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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 Jun 30 2020
Journal Name
Membranes
Experimental and Theoretical Analysis of Lead Pb2+ and Cd2+ Retention from a Single Salt Using a Hollow Fiber PES Membrane
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The present work reports the performance of three types of polyethersulfone (PES) membrane in the removal of highly polluting and toxic lead Pb2+ and cadmium Cd2+ ions from a single salt. This study investigated the effect of operating variables, including pH, types of PES membrane, and feed concentration, on the separation process. The transport parameters and mass transfer coefficient (k) of the membranes were estimated using the combined film theory-solution-diffusion (CFSD), combined film theory-Spiegler-Kedem (CFSK), and combined film theory-finely-porous (CFFP) membrane transport models. Various parameters were used to estimate the enrichment factors, concentration polarization modulus, and Péclet number. The pH values signif

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Publication Date
Mon Jul 01 2013
Journal Name
2013 35th Annual International Conference Of The Ieee Engineering In Medicine And Biology Society (embc)
A preliminary investigation of the effect of force variation for myoelectric control of hand prosthesis
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Publication Date
Wed Aug 12 2015
Journal Name
J. Genet. Environ. Resour. Conserv
Effect of arbuscular mycorrhizal fungi as a biocontrol agent and organic matter against fusarium wilt in tomato
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The objective of this investigation was to study the effects of a mixture of three arbuscular mycorrhizae (Glomus etunicatum, G. leptotichum and Rhizophagus intraradices) on the development of fusarium wilt disease in tomato plants in the presence and absence of organic matter (peatmoss). Results indicated an increase in mycorrhizal root dry weight especially in the presence of the organic matter, on the other hand this parameter was significantly decreased when Fusarium oxysporum f. sp. Lycopersiciwas added simultaneously with the mycorrhiza, Moreover, mycorrhiza and organic matter significantly reduced the damping off seedling disease, disease severity and rate of infection of tomato leaves and roots caused by the pathogenic fungus, These

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Publication Date
Thu Dec 01 2022
Journal Name
Journal Of Medicine And Life
Renal stone density on native CT-scan as a predictor of treatment outcomes in shock wave lithotripsy
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Extracorporeal shock wave lithotripsy (ESWL) is considered a standard treatment for nephrolith or kidney stones measuring less than 20 mm. Anatomical, machine-related, and stone factors play pivotal roles in treatment outcomes, the latter being the leading role. This paper examined the relationship between stone density on native CT scans and ESWL treatment to remove renal stones concerning several treatments. One hundred and twenty patients (64 males and 56 females) were enrolled and completed the study from April 2019 to September 2020. Inclusion criteria were a single renal pelvis stone of 5–20 mm to be treated for the first time in adult patients with no urinary or musculoskeletal anatomical abnormalities. We assessed patients

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Publication Date
Wed May 10 2023
Journal Name
Journal Of Planner And Development
Analysis and evaluation of related factors affecting community Participation as a policy to upgrade residential slums area
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have suffered from deteriorating residential neighborhoods, poor economic, social and urban living conditions of the population and deteriorating the infrastructural and superior services. These problems were the secretions of these cities' rapid urbanization. Based on the principles of sustainable urban planning and in order to achieve adequate opportunities for the lives of the population and provide them with sustainable livelihoods, policies have emerged to upgrade along the lines of community participation and programmes to reform and develop those neighbourhoods, raise their efficiency and make them livable. Thus, the problem of research was identified "The absence of a comprehensive cognitive perception of the most prominent facto

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Publication Date
Wed Oct 01 2014
Journal Name
Journal Of Economics And Administrative Sciences
Spatial Regression Model Estimation for the poverty Rates In the districts of Iraq in 2012
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Theresearch took the spatial autoregressive model: SAR and spatial error model: SEM in an attempt to provide a practical evident that proves the importance of spatial analysis, with a particular focus on the importance of using regression models spatial andthat includes all of them spatial dependence, which we can test its presence or not by using Moran test. While ignoring this dependency may lead to the loss of important information about the phenomenon under research is reflected in the end on the strength of the statistical estimation power, as these models are the link between the usual regression models with time-series models. Spatial analysis had

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Publication Date
Sun Jan 01 2023
Journal Name
Isvs E-journal
Preserving the Past and Building the Future: A Sustainable Urban Plan for Mosul, Iraq
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Preserving the Past and Building the Future: A Sustainable Urban Plan for Mosul, Iraq

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Publication Date
Mon Dec 26 2016
Journal Name
Iraqi Journal Of Market Research And Consumer Protection
ESTIMATION OF THE CHEMICAL COMPONENTS OF WASTES PRESSED GRAPES A STUDY THE EFFECT OF THERMAL EXTRACTS TRANSACTIONS IN INHIBITING THE GROWT OF MICROORGANISMS.: ESTIMATION OF THE CHEMICAL COMPONENTS OF WASTES PRESSED GRAPES A STUDY THE EFFECT OF THERMAL EXTRACTS TRANSACTIONS IN INHIBITING THE GROWT OF MICROORGANISMS.
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The chemical composition of wastes of pressed grapes and found that the main components of wastes of pressed grapes, represented by the percentage of moisture was 6.47%, and the proportions are 3.71%. Either carbohydrates amounted to 85.77 %, either in fat models using petroleum ether Petroleum ether) was the increase of 0.27%. estimated the percentage of ash in the sampls was 3.78%, either fiber reached 69.47 %,, in addition to the test extracts towards the growth of seven types of bacteria, which included Bacillus subtilis, Bacillus cereus, Bacillus stearothermophilus, Escherishia coli, Staphylococcus aureus, Salmonella typhimurium and Pseudomonas fluorescens and yeast Candida albicans and Kluyveromyces marxianus, ( diffusion method ).

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Publication Date
Wed Jan 01 2020
Journal Name
Veterinary World
Babesia canis spp. in dogs in Baghdad Province, Iraq: First molecular identification and clinical and epidemiological study
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Aim: The aim of this study was to investigate babesiosis in dogs of different breeds and ages and of both sexes in Baghdad Province by molecular detection of Babesia canis using conventional polymerase chain reaction (PCR) and sequencing followed by phylogenetic analyses. Materials and Methods: Blood samples were collected from 310 dogs of different ages and breeds, and of both sexes in different areas of Baghdad Province from December 2018 to September 2019; during clinical examinations, body temperature, pulse, respiratory rate, and signs of diseases were recorded. PCR was used to amplify a specific 450-bp fragment of the 18S rRNA gene of B. canis. PCR products were sequenced, and MEGA 6.0 software was used for analysis. Chi-squar

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Publication Date
Wed Oct 25 2023
Journal Name
College Of Islamic Sciences
Provisions for a Muslim to be naturalized with the citizenship of non-Muslim countries
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Praise to Allah, Lord of the Worlds. Thank you very much. Blessed. As his face should be majestic and great. His authority, and may peace and blessings be upon our master Muhammad, a perpetual blessing until the Day of Judgment

And upon the God of purity, His righteous companions, and those who follow them in righteousness until the Day of Judgment. But after:-

Anyone who looks into the history of nations, peoples, and the conditions of human beings will see that naturalization as a person’s affiliation to a particular state is something that happened only in recent centuries. In ancient times, a person’s loyalty was to the tribe to which the person belonged, and he was integrated into it and attributed to it, and in

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