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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 Feb 20 2024
Journal Name
Baghdad Science Journal
A New Strategy to Modify Hopfield by Using XOR Operation
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The Hopfield network is one of the easiest types, and its architecture is such that each neuron in the network connects to the other, thus called a fully connected neural network. In addition, this type is considered auto-associative memory, because the network returns the pattern immediately upon recognition, this network has many limitations, including memory capacity, discrepancy, orthogonally between patterns, weight symmetry, and local minimum. This paper proposes a new strategy for designing Hopfield based on XOR operation; A new strategy is proposed to solve these limitations by suggesting a new algorithm in the Hopfield network design, this strategy will increase the performance of Hopfield by modifying the architecture of t

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Publication Date
Wed Jun 11 2003
Journal Name
Iraqi Journal Of Laser
Microdrop Size Measurement in a Mixing Unit Using Laser Technique
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One of the troublesome duties in chemical industrial units is determining the instantaneous drop size distribution, which is created between two immiscible liquids within such units. In this work a complete system for measuring instantaneous droplet size is constructed. It consists of laser detection system (1mW He-Ne laser), drop generation system (turbine mixer unit), and microphotography system. Two immiscible liquids, water and kerosene were mixed together with different low volume fractions (0.0025, 0.02) of kerosene (as a dispersed phase) in water (as a continuous phase). The experiments were carried out at different rotational speed (1180- 2090 r.p.m) of the turbine mixer. The Sauter mean diameter of the drops was determined by la

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Publication Date
Wed Jun 29 2022
Journal Name
Iraqi Journal Of Chemical And Petroleum Engineering
Measuring Dyes Concentration Using a Low-Cost Visible-Light Spectrophotometer
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   A low-cost, RGB LED-based visible-light spectrophotometer was designed to measure dyes concentration. Dyes are widely used as indicators or coloring agents in different applications and knowing their concentration is an essential part for many studies. The proposed spectrophotometer provides many functionalities that clones the traditional expensive spectrophotometers for a budged price under $50. It was aimed to provide a versatile tool for instructors and educators to teach their students the fundamental concepts behind spectrophotometry. Malachite green, methyl red, and methyl orange dyes were chosen to be good samples to show the integrity of the proposed spectrophotometer in terms of accuracy, repeatability, and sensitivity as

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Publication Date
Mon Jan 01 2024
Journal Name
Lecture Notes In Networks And Systems
Using Machine Learning to Control Congestion in SDN: A Review
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Publication Date
Mon Jun 01 2020
Journal Name
Journal Of Engineering
The The Use of Copper and Aluminum Electrodes for Energy Production in a Microbial Fuel Cell
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Microbial fuel cell is a device that uses the microorganism metabolism for the production of electricity under specific operating conditions. Double chamber microbial fuel cell was tested for the use of two cheap electrode materials copper and aluminum for the production of electricity under different operating conditions. The investigated conditions were concentration of microorganism (yeast) (0.5- 2 g/l), solutions temperature (33-45 oC) and concentration of glucose as a substrate (1.5- 6 g/l). The results demonstrated that copper electrode exhibit good performance while the performance of aluminum is poor. The electricity is generated with and without the addition of substrate. Addition of glucose substrate

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Publication Date
Thu Jan 02 2020
Journal Name
Journal Of The College Of Languages (jcl)
The newspaper is a field for the use of phraseologism: Газета как сфера использованиея фразеологических единиц
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Idiomatic expressions in Russian journalism make one important borrowed means for making a dialogue with the receiver's intellect in so far as it has the distinct feature of  having clarity and exactness of meaning. The meaning is seen as a shortcut for covering a series of concepts and details so as to arrive at the intended meaning. This is done by stimulating the reader by the use of certain clear idioms. The use of such idioms in a journalistic text is not for a linguistic purpose only, but it is a cultural and social phenomenon reflecting the type of current changes in the society and it aims at discoursing with the reader's mind. This paper is a practi

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Publication Date
Mon Dec 30 2013
Journal Name
Iraqi Journal Of Chemical And Petroleum Engineering
Mass Transfer Enhancement Using Extensions as Turbulence Promoters
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Mass transfer was studied using a rotating cylinder electrode with different lengths of legs acting as turbulence promoters. Two types of rotating cylinder ,made of brass, were examined : an enhanced cylinder one, with four rectangular extensions 10 mm long, 10 mm wide, and 1mm thick, and an enhanced cylinder two with four longitudes 30 mm long,10 mm wide, and 1mm thick. The best performance was obtained for enhanced cylinder two at low rotation speeds while enhanced cylinder one was realized at high rotation speeds. The mass transfer enhancement as compared with a normal rotating cylinder electrode, devoid of promoters, is 53% or 58% higher. The enhancement percentage decreased as rotation speeds increased further, since, seemingly, ful

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Publication Date
Fri Jan 01 2021
Journal Name
Aip Conference Proceedings
A study of the safety and security conditions followed in the X-ray clinics in the Al-Amiriya-Baghdad
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Publication Date
Wed May 01 2024
Journal Name
Journal Of Madenat Alelem College
Study 1,4- Naphthoquinone Derivative and Biological Activity: A Review
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In this work, we focused on studying 1,4-naphthoquinones and their derivatives, and knowing the methods of preparing them using different auxiliary agents and forming derivatives containing heterocyclic rings, active groups and saturated rings containing heterogeneous elements . In addition, due to their strong antibacterial, antifungal and anticancer activity, 1,4-naphthoquinone compounds biological importance and are considered a source of various pharmaceutical compounds.

Publication Date
Sun Dec 22 2024
Journal Name
Journal Of Petroleum Research And Studies
Optimizing Well Placement with Genetic Algorithms: A Case Study
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Maximizing the net present value (NPV) of oil field development is heavily dependent on optimizing well placement. The traditional approach entails the use of expert intuition to design well configurations and locations, followed by economic analysis and reservoir simulation to determine the most effective plan. However, this approach often proves inadequate due to the complexity and nonlinearity of reservoirs. In recent years, computational techniques have been developed to optimize well placement by defining decision variables (such as well coordinates), objective functions (such as NPV or cumulative oil production), and constraints. This paper presents a study on the use of genetic algorithms for well placement optimization, a ty

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