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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
Wed Jun 30 2021
Journal Name
Iraqi Journal Of Chemical And Petroleum Engineering
Advanced Study of Promoted Pt /SAPO-11 Catalyst for Hydroisomerization of the n-Decane Model and Lube Oil
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   SAPO-11 is synthesized from silicoaluminophosphate in the presence of di-n-propylamine as a template. The results show that the sample obtained has good crystallinity, 396m2/g BET surface area, and 0.35 cm3/g pore volume. The hydroisomerization activity of (0.25)Pt (1)Zr (0.5)W/SAPO-11 catalyst was determined using n-decane and base oil. All hydroisomerization experiments of n-decane were achieved at a fixed bed plug flow reactor at a temperature range of 200-275°C and  LHSV 0.5-2h-1.  The results show that the n-decane conversion increases with increasing temperature and decreasing LHSV, the maximum conversion of 66.7 % was achieved at temperature 275°C and LHSV of 0.5 h-1

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Publication Date
Sun Sep 30 2012
Journal Name
Iraqi Journal Of Chemical And Petroleum Engineering
Polyvinyl Alcohol – Sodium Nitrite Water Soluble Composite as a Corrosion Inhibitor for Mild Steel in Simulated Cooling Water
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The inhibitive action of polyvinyl alcohol –sodium nitrite (PVASN) composite on the corrosion of mild steel in simulated cooling water (SCW) has been investigated by weight loss and potentiodynamic polarization. The effect of composite concentration (PVA/SN) , pH, and exposure time on corrosion rate of mild steel were verified using 2 levels factorial design and surface response analysis through weight loss approach, while the electrochemical measurements were used to study the behavior of mild steel in (SCW) with pH between 6 and 8 and in absence and presence of (PVA) in solution containing different concentration of NaNO2. It was verified that all three main variables studied were statistically significant while their interaction is

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Publication Date
Tue May 30 2023
Journal Name
Rawal Medical Journal
Elevated lactate dehydrogenase (LDH) and C- reactive protein (CRP) level as a risk factor for critical COVID-19
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Abstract Objective: To identify correlation of elevated LDH & CRP levels with the outcomes of COVID-19. Methodology: The cross-sectional retrospective study consisted of 200 COVID-19 patients who presented at a private clinical in Baghdad, Iraq. It was carried out from February 2021 to February 2022. Data included age, gender and clinical presentation. Blood samples were taken for high sensitivity CRP and LDH in the serum. Results: Out of 200 patients, 50 were critical and 150 severe according to clinical features. LDH and CRP showed a significant increase (p=0.000) in critical patients. This group involved admission to the respiratory intensive care unit requiring mechanical ventilation than in patients with severe COVID-19 (760.5±6.3 vs.

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Publication Date
Thu Jan 25 2024
Journal Name
Iraqi Journal Of Agricultural Sciences
SPRAYING NANO CHITOSAN LOADED WITH NPK, NETTEL AND GREEN TEA EXTRACTS AS A TOOL FOR IMPROVEMENT POTATO PRODUCTIVITY
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This study was aimed to evaluate the effect of spraying nano chitosan loaded with NPK fertilizer and nettle leaf and green tea extracts on the growth and productivity of potato for the spring and fall seasons of 2021.It was conducted at private farm in Wasit Governorate, Iraq, as a factorial experiment (5 × 5) within randomized complete block design using three replicates. The first factor included spraying with four concentrations of chitosan nanoparticles loaded with NPK fertilizer 0, 10. 15 and 20% in addition to chemical fertilization treatment, the second factor was spraying nettle leaf extract 25 and 35 gL-1 and green tea extract with 2 and 4 g.L-1, in addition to the control treatment, spraying with distilled water only. The

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Publication Date
Fri Jun 01 2018
Journal Name
Journal Of The College Of Languages (jcl)
האלמנטים המשותפים בשיריהם של משה בן עזרא ואבו פיראס אלחמדני (מחקר השוואתי) Elements common in the poems of Musa son of Izra and Abu Firas al-Hamdani (A comparative study)
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Abstract:

     Musa son of Yaqoob son of Izra, the Spanish poet, linguist, and  philosopher, was born in Granada. He has many poems representing  types of poetry. Also, he had important books, such as "the Poetry of Israel" and "Contemplative Research". He is knowledgeable in both Hebrew and Arabic, because most of his books were written in Arabic and the then translated to Hebrew. It seemed that he was influenced by Arab poets, specifically Abo Firas, and borrowed many issues, such as comparison, repetition, exaggeration, etc. and included them in his poetry.

     All know that Arabic literature clearly influenced Hebrew literature in the Spanish era. Ara

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Publication Date
Tue Nov 09 2021
Journal Name
Abu Dhabi International Petroleum Exhibition & Conference
Numerical Simulation of Gas Lift Optimization Using Artificial Intelligence for a Middle Eastern Oil Field
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Abstract<p>Artificial lift techniques are a highly effective solution to aid the deterioration of the production especially for mature oil fields, gas lift is one of the oldest and most applied artificial lift methods especially for large oil fields, the gas that is required for injection is quite scarce and expensive resource, optimally allocating the injection rate in each well is a high importance task and not easily applicable. Conventional methods faced some major problems in solving this problem in a network with large number of wells, multi-constrains, multi-objectives, and limited amount of gas. This paper focuses on utilizing the Genetic Algorithm (GA) as a gas lift optimization algorit</p> ... Show More
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Publication Date
Tue Mar 01 2016
Journal Name
Journal Of Engineering
A reformation Study about the Construction Management in the Primary Stage Curricula’s for the Civil Engineering in Some of the Iraqi Universities
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There is no doubt that the field of education and teaching (in any country and whatever its ruling system varies “d”) is considered one of the most specific and sensitive field, because it is related to the building of human. And as the human is a purpose (aim) and the means in the same time and he is the strategist capital, so he way of his rearing, education, choosing the educator, methods of working and the aims are considered serious matters.

     The educational process has aim determined by the society for him self through its working establishments in this field and these are the official and public establishments. And as he feels that the establishments have failed to achieve its d

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Publication Date
Mon Oct 02 2023
Journal Name
Journal Of Engineering
Transport Assessment Using Bayesian Method to Determine Ride-Hailing in Kula Lumpur: A Case Study
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This research was designed to investigate the factors affecting the frequency of use of ride-hailing in a fast-growing metropolitan region in Southeast Asia, Kuala Lumpur. An intercept survey was used to conduct this study in three potential locations that were acknowledged by one of the most famous ride-hailing companies in Kuala Lumpur. This study used non-parametric and machine learning techniques to analyze the data, including the Pearson chi-square test and Bayesian Network. From 38 statements (input variables), the Pearson chi-square test identified 14 variables as the most important. These variables were used as predictors in developing a BN model that predicts the probability of weekly usage frequency of ride-hai

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Publication Date
Fri Sep 30 2022
Journal Name
Iraqi Journal Of Chemical And Petroleum Engineering
Cadmium Removal Using Bio-Electrochemical Reactor with Packed Bed Rotating Cylindrical Cathode: A Kinetics Study
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   The kinetics of removing cadmium from aqueous solutions was studied using a bio-electrochemical reactor with a packed bed rotating cylindrical cathode. The effect of applied voltage, initial concentration of cadmium, cathode rotation speed, and pH on the reaction rate constant (k) was studied. The results showed that the cathodic deposition occurred under the control of mass transfer for all applied voltage values ​​used in this research. Accordingly, the relationship between logarithmic concentration gradient with time can be represented by a first-order kinetic rate equation. It was found that the rate constant (k) depends on the applied voltage, the initial cadmium concentration, the pH and the rotational speed of cathode. It

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Publication Date
Sun Feb 03 2019
Journal Name
Iraqi Journal Of Physics
A study of the characterization of CdS/PMMA nanocomposite thin film
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Nanocomposites of polymer material based on CdS as filler
material and poly methyl methacrylate (PMMA) as host matrix have
been fabricated by chemical spray pyrolysis method on glass
substrate. CdS particles synthesized by co-precipitation route using
cadimium chloride and thioacetamide as starting materials and
ammonium hydroxide as precipitating agent. The structure is
examined by X-ray diffraction (XRD), the resultant film has
amorphous structure. The optical energy gap is found to be (4.5,
4.06) eV before and after CdS addition, respectively. Electrical
activation energy for CdS/PMMA has two regions with values of
0.079 and 0.433 eV.

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