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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
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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Publication Date
Fri Mar 31 2017
Journal Name
Iraqi Journal Of Pharmaceutical Sciences ( P-issn 1683 - 3597 E-issn 2521 - 3512)
A Study of the Furocoumarin Derivative of Ruta Chalepensis L. (Rutaceae)
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  The content of Furocoumarin derivatives (Psoralens) of Ruta Chalepensis L. (Whole plant) was studied by simple extraction with petroleum ether (b.p. 60-80Co). The results indicated that the plant contains a total of about (0.015%).

       Investigation of these compounds by thin layer chromatography (TLC) revealed the presence of at least four compounds of which methoxsalen (8-methoxypsoralen) was isolated.     It was identified and authenticated with a standard by spectral method, IR, NMR, Mass spectra and HPLC.This plant could be considered as a good source for supplying this compound, which is widely used in dermatological preparations.

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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
Wed Jan 29 2020
Journal Name
Advances In Rheumatology
Neutrophil/lymphocyte and platelet/lymphocyte ratios as potential markers of disease activity in patients with Ankylosing spondylitis: a case-control study
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Abstract<sec> <title>Background

The neutrophil/ lymphocyte ratio (NLR) and platelet/lymphocyte ratio (PLR) have the potential to be inflammatory markers that reflect the activity of many inflammatory diseases. The aim of this study was to evaluate the NLR and PLR as potential markers of disease activity in patients with ankylosing spondylitis.

Methods

The study involved 132 patients with ankylosing spondylitis and 81 healthy controls matched in terms of age and gender. Their sociodemographic data, disease activity scores using the Bath Ankylosing

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Publication Date
Mon Sep 23 2019
Journal Name
Baghdad Science Journal
New Approach for Solving Three Dimensional Space Partial Differential Equation
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This paper presents a new transform method to solve partial differential equations, for finding suitable accurate solutions in a wider domain. It can be used to solve the problems without resorting to the frequency domain. The new transform is combined with the homotopy perturbation method in order to solve three dimensional second order partial differential equations with initial condition, and the convergence of the solution to the exact form is proved. The implementation of the suggested method demonstrates the usefulness in finding exact solutions. The practical implications show the effectiveness of approach and it is easily implemented in finding exact solutions.

       Finally, all algori

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Publication Date
Sun Sep 30 2012
Journal Name
College Of Islamic Sciences
He saw a linguistic study, in the Noble Qur’an
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In the name of God, praise be to God, and prayers and peace be upon the best of God’s creation, Muhammad bin Abdullah, and upon his family and companions, and from his family:
And after:
     He saw from verbs that transcend one effect if it is visual and to two effects if it is heart and this action has several strokes and it is an awareness of the sense and illusion and imagination and reason and in addition to that it has many meanings dealt with in the glossary books and as for what the verb included in the audio studies it is the explanation and deletion and slurring The heart of my place. As for what the grammatical studies included, it focuses on one or two effects according to its l

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Publication Date
Thu Dec 30 2021
Journal Name
College Of Islamic Sciences
Controls Scanning on the slippers: a study fiqhiat Comparison
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Controls Scanning on the slippers a study fiqhiat Comparison

The subject of this research is an important topic, which is frequently repeated, and people need to know its wisdom, and has made it in front and the preface and three detectives, showed through discussion the meaning of the survey on the socks, its wisdom, its rules and conditions, and the duration of the survey on it, spoiled and reasoned and compared to the doctrinal doctrines, And the most correct statement of words I have concluded with a number of things, as follows:

  1. The need to ensure that the slippers are clean, visible and inwa

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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
Sat Apr 02 2022
Journal Name
Journal Of Accounting And Financial Studies ( Jafs )
The Role of Artificial Intelligence in achieving Ambidextrous Performance A case study in a sample of private banks
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The research aims to shed light on the role of artificial intelligence in achieving Ambidexterity performance, as banks work to take advantage of modern technologies, artificial intelligence is an innovation that is expected to have a long-term impact, as well as banks can improve the quality of their services and analyze data to ensure that customers' future needs are understood. . The Bank of Baghdad and the Middle East Bank were chosen as a community for the study because they had a role in the economic development of the country as well as their active role in the banking market. A sample of department managers was highlighted in collecting data and extracting results based on the checklist, which is the main tool for the stu

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