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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 2023
Journal Name
Biochemical Engineering Journal
Immobilization of mixed cells by Flaxseeds (Linum usitatissimum) extract as new nonconventional biocarrier for biodegradation of sodium dodecyl sulfate
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Publication Date
Wed Sep 01 2021
Journal Name
International Journal Of Nonlinear Analysis And Application
Suggested methods for prediction using semiparametric regression function
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Ferritin is a key organizer of protected deregulation, particularly below risky hyperferritinemia, by straight immune-suppressive and pro-inflammatory things. , We conclude that there is a significant association between levels of ferritin and the harshness of COVID-19. In this paper we introduce a semi- parametric method for prediction by making a combination between NN and regression models. So, two methodologies are adopted, Neural Network (NN) and regression model in design the model; the data were collected from مستشفى دار التمريض الخاص for period 11/7/2021- 23/7/2021, we have 100 person, With COVID 12 Female & 38 Male out of 50, while 26 Female & 24 Male non COVID out of 50. The input variables of the NN m

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Publication Date
Tue Dec 01 2009
Journal Name
Journal Of Economics And Administrative Sciences
Using Artificial Neural Network Models For Forecasting & Comparison
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The Artificial Neural Network methodology is a very important & new subjects that build's the models for Analyzing, Data Evaluation, Forecasting & Controlling without depending on an old model or classic statistic method that describe the behavior of statistic phenomenon, the methodology works by simulating the data to reach a robust optimum model that represent the statistic phenomenon & we can use the model in any time & states, we used the Box-Jenkins (ARMAX) approach for comparing, in this paper depends on the received power to build a robust model for forecasting, analyzing & controlling in the sod power, the received power come from

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Publication Date
Wed Feb 01 2023
Journal Name
Trends Technological And Science ,engineering
Automated Sorting for Tomatoes using Artificial Neural Network
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A .technology analysis image using crops agricultural of grading and sorting the test to conducted was experiment The device coupling the of sensor a with camera a and 75 * 75 * 50 dimensions with shape cube studio made-factory locally the study to studio the in taken were photos and ,)blue-green - red (lighting triple with equipped was studio The .used were neural artificial and technology processing image using maturity and quality ,damage of fruits the of characteristics external value the quality 0.92062, of was value regression the damage predict to used was network neural artificial The .network the using scheme regression a of means by 0.98654 of was regression the of maturity and 0.97981 of was regression the of .algorithm Marr

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Publication Date
Wed Jan 01 2025
Journal Name
Veterinary World
Comparison of the sequences of the viral capsid protein 1 and viral capsid protein 2 encoded genes in symptomatic and asymptomatic cases of canine parvovirus 2 in dogs
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Background and Aim: Canine parvovirus 2 (CPV-2) is a highly contagious virus that infects wild and domestic canines. Despite the use of a routine vaccination protocol, it is endemic in Iraq. The genetic drift of CPV-2 is a major issue worldwide because it abrogates virus control. In Iraq, there is a knowledge gap regarding the genetic sequences of asymptomatic and symptomatic CPV-2 cases. Therefore, this study aimed to perform a genetic analysis of viral capsid protein 1 (VP1) and viral capsid protein 2 (VP2), two major capsid-encoding genes, to demonstrate the possible role of certain mutations in triggering infection. Materials and Methods: Symptomatic and asymptomatic cases (n = 100/each) were tested by a polymerase chain reacti

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Publication Date
Thu Sep 13 2018
Journal Name
Baghdad Science Journal
Studying Biomimetic Coated Niobium as an Alternative Dental Implant Material to Titanium (in vitro and in vivo study)
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Commercially pure titanium (cpTi) is widely used as dental implant material although it was found that titanium exhibited high modulus of elasticity and the lower corrosion tendency in oral environment. Niobium(Nb) was chosen for this study as an alternative to cpTi implant material due to its bioinert behavior and good elastic modulus and moderate cost in addition to corrosion resistance. This study was done to evaluate the effect of biomimetic coating on the surface properties of the commercially pure titanium and niobium implants by in vitro and in vivo experiments. The in vitro study was involved etching the samples of each material in HCl then soaking in 10M NaOH aqueous solution. These samples were then immersed in a 5 times concent

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Publication Date
Wed Jun 01 2022
Journal Name
Journal Of The College Of Languages (jcl)
Reduced and Citation Forms as Produced by Iraqi EFL University Students at Duhok University An Error Analytic Study
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English is spoken by its native speakers in two different forms. Reduced form which marks the colloquial and rapid speech so that it is easily produced and a citation or unreduced form which is a characteristic of careful, emphasized and slow speech.

      This paper investigates Iraqi EFL university students’ production of the two forms mentioned above. The sample chosen includes twenty fourth year students, of which ten are males and the other ten are females from the Department of English of the College of Languages of the University of Duhok in Kurdistan Region of Iraq in the academic year 2020-2021.  The material tested is six connective words which represent the commonest ones in every-day co

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Publication Date
Sat Oct 01 2022
Journal Name
Al–bahith Al–a'alami
The evolution of the press image in the Iraqi press (An analytical study of the pictures of the first page of Al-Sabah newspaper for the year)
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This research sheds light on the development that has occurred on the use of press pictures in the Iraqi press by analyzing the form and content of the images used in (Al-Sabaah) newspaper for the 2012 model. The researcher's interest in this topic for what represented by the press picture of a way to highlight and attract the reader's attention to the substance journalist who represents the goals behind the newspaper publishing.

This research is divided into three sections. The first one dealt with the methodological framework of the research, and the second part addressed the aspect of press pictures and its history and technological development, while the third section devoted to the study of the development of the form and co

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Publication Date
Sun Mar 03 2013
Journal Name
Baghdad Science Journal
Modifying Plaque assay and Clearance test as tools in determination of phage typing for E. Coli bacterial interspecies
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Bacteriophage of E. Coli interspecies from sewage samples were isolated , the phage particles were isolated from two different sewage samples . The first sample was collected from sewage sample of Baghdad university and the second sample was isolated from domestic sewage sample , first sample showed phages specialized for three E. Coli interspecies bacteria (first plate ) and two E. Coli interspecies bacteria (second plate ) , meanwhile second sample showed phage specialized for two E. Coli. interspeciesThe study of appearance of E coli phages from first sample showed three types of E. coli phages with different size of inhibition zone ( 1 , 0.7,0.5 )Cm respectively ( first plate ) , meanwhile E. Coli interspecies bacteria showed phages

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Publication Date
Fri Nov 01 2024
Journal Name
Plos One
Psychological flow and mental immunity as predictors of job performance for mental health care practitioners during COVID-19
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Background Numerous studies indicated that workers in the health sector suffer from work stress, hassles, and mental health problems associated with COVID-19, which negatively affect the completion of their job tasks. These studies pointed out the need to search for mechanisms that enable workers to cope with job stress effectively. Objectives This study investigated psychological flow, mental immunity, and job performance levels among the mental health workforce in Saudi Arabia. It also tried to reveal the psychological flow (PF) and mental immunity (MI) predictability of job performance (JP). Method A correlational survey design was employed. The study sample consisted of 120 mental health care practitioners (therapists, psychologists, co

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