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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
Mon May 01 2017
Journal Name
Energy Procedia
A Coupled Model of the Linear Joule Engine with Embedded Tubular Permanent Magnet Linear Alternator
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Publication Date
Thu Aug 13 2020
Journal Name
Asia Pacific Journal Of Molecular Biology And Biotechnology
The anticancer molecular mechanism of Carnosol in human cervical cancer cells: An in vitro study
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Carnosol, a phenolic diterpene, is one of the effective anticancer agents naturally occurring in rosemary, sage, parsley, and oregano. The chemoresistance problem increased with the routinely used chemotherapy. Therefore, the efforts to find a substitute with safe and low cost have become crucial worldwide. The current study attempts to inspect the anticancer molecular mechanisms of Carnosol on modulating up- and down- regulation of multiple genetic carcinogenesis pathways. The cytotoxicity of Carnosol on Hela cells was evaluated by MTS assay. Flow cytometry was used to assess apoptosis and cell cycle arrest. The apoptotic morphological changes were obvious by dual apoptosis assay. The differential gene expression after treatment wi

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Publication Date
Fri Jan 01 2021
Journal Name
Annals Of The Romanian Society For Cell Biology
Molecular study to the fungus Neosetophomasamarorum was isolated from Al Chabaish marsh, South of Iraq
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IA Ali, FK Emran, DF Salloom, Annals of the Romanian Society for Cell Biology, 2021

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Publication Date
Mon Jul 01 2019
Journal Name
Journal Of Educational And Psychological Researches
Constructing a Scale for the Nine Types of Students Personality: Constructing a Scale for the Nine Types of Students Personality
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Abstract

The current research aims to construct a scale for the nine types of students’ personality according to Rob Fitzel model. To do this, (162) items were formed that present the nine types of personality with (18) items for each type. To test the validity of the scale, a sample of (584) students of Al-Mustansrya University were chosen. The data of their responses was analyzed by using factor analysis. The findings explored (9) factors as one factor for each type of personality with (12) items for each one. Then, the reliability of the scale was found by using the test-retest method and Alfa Cronbach method.

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Publication Date
Thu Dec 14 2023
Journal Name
4th International Conference Of Modern Technologies In Agricultural Sciences
A study of the Effect of Diesel Oil Contamination with Glycol on the Performance of a Diesel Engine
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The performance of a diesel engine was tested with diesel oil contaminated with glycol at the engineering workshop/Department of Agricultural Machines and Equipment / College of the Agricultural Engineering Sciences at the University of Baghdad. To investigate the impact of different concentrations of glycol on the performance of a diesel engine, an experimental water-cooled four-stroke motor was utilized, with oil containing 0, 100, and 200 parts per million (ppm). Specific fuel consumption, thermal efficiency, friction power, and exhaust gas temperature were examined as performance indicators. To compare the significance of the treatments, the study employed a full randomization design (CRD), with three replicates for each treatment at th

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Publication Date
Fri Dec 01 2023
Journal Name
Iop Conference Series: Earth And Environmental Science
A study of the Effect of Diesel Oil Contamination with Glycol on the Performance of a Diesel Engine
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Abstract<p>The performance of a diesel engine was tested with diesel oil contaminated with glycol at the engineering workshop/Department of Agricultural Machines and Equipment / College of the Agricultural Engineering Sciences at the University of Baghdad. To investigate the impact of different concentrations of glycol on the performance of a diesel engine, an experimental water-cooled four-stroke motor was utilized, with oil containing 0, 100, and 200 parts per million (ppm). Specific fuel consumption, thermal efficiency, friction power, and exhaust gas temperature were examined as performance indicators. To compare the significance of the treatments, the study employed a full randomization des</p> ... Show More
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Publication Date
Fri Dec 01 2023
Journal Name
Iop Conference Series: Earth And Environmental Science
A study of the Effect of Diesel Oil Contamination with Glycol on the Performance of a Diesel Engine
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Abstract<p>The performance of a diesel engine was tested with diesel oil contaminated with glycol at the engineering workshop/Department of Agricultural Machines and Equipment / College of the Agricultural Engineering Sciences at the University of Baghdad. To investigate the impact of different concentrations of glycol on the performance of a diesel engine, an experimental water-cooled four-stroke motor was utilized, with oil containing 0, 100, and 200 parts per million (ppm). Specific fuel consumption, thermal efficiency, friction power, and exhaust gas temperature were examined as performance indicators. To compare the significance of the treatments, the study employed a full randomization des</p> ... Show More
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Publication Date
Mon Jan 01 2024
Journal Name
Medical Research Archives
Genetic Polymorphism for the Gene Encoding Endoplasmic Reticulum Aminopeptidase-1 (ERAP-1) in Iraqi Patients with Ankylosing Spondylitis
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Ankylosing spondylitis (AS) is a common, highly heritable inflammatory arthritis affecting primarily the spine and pelvis. This study was aimed to investigate the relationship between the rs27044 polymorphism in Endoplasmic reticulum aminopeptidase-1 (ERAP-1) with the susceptibility and severity of AS correlated with some biochemical markers such as hematological parameter (Erythrocytes sedimentation rate (ESR)) and immunological parameters (C-reactive protein (CRP), Human leukocyte antigen-B27 (HLA-B27), Interlukin-6 (IL-6) and Interlukin-23 (IL-23)), and oxidative stress parameters (Glutathione (GSH) and Malondialdehyde (MDA)) in a sample of Iraqi population. A total of 60 blood samples were collected from AS patients requited Rhe

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Publication Date
Fri Feb 08 2019
Journal Name
Iraqi Journal Of Laser
Writing of a Bragg Grating on a D-shaped Optical Fiber Using the KrF Excimer Laser
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Fiber Bragg Grating has many advantages where it can be used as a temperature sensor, pressure sensor or even as a refractive index sensor. Designing each of this fiber Bragg grating sensors should include some requirements. Fiber Bragg grating refractive index sensor is a very important application. In order to increase the sensing ability of fiber Bragg gratings, many methods were followed. In our proposed work, the fiber Bragg grating was written in a D-shaped optical fiber by using a phase mask method with KrFexcimer. The resultant fiber Bragg grating has a high reflectivity 99.99% with a Bragg wavelength of 1551.2 nm as a best result obtained from a phase mask with a grating period of 1057 nm. In this work it was found that the rota

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Publication Date
Sun Mar 13 2011
Journal Name
Baghdad Science Journal
Using of Rustumiya sewage water for irrigation:1- its effect on some soil properties and corn growth
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This study is conducted to investigate the validity of using different levels of Rustumiya sewage water for irrigation and their effects on corn growth and some of the chemical properties of the soil such as electrical conductivity and soil pH in extract soil paste , the micro nutrient content in soil and plant which are ( Fe , Mn , Zn , Cu , Cd , Pb ). Three levels of sewage water ( 0 , 50 , 100 )% in two stages were used ,the three levels of wastewater ( without soil fertilization ) were used in the first stage , Where 80 Kg N /D+50Kg P2O5 /D was added to the soil as fertilizer in the control (0%) treatment and 40 Kg N/D+25Kg P2O5/D were added to 50 and 100% levels in the second stage .Corn seeds were planted in 12kg plastic pots in Com

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