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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
Thu Sep 01 2011
Journal Name
Journal Of Economics And Administrative Sciences
Determination Of The Efficient Production Plans For Al-Shaheed Public Company By Using Tatget Motad Model Under Risk And Uncertainty
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The research aims to derive the efficient industrial plans for Al – shaheed public company under risk by using Target MOTAD as a linear alternative  model for the quadratic programming models.

The results showed that there had been a sort of (trade- off) between risk and the expected gross margins. And if the studied company strives to get high gross margin, it should tolerate risk and vice versa. So the management  of Al- Shaheed Company to be invited to apply the suitable procedures in the production process, in order to get efficient plans that improves it's  performance .

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Publication Date
Sat Jan 01 2022
Journal Name
Journal Of Sport Sciences
The effect of using the McCarthy model according to cognitive style (rigid- flexibility) in learning some skills in artistic gymnastics for women
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The aim of the research is to identify the cognitive method (rigidity flexibility) of third-stage students in the collage of Physical Education and Sports Sciences at The University of Baghdad, as well as to recognize the impact of using the McCarthy model in learning some of skills in gymnastics, as well as to identify the best groups in learning skills, the experimental curriculum was used to design equal groups with pre test and post test and the research community was identified by third-stage students in academic year (2020-2021), the subject was randomly selected two divisions after which the measure of cognitive method was distributed to the sample, so the subject (32) students were distributed in four groups, and which the pre te

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Publication Date
Tue Mar 24 2009
Journal Name
كتاب الوقائع /المؤتمر العلمي الثالث لكلية العلوم جامعة بغداد
Using antibiotics as mutagenic and curing agents for Prodigiosin Production By Serratia marcescens
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The effect of different antibiotics on growth pigment and plasmid curing of Serratia marcescens were studied, S. marcescens was cultured in media containing(16_500)µg/ml of antibiotics, curing mutants unable to produce prodigiosin and lost one plasmid band were obtained of of ampicillin, amoxillin, antibiotics concentrations (64 500) µg/ml metheprim, ultracloxam, azithromycin, cephalexin and erythromycin treated with (350 500) µg/ml of The mutant cells rose- light color and and refampicin revealed S.marcescens inhibited ciprodar and tetracyclin, lincomycin did not lost the plasmid band chlaforan

Publication Date
Wed Oct 26 2022
Journal Name
Petroleum Science And Technology
Building 3D geological model using non-uniform gridding for Mishrif reservoir in Garraf oilfield
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Publication Date
Sat Aug 01 2020
Journal Name
Jordan Journal Of Physics
Theoretical Simulation of Backscattering Electron Coefficient for SixGe1-x/Si Heterostructure as a Function of Primary Electron Beam Energy and Ge Concentration
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Abstract: This study aims to investigate the backscattering electron coefficient for SixGe1-x/Si heterostructure sample as a function of primary electron beam energy (0.25-20 keV) and Ge concentration in the alloy. The results obtained have several characteristics that are as follows: the first one is that the intensity of the backscattered signal above the alloy is mainly related to the average atomic number of the SixGe1-x alloy. The second feature is that the backscattering electron coefficient line scan shows a constant value above each layer at low primary electron energies below 5 keV. However, at 5 keV and above, a peak and a dip appeared on the line scan above Si-Ge alloy and Si, respectively, close to the interfacing line

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Publication Date
Tue Dec 01 2015
Journal Name
Journal Of Al-nahrain University-science
Synthesis of Polyacrylamides from Derivatives 2-Aminobenzothiazole and also Preparation of Dibutylphthalate as a Plasticizer to Estimate Plasticization Behaviour for Prepared Polymers
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Publication Date
Sat Feb 01 2020
Journal Name
Journal Of Economics And Administrative Sciences
Evaluation of banking performance according to the CAMELS model An applied study of Al-Mansour Investment Bank for the period 2014-2018.
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The banking sector has a significant impact on the economic growth of the country, and the importance of this sector must assess its financial performance from time to time, to measure the situation related to money for each bank and how to put the supervision of the efficiency of the full. The research aims at evaluating the financial performance according to the elements of the CAMELS model, which including capital adequacy, asset quality, management efficiency, profitability, liquidity, and market risk sensitivity. The research included the study of Al-Mansour Investment Bank during the period from 2014 to 2018. The base capital ratio was used to total assets to measure capital adequacy The proportion of investments to total a

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Publication Date
Wed Apr 01 2020
Journal Name
Technology Reports Of Kansai University
Complex of Lascoux in the General Case of Three Rows
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Publication Date
Thu May 02 2013
Journal Name
Al-mustansiriyah
Synthesis, Spectroscopic and Biological Studies of a New some Complexes with N-Pyridine-2-Y1 methyl-benzene-1, 2-diamine.
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Publication Date
Sun Jul 08 2018
Journal Name
Journal Of Global Pharma Technology
Association of Insulin-Like Growth Factor 2 Apa 1 A820G (rs680) Polymorphism with Thyroid Dysfunction in a Sample Iraqi Patien
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