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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 Jul 01 2012
Journal Name
Journal Of Computer Science
Peer-to-Peer Video Conferencing Using Hybrid Content Distribution Model
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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
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
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 Feb 15 2026
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 average drag estimated on

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Publication Date
Sun Dec 02 2018
Journal Name
Journal Of The College Of Education For Women
The Role of Local Satellite Channels in the formation of knowledge and trends of the Iraqi Public Towards Terrorism: A Field Study
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Terrorism is a global phenomenon that engulfs most regions of the world to varying degrees. Media outlets are aware of the many incidents of violence and terrorism that have increased in recent times. The differences between the size of the phenomenon in different societies are the causes and severity of the phenomenon. On the role of local satellite channels in shaping the knowledge and trends of the Iraqi public towards the events of terrorism, in light of the assumptions of reliance on the media. The importance of this study is that it assesses the role of local satellite channels in the formation of knowledge and trends The study seeks to know the extent of exposure of the Iraqi public to local satellite channels, and to reveal the e

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Publication Date
Sun Aug 31 2025
Journal Name
Journal Of Science In Medicine And Life
Serum Endothelial Specific Molecule 1(EMS 1) and Uric Acid Levels in Severe Preeclampsia
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Publication Date
Sun Sep 03 2017
Journal Name
Baghdad Science Journal
Kinetic and Mechanistic Studies for the Gas-phase Reaction of Ozone with 2, 3-Dimethyl-2-Butene and 1, 3-Butadiene
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The reactions of ozone with 2,3-Dimethyl-2-Butene (CH3)2C=C(CH3)2 and 1,3-Butadiene CH2=CHCH=CH2 have been investigated under atmospheric conditions at 298±3K in air using both relative and absolute rate techniques, and the measured rate coefficients are found to be in good agreement in both techniques used. The obtained results show the addition of ozone to the double bond in these compounds and how it acts as function of the methyl group substituent situated on the double bond. The yields of all the main products have been determined using FTIR and GC-FID and the product studies of these reactions establish a very good idea for the decomposition pathways for the primary formed compounds (ozonides) and give a good information for the effe

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Publication Date
Mon Apr 04 2011
Journal Name
Ibn Al-haitham J.for Pure &appl.sci
Anew Spectrophotometric Method For The Determination of La (III) With 3-Hydroxy -4-(2-hydroxy –Phenyl azo)Naphthalene -1-Sulfonic Acid
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A simple, rapid and sensitive spectrophotometric method has been proposed for the determination of La (III) using 3-hydroxy -4-(2-hydroxy-phenyl azo) naphthalene -1- sulfonic acid as a chromogenic reagent. This method is based on the formation of a red-pink colored complex, upon the reaction of La(III) with the reagent in an alkaline medium (pH= 9.50), having a maximum absorbance at 459 nm. Beer's law is valid in the concentration range 0.512 µg.ml-1 with a Sandell's sensitivity value of 0.0188 µg.cm-2 and molar absorptivity of 7376.12 L.mol-1.cm-1. The stoichiometric composition of the chelate is 1:3. The effect of the presence of different cations as interferants in the determination of La(III) under the given optimum conditions wer

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Publication Date
Sun Jan 01 2017
Journal Name
International Journal Of Advanced Computer Science And Applications
A Proposed Framework to Investigate the User Acceptance of Personal Health Records in Malaysia using UTAUT2 and PMT
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