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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
Fri Oct 20 2023
Journal Name
Al-ameed Journal For Medical Research And Health Sciences
Perceptions of Nursing Students about COVID-19 Transmission: A Multi University Study
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Publication Date
Sun Feb 20 2022
Journal Name
Papers In Physics
Electronic and optical properties of nickel-doped ceria: A computational modelling study
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Cerium oxide (CeO2), or ceria, has gained increasing interest owing to its excellent catalytic applications. Under the framework of density functional theory (DFT), this contribution demonstrates the eect that introducing the element nickel (Ni) into the ceria lattice has on its electronic, structural, and optical characteristics. Electronic density of states (DOSs) analysis shows that Ni integration leads to a shrinkage of Ce 4f states and improvement of Ni 3d states in the bottom of the conduction band. Furthermore, the calculated optical absorption spectra of an Ni-doped CeO2 system shifts towards longer visible light and infrared regions. Results indicate that Ni-doping a CeO2 system would result in a decrease of the band gap. Finally,

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Publication Date
Thu Jun 09 2022
Journal Name
Iraqi Journal Of Pharmaceutical Sciences ( P-issn 1683 - 3597 E-issn 2521 - 3512)
Safety Profile of Biological Drugs in Clinical Practice: A Retrospective Pharmacovigilance Study
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Biological drugs have an active substance that is made by a living organism or derived from a living organism. They are one of the important therapy options used in a wide range of diseases especially life-threatening diseases. Biological therapy opens new opportunities for treating different diseases for which drug therapy is minimal, but they have considerable differences in the safety consequences in comparison with non-biological drugs. The aim of the current study was to assess the post-marketing safety profile of biological drugs used in Iraqi hospitals by the analysis of the reported adverse drug reactions regarding their severity, seriousness, preventability, expectedness, and outcome. It is a retrospective study of the individu

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Publication Date
Tue Sep 09 2025
Journal Name
Wasit Journal Of Sports Sciences
The impact of the Needham model on learning the skills of dribbling and handling in football for students
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Publication Date
Wed Jun 30 2021
Journal Name
Journal Of Economics And Administrative Sciences
The role of strategic memory in the successful use of the COSO model for auditing human resource management
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The main purpose of the research is to diagnose the importance of the role that strategic memory plays with its three variables (content, structure, and processes) in helping the human resource department to use the COSO model with its five components (culture and governance, strategy and objectives, performance, communications and information, and feedback) in auditing activities and tasks Her own. As the research problem emphasized the existence of a lack of cognitive perception, of the importance of strategic memory, and the investment of its components in the rationalization of the application of the COSO model. and therefore it can be emphasized that the importance of the research is to provide treatments for problems relate

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Publication Date
Mon Aug 31 2020
Journal Name
Journal Of Research In Medical And Dental Science
The Effect of Super Oxidized Water Mouthwash on the Level of IL 1? in Gingival Crevicular Fluid for Patients with Gingivitis Randomized Clinical Trial
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Background: One of the most predominant periodontal diseases is the plaque induced gingivitis. For the past 20 years, super-oxidized solutions have be..

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Publication Date
Mon Mar 23 2020
Journal Name
Journal Of Engineering
Drag Reduction Using Passive Methods on KIA PRIDE Car Model
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An experimental study on a KIA pride (SAIPA 131) car model with scale of 1:14 in the wind tunnel was made beside the real car tests. Some of the modifications to passive flow control which are (vortex generator, spoiler and slice diffuser) were added to the car to reduce the drag force which its undesirable characteristic that increase fuel consumption and exhaust toxic gases. Two types of calculations were used to determine the drag force acting on the car body. Firstly, is by the integrating the values of pressure recorded along the pressure taps (for the wind tunnel and the real car testing), secondly, is by using one component balance device (wind tunnel testing) to measure the force. The results show that, the avera

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Publication Date
Fri Jan 01 2021
Journal Name
Journal Of Economics And Administrative Sciences
Predicting Social Security Fund compensation in Iraq using ARMAX Model
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Time series have gained great importance and have been applied in a manner in the economic, financial, health and social fields and used in the analysis through studying the changes and forecasting the future of the phenomenon. One of the most important models of the black box is the "ARMAX" model, which is a mixed model consisting of self-regression with moving averages with external inputs. It consists of several stages, namely determining the rank of the model and the process of estimating the parameters of the model and then the prediction process to know the amount of compensation granted to workers in the future in order to fulfil the future obligations of the Fund. , And using the regular least squares method and the frequ

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Publication Date
Sat Oct 20 2018
Journal Name
Journal Of Economics And Administrative Sciences
Bayesian Tobit Quantile Regression Model Using Four Level Prior Distributions
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Abstract:

      In this research we discussed the parameter estimation and variable selection in Tobit quantile regression model in present of multicollinearity problem. We used elastic net technique as an important technique for dealing with both multicollinearity and variable selection. Depending on the data we proposed Bayesian Tobit hierarchical model with four level prior distributions . We assumed both tuning parameter are random variable and estimated them with the other unknown parameter in the model .Simulation study was used for explain the efficiency of the proposed method and then we compared our approach with (Alhamzwi 2014 & standard QR) .The result illustrated that our approach

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Publication Date
Sun Jul 01 2012
Journal Name
Journal Of Computer Science
Peer-to-Peer Video Conferencing Using Hybrid Content Distribution Model
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