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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 Dec 31 2017
Journal Name
Iraqi Journal Of Chemical And Petroleum Engineering
Study and Analysis of Concentric Shell and Double Tube Heat Exchanger Using Tio2 Nanofluid
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In this paper, nanofluid of TiO2/water of concentrations of 0.002% and 0.004% volume was used. This nanofluid was flowing through heat exchanger of shell and concentric double tubes with counter current flow to the hot oil. The thermal conductivity of nanofluid is enhanced with increasing concentrations of the TiO2, this increment was by 19% and 16.5% for 0.004% and 0.002% volume respectively relative to the base fluid (water). Also the heat transfer coefficient of the nanofluid is increased as Reynold's number and nanofluid concentrations increased too. The heat transfer coefficient is increased by 66% and 49% for 0.004% and 0.002% volume respectively relative to the base fluid. This study showed that the friction

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Publication Date
Thu Dec 28 2017
Journal Name
Al-khwarizmi Engineering Journal
Simulation Study of Mass Transfer Coefficient in Slurry Bubble Column Reactor Using Neural Network
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The objective of this study was to develop neural network algorithm, (Multilayer Perceptron), based correlations for the prediction overall volumetric mass-transfer coefficient (kLa), in slurry bubble column for gas-liquid-solid systems. The Multilayer Perceptron is a novel technique based on the feature generation approach using back propagation neural network. Measurements of overall volumetric mass transfer coefficient were made with the air - Water, air - Glycerin and air - Alcohol systems as the liquid phase in bubble column of 0.15 m diameter. For operation with gas velocity in the range 0-20 cm/sec, the overall volumetric mass transfer coefficient was found to decrease w

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Publication Date
Thu Oct 31 2013
Journal Name
Al-khwarizmi Engineering Journal
An Investigation Study of Thinning Distribution in Single Point Incremental Forming Using FEM Analysis
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Single Point Incremental Forming (SPIF) is a forming technique of sheet material based on layered manufacturing principles. The sheet part is locally deformed through horizontal slices. The moving locus of forming tool (called as toolpath) in these slices constructed to the finished part was performed by the CNC technology. The toolpath was created directly from CAD model of final product. The forming tool is a Ball-end forming tool, which was moved along the toolpath while the edges of sheet material were clamped rigidly on fixture.

This paper presented an investigation study of thinning distribution of a conical shapes carried out by incremental forming and the validation of finite element method to evaluate the limits of the p

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Publication Date
Tue May 01 2018
Journal Name
Journal Of Physics: Conference Series
Study of vegetation cover distribution using DVI, PVI, WDVI indices with 2D-space plot
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Publication Date
Thu Nov 02 2023
Journal Name
Journal Of Engineering
Numerical Study of Piled Raft Foundation in Non-Homogeneous Soil Using Finite Element Method
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This paper analyzes a piled-raft foundation on non-homogeneous soils with variable layer depth percentages. The present work aims to perform a three-dimensional finite element analysis of a piled-raft foundation subjected to vertical load using the PLAXIS 3D software. Parametric analysis was carried out to determine the effect of soil type and initial layer thickness. The parametric study showed that increasing the relative density from 30 % to 80 % of the upper sand layer and the thickness of the first layer has led to an increase in the ultimate load and a decrease in the settlement of piled raft foundations for the cases of sand over weak soil.  In clay over weak soil, the ultimate load of the piled raft foundation w

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Publication Date
Tue Jan 01 2019
Journal Name
Opcion, Año
The effect of the -Zahorik- model on acquiring grammatical concepts among students of the College of Administration and Economics/University of Baghdad
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Publication Date
Tue Nov 01 2016
Journal Name
Journal Of Economics And Administrative Sciences
Analysis of The Effect of The Administration of Communications Towers in The Selling Prices of Residential Real estate )New University Village Model(
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Abstract                          

 Should be the goal of Government controls, including environmental controls and safety laws to protect citizens from the harmful effects of negative secreted by human's additions and changes in the environment. and perhaps the protection aspects of the protection of citizens from the adverse effects of communications towers, including those produced by towers of health effects. The people the right to choose the nature of the physical environment, which should not be imposed on them by others. Communications towers are one of the main problems that have been

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Publication Date
Tue May 26 2026
Journal Name
Revista Iberoamericana De Psicología Del Ejercicio Y El Deporte, Issn 1886-8576, Vol. 17, Nº. 1, 2022, Págs. 33-35
The Effect of Using Therapeutic Physical Exercises Accompanying Physical Therapy in the Rehabilitation of Lumbar Disc Herniation for Football Players Aged (25-25)
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Autorías: Imad Kadhim Khlaif, Talib Faisal Shnawa. Localización: Revista iberoamericana de psicología del ejercicio y el deporte. Nº. 1, 2022. Artículo de Revista en Dialnet.

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Publication Date
Tue May 26 2026
Journal Name
Journal Of Baghdad College Of Dentistry
Bone density determination for the maxilla and the mandible in different age groups by using computerized tomography (Part I)
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Background: Mini implant stability is primarily related to local bone density; no studies have evaluated bone density related to mini implant placement for orthodontic anchorage between different age groups in the maxilla and the mandible. The present research aims to evaluate side, gender, age, and regional differences in bone density of the alveolar bone at various orthodontic implant sites. Materials and method: Fifty three individuals who were divided into two groups according to their age into: group I (ages 16-20 years) and group II (ages 21-29 years) had subjected to clinical examination, then 64-multislice computed tomography scan data were evaluated and bone density was measured in Hounsfield unit at 102 points (51 in the maxilla

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Publication Date
Mon Jan 02 2023
Journal Name
Pakistan Heart Jornal
The Effect of the Strategy of Differentiated Education According to the Auditory Learning Style by Using Assistance in Learning the Back Kick (T-Chagi) for the Young Players of …
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