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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 Oct 29 2025
Journal Name
The Indonesian Biomedical Journal
Genotype Combination of rs1042044 and rs6458093 in GLP-1R as A Genetic Risk for Osteoporosis in Postmenopausal Iraqi Women
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BACKGROUND: Many genetic factors are known to be related to osteoporosis, and currently the role of the glucagon-like peptide-1 receptor (GLP-1R) gene in bone health has been studied intensively. Some variation of this gene, such as rs1042044 and rs6458093, are known to be linked to metabolic diseases and lower bone mineral density, however their specific contribution to osteoporosis remains largely unexplored. Therefore, this study was conducted to investigate the combined genotypic effect of rs1042044 and rs6458093 as a genetic risk factor for osteoporosis in postmenopausal Iraqi women.METHODS: Blood samples from 75 osteoporosis patients and 75 healthy controls, aged 45-85, were collected. DNA was extracted, and a region of GLP-1R

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Publication Date
Sun Jun 05 2016
Journal Name
Baghdad Science Journal
Local wheat peel as a solid surface to remove Azure B dye from aqueous solution:Equilibrium isotherms and thermodynamic study
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In this research local wheat peel was used as an adsorbent surface for removal of Azure B (AB) dye from the aqueous solution. The adsorption process was performed at different experimental parameters, equilibrium time, temperature, ionic strength and solution pH. The isotherms of adsorption are of H-type as compared with Giles curves and the adsorption data were coincide with Freundlich equation. The adsorption kinetic data were analyzed using pseudo- first and second order kinetic models. The effect of temperature was studied and the amount of dye adsorbed was found to increase with the increasing of temperature from 25 to 50 oC. The values of thermodynamic functions like enthalpy and entropy have been estimated. The quantity of adso

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Publication Date
Mon Sep 01 2014
Journal Name
Al-khwarizmi Engineering Journal
Trajectory Tracking Control for a Wheeled Mobile Robot Using Fractional Order PIaDb Controller
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Nowadays, Wheeled Mobile Robots (WMRs) have found many applications as industry, transportation, inspection, and other fields. Therefore, the trajectory tracking control of the nonholonomic wheeled mobile robots have an important problem. This work focus on the application of model-based on Fractional Order  PIaDb (FOPID) controller for trajectory tracking problem. The control algorithm based on the errors in postures of mobile robot which feed to FOPID controller to generate correction signals that transport to  torque for each driven wheel, and by means of dynamics model of mobile robot these torques used to compute the linear and angular speed to reach the desired pose. In this work a dynamics model of

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Publication Date
Fri Jan 01 2016
Journal Name
Machine Learning And Data Mining In Pattern Recognition
A New Strategy for Case-Based Reasoning Retrieval Using Classification Based on Association
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Publication Date
Thu Feb 01 2018
Journal Name
Journal Of Engineering
Using a New Modification on Wind Turbine Ventilator for Improving Indoor Air Quality
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This paper describes a newly modified wind turbine ventilator that can achieve highly efficient ventilation. The new modification on the conventional wind turbine ventilator system may be achieved by adding a Savonius wind turbine above the conventional turbine to make it work more efficiently and help spinning faster. Three models of the Savonius wind turbine with 2, 3, and 4 blades' semicircular arcs are proposed to be placed above the conventional turbine of wind ventilator to build a hybrid ventilation turbine. A prototype of room model has been constructed and the hybrid turbine is placed on the head of the room roof. Performance's tests for the hybrid turbine with a different number of blades and different values o

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Publication Date
Tue Mar 10 2020
Journal Name
Journal Of Research On The Lepidoptera
Study of the Association of Glucagon like Peptide-1 Receptors (GLP-1R) Gene Polymorphism and GLP-1 Hormone Levels in Type 2 Diabetics Patients in Iraq
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Publication Date
Sun Jan 25 2026
Journal Name
Journal Of Baghdad College Of Dentistry
A study to compare the cleaning efficiency of different irrigation systems for macro debris removal in instrumented canals (An in vitro study)
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Background: Irrigation of the canal system permits removal of residual tissue in the canal anatomy that cannot be reached by instrumentation of the main canals so the aim of this study was to compare and evaluate the efficiency of conventional irrigation system, endoactivator sonic irrigation system,P5 Newtron Satelec passive ultrasonic irrigation and Endovac irrigation system in removing of dentin debris at three levels of root canals and to compare the percentage of dentin debris among the three levels for each irrigation system. Materials and methods: Forty extracted premolars with approximately straight single root canals were randomly distributed into 4 tested groups of 10 teeth each. All canals were prepared with Protaper Universal ha

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Publication Date
Fri Sep 30 2022
Journal Name
Journal Of Economics And Administrative Sciences
Robust Estimation OF The Partial Regression Model Using Wavelet Thresholding
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            Semi-parametric regression models have been studied in a variety of applications and scientific fields due to their high flexibility in dealing with data that has problems, as they are characterized by the ease of interpretation of the parameter part while retaining the flexibility of the non-parametric part. The response variable or explanatory variables can have outliers, and the OLS approach have the sensitivity to outliers. To address this issue, robust (resistance) methods were used, which are less sensitive in the presence of outlier values in the data. This study aims to estimate the partial regression model using the robust estimation method with the wavel

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Publication Date
Mon Oct 03 2022
Journal Name
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THE SEEDS OF ECOCRITICISM: A STUDY IN THE POETRY OF JOHN CLARE
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Nowadays, the worldwide issue of the environment occupies the minds not only of ecological experts and politicians but also is addressed in cultural fields and literature in particular. The conceptualization of ecocriticism, whether in the ecological field or cultural studies, has come as a response to the increasing public awareness of numerous environmental crises. Most ecocritics regard John Clare (1793-1864) as a 'proto-ecological' British poet since his poetry incorporates ecological issues which were not then categorized as they are now. The study offers a precise illustration of ecocriticism coupled with a number of the most significant ecological concepts proven in selected poems by John Clare. The ecocritical reading of Clare's po

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Publication Date
Sat Oct 01 2022
Journal Name
Case Studies In Thermal Engineering
Comparative assessment of the performance and combustion attributes of a free piston linear generator fuelled with CNG and CNG-CO2
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