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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 Jun 10 2010
Journal Name
Iraqi Journal Of Laser
Experimental Investigation of a Laser Wireless Video Communication System Using Intensity Modulated /Direct Detection Technique
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In this work Laser wireless video communication system using intensity modualtion direct
detection IM/DD over a 1 km range between transmitter and receiver is experimentally investigated and
demonstrated. Beam expander and beam collimeter were implemented to collimete laser beam at the
transmitter and focus this beam at the receiver respectively. The results show that IM/DD communication
sysatem using laser diode is quite attractive for transmitting video signal. In this work signal to noise
ratio (S/N) higher than 20 dB is achieved in this work.

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Publication Date
Tue Oct 26 2021
Journal Name
Series On Biomechanics
Monitoring and analysis of plantar pressure map and foot motions using a wearable sensing system
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Publication Date
Thu Jun 01 2023
Journal Name
Baghdad Science Journal
Design and construction of anair pollution detection system using a laser beam and absorption spectroscopy
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Air pollution is one of the important problems facing Iraq. Air pollution is the result of uncontrolled emissions from factories, car exhaust electric generators, and oil refineries and often reaches unacceptable limits by international standards. These pollutants can greatly affect human health and regular population activities. For this reason, there is an urgent need for effective devices to monitor the molecular concentration of air pollutants in cities and urban areas. In this research, an optical system has been built consisting of aHelium-Neonlaser,5mWand at 632.8 nm, a glass cell with a defined size, and a power meter(Gentec-E-model: uno) where a scattering of the laser beam occurs due to air pollution. Two pollutants were examin

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Publication Date
Sat Sep 30 2023
Journal Name
Iraqi Journal Of Chemical And Petroleum Engineering
Removal of Lead Ions from Wastewater by using a Local Adsorbent from Charring Tea Wastes
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   Adsorption of lead ions from wastewater by native agricultural waste, precisely tea waste. After the activation and carbonization of tea waste, there was a substantial improvement in surface area and other physical characteristics which include density, bulk density, and porosity. FTIR analysis indicates that the functional groups in tea waste adsorbent are aromatic and carboxylic. It can be concluded that the tea waste could be a good sorbent for the removal of Lead ions from wastewater. Different dosages of the adsorbents were used in the batch studies. A random series of experiments indicated a removal degree efficiency of lead reaching (95 %) at 5 ppm optimum concentration, with adsorbents R2 =97.75% for tea. Three mo

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Publication Date
Tue Aug 01 2023
Journal Name
Baghdad Science Journal
Performance Evaluation of a Triple Concentric Tube Heat Exchanger Using Deionized Water and Oil-40
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This study examines experimentally the performance of a horizontal triple concentric tube heat exchanger TCTHE made of copper metal using water as cooling fluid and oil-40 as hot fluid. Hot fluid enters the inner annular tube of the TCTHE in a direction at a temperature of 50, 60 and 70 oC and a flow rate of 20 l/hr. On the other hand, the cooling fluid enters the inner tube and the outer annular tube in the reverse direction (counter current flow) at a temperature of 25 oC and flow rates of 10, 15, 20, 25, 30 and 35 l/hr. The TCTHE is composed of three copper tubes with outer diameters of 34.925 mm, 22.25 mm, and 9.525 mm, and thicknesses of 1.27 mm, 1.143 mm, and 0.762 mm, respectively. TCTHE tube's length was 670

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Publication Date
Fri Jan 31 2025
Journal Name
Open Veterinary Journal
<b>Histopathological effects of repeated 14-day administration of rizatriptan benzoate in a nitroglycerin-induced migraine rabbit model</b>
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Background: Migraine is one of multiple attack neurological conditions that causes moderate to severe headaches with no defined pathophysiology and few animal models. Aim: Establishing an animal model that reproduces migraine-like action is important in medical research to identify the mechanism underlying this disorder. Additionally, it facilitates the availability and reliability of new models that may act as human surrogate models. Method: Rabbits were divided into four groups. Negative group, migraine group, rizatriptan- nitroglycerin group, and rizatriptan group. The frequency of head scratching and the histopathological changes in the brain, liver, kidney, and heart for groups were evaluated in all groups. Results: T

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Publication Date
Sun May 23 2021
Journal Name
Egyptian Journal Of Chemistry
Thermodynamic study of adsorption of a mixture of Nolvadex and nanoparticle ferric oxide that prepared on the surface of activated charcoal
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Publication Date
Sun Nov 24 2024
Journal Name
Polymer-plastics Technology And Materials
Li <sub>2</sub> CO <sub>3</sub> as a Modifier for PVA/PVP/PEG Blend Polymer Electrolytes: Effects on Structural Integrity, Electrical Performance, Thermal Behavior and Optical Properties
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Publication Date
Thu Jan 02 2025
Journal Name
Ibn Al-haitham Journal For Pure And Applied Sciences
Morphological and Molecular studies of Acanthobra marmid Heckel, 1843 (Piscies, Cypriniformes, Leuciscidae) from the Middle of Iraq
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Leuciscidae species are the abundant and widely distributed fish species in Iraq's inland waters. They are complex species, and morphology makes them difficult to identify. Molecular analysis achieved and confirmed the morphological characters. Twenty specimens of Acanthobrama marmid were collected from two localities at Tigris River, in the middle of Iraq; 15 specimens from the Al-Zubaydia sub-district and five specimens from Al-Tharthar Lake. We used the mitochondrial DNA cytochrome b (cytb) gene to sequence the DNA of A. marmid. The following analysis are compared the sequences with those of other fish genera and species found in the Gene Bank. The barcoding result (DNA sequencing) in fishes found in the same family (Leuciscidae) showed

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Publication Date
Wed Jun 01 2016
Journal Name
Journal Of Engineering
Management Model for Evaluation and Selection of Engineering Equipment Suppliers for Construction Projects in Iraq
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Engineering equipment is essential part in the construction project and usually manufactured with long lead times, large costs and special engineering requirements. Construction manager targets that equipment to be delivered in the site need date with the right quantity, appropriate cost and required quality, and this entails an efficient supplier can satisfy these targets. Selection of engineering equipment supplier is a crucial managerial process .it requires evaluation of multiple suppliers according to multiple criteria. This process is usually performed manually and based on just limited evaluation criteria, so better alternatives may be neglected. Three stages of survey comprised number of public a

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