 2023
Journal Name
Materials Chemistry And Physics
BC2N nanotube as a promising anode for rechargeable calcium ion batteries
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Because of cost-effective production and abundant resources of calcium, Ca-ion batteries (CIBs) are an appropriate option to alternate Li-ion batteries (LIBs). A new category of anode materials for CIBs has emerged since the successful synthesis of carbon nanotubes, which are B and N doped derivatives of it. For high-performance CIBs, BC2N nanotube (BC2NNT) has been studied as promising anode materials. In order to comprehend electrochemical attributes, cycling stability, and adsorption behavior of BC2NNT, first-principles computations have been executed. Based on nuclear magnetic resonance computations, two types of hexagonal rings (B2C2N2 (I) and BC4N (II)) were specified that are non-aromatic. Ca has adsorption on B2C2N2 and BC4N with ad

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Publication Date
Sun Mar 15 2020
Journal Name
Journal Of The College Of Education For Women
Data-Driven Approach for Teaching Arabic as a Foreign Language: Eygpt
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Corpus linguistics is a methodology in studying language through corpus-based research. It differs from a traditional approach in studying a language (prescriptive approach) in its insistence on the systematic study of authentic examples of language in use (descriptive approach).A “corpus” is a large body of machine-readable structurally collected naturally occurring linguistic data, either written texts or a transcription of recorded speech, which can be used as a starting-point of linguistic description or as a means of verifying hypotheses about a language.  In the past decade, interest has grown tremendously in the use of language corpora for language education. The ways in which corpora have been employed in language pedago

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Publication Date
Mon Jun 01 2020
Journal Name
Journal Of Engineering
GIS as A Tool for Expansive Soil Detection at Sulaymaniyah City
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Geotechnical engineering like any other engineering field has to develop and cope with new technologies. This article intends to investigate the spatial relationships between soil’s liquid limit (LL), plasticity index (PI) and Liquidity index (LI) for particular zones of Sulaymaniyah City. The main objective is to study the ability to produce digital soil maps for the study area and determine regions of high expansive soil. Inverse Distance Weighting (IDW) interpolation tool within the GIS (Geographic Information System) program was used to produce the maps. Data from 592 boreholes for LL and PI and 245 boreholes for LI were used for this study. Layers were allocated into three depth ranges (1 to 2, 2 to 4 and 4 to 6)

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Publication Date
Fri Dec 30 2011
Journal Name
Al-kindy College Medical Journal
Postprandial Hyperglycemia as a Significant Risk Factor for Coronary Heart Disease
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Background: The highest concentrations of
blood glucose during the day are usually found
postprandialy. Postprandial hyperglycemia (PPH)
is likely to promote or aggravate fasting
hyperglycemia. Evidence in recent years suggests
that PPH may play an important role in functional
& structural disturbances in different body organs
particularly the cardiovascular system.
Objective: To evaluate the effect of (PPH) as a
risk factor for coronary Heart disease in Type 2
diabetic patients.
Methods: Sixty-three type2 diabetic patients
were included in this study. All have controlled
fasting blood glucose, with HbA1c correlation.
They were all followed for five months period
(from May to October 2008)

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