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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 15 2017
Journal Name
International Journal Of Computer Applications
Assessment of Annual Wind Energy Potential at Three Sites in Iraq for Wind Energy Applications
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Assessment of annual wind energy potential for three selected sites in Iraq has been analyzed in the present work. The wind velocities data from August 2014 to July 2015 were collected from the website of Weather Underground Organization (WUO) at stations elevation (35m, 32m, and 17m) for Baghdad, Najaf, and Kut Al-Hai respectively. Extrapolation of stations elevation and wind velocities was used to estimate wind velocities at (60m, 90m, and 120m). The objectives are to analyze the wind speed data and assess the wind energy potential for wind energy applications. Computer code for MATLAB software has been developed to solve the mathematical model. The results are presented as a monthly and annual average for wind velocities, standard deviat

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Publication Date
Sat Dec 01 2018
Journal Name
Journal Of Economics And Administrative Sciences
Compare Estimate Methods of Parameter to Scheffʼe Mixture Model By Using Generalized Inverse and The Stepwise Regression procedure for Treatment Multicollinearity Problem
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Mixture experiments are response variables based on the proportions of component for this mixture. In our research we will compare the scheffʼe model with the kronecker model for the mixture experiments, especially when the experimental area is restricted.

     Because of the experience of the mixture of high correlation problem and the problem of multicollinearity between the explanatory variables, which has an effect on the calculation of the Fisher information matrix of the regression model.

     to estimate the parameters of the mixture model, we used the (generalized inverse ) And the Stepwise Regression procedure

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Publication Date
Tue Jun 01 2021
Journal Name
Baghdad Science Journal
Three-Dimensional Nonlinear Integral Operator with the Modelling of Majorant Function
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In this paper, the process for finding an approximate solution of nonlinear three-dimensional (3D) Volterra type integral operator equation (N3D-VIOE) in R3 is introduced. The modelling of the majorant function (MF) with the modified Newton method (MNM) is employed to convert N3D-VIOE to the linear 3D Volterra type integral operator equation (L3D-VIOE). The method of trapezoidal rule (TR) and collocation points are utilized to determine the approximate solution of L3D-VIOE by dealing with the linear form of the algebraic system. The existence of the approximate solution and its uniqueness are proved, and illustrative examples are provided to show the accuracy and efficiency of the model.

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Publication Date
Sun Jul 01 2018
Journal Name
Journal Of Global Pharma Technology
Preparation, Characterization and Biological Activity of New Derivatives of 3-Cyclic Oxazepine, 3-Cyclic Lactam and 3- Aminomethyl Imidazo (1, 2-a) Benzthiazol
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In this work a series of fourteen new compounds were synthesized. Compound [1] was formed from the reaction of 2-aminobenzothiazole and p-bromophenacyl bromide. Aldehyde group [2] was obtained from the reaction of compound [1] with pocl3 in presence of DMF and CHCl3 .After that shiff bases have been synthesized from the reaction of compound [2] with different aromatic amine to give new shiff bases [3- 5]. These new shiff bases have been reduced to their corresponding amine [6-8] by means of sodium borohydride. Then reaction of shiff bases [3-5] with phenyl isocyanate gives 3-cyclic lactam derivatives [9-11]. 3-cyclic Oxazepine derivatives [12-14] were obtained by reaction of shiff bases [3-5] with succinic anhydride. These new formed co

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Publication Date
Wed Mar 01 2023
Journal Name
Journal Of Engineering
Effect of a Parked Car Orientation on a Temperature Distribution and Cooling Load Calculation: Experimental Study
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When a vehicle is left parked in the sun for an extended period, the gathered heat causes damage to several interiors within the cabin and causes discomfort for people and animals left inside the car. In the present work, the effect of the orientation of a parked white minibus on temperature distribution and cooling load calculation is studied experimentally in an open environment. Two different cases were studied facing south and facing east. For several hours, the temperature inside the car cabin had been monitored and measured at five separate locations. The cooling load calculations are carried out based on the experimental measurements. The results show that the overheating of parked cars always happens as a result

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Publication Date
Sun Jan 01 2023
Journal Name
The Egyptian Journal Of Hospital Medicine
The Effect of a Program Using Auxiliary Tools to Improve The Long Passing Skill of Football Juniors
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Publication Date
Mon Jul 21 2014
Journal Name
Sensors
Reduction of the Dimensionality of the EEG Channels during Scoliosis Correction Surgeries Using a Wavelet Decomposition Technique
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This paper presents a comparison between the electroencephalogram (EEG) channels during scoliosis correction surgeries. Surgeons use many hand tools and electronic devices that directly affect the EEG channels. These noises do not affect the EEG channels uniformly. This research provides a complete system to find the least affected channel by the noise. The presented system consists of five stages: filtering, wavelet decomposing (Level 4), processing the signal bands using four different criteria (mean, energy, entropy and standard deviation), finding the useful channel according to the criteria’s value and, finally, generating a combinational signal from Channels 1 and 2. Experimentally, two channels of EEG data were recorded fro

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Publication Date
Sat Jan 01 2022
Journal Name
Proceeding Of The 1st International Conference On Advanced Research In Pure And Applied Science (icarpas2021): Third Annual Conference Of Al-muthanna University/college Of Science
Efficient approach for solving high order (2+1)D-differential equation
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Publication Date
Sat Sep 24 2022
Journal Name
Arab World English Journal
A Critical Stylistic Study of the Notion of Women Empowerment in the Mona Lisa Smile (2003)
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This study unveils the ideologies of women empowerment encoded in the Mona Lisa Smile movie (2003). It reveals how the stereotypical image of women born only to be wives and do the duties of upbringing and housework is challenged. Katherine Ann Watson (Julia Roberts), the main character in the movie, wants to make a difference in the next generation of women. She rejects the imposed traditional ideologies. Linguistically, she opposes conventional thinking and seeks to persuade her students that life is about more than getting married. The primary focus of this study is to examine and clarify how the characters’ linguistic choices convey their ideologies concerning the notion of women empowerment. To do this, the researchers apply

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Publication Date
Sat Sep 30 2023
Journal Name
Journal Of The College Of Education For Women
The Problem of Paradox and its Manifestations: A Study in the Titles of Najm Wali's Novels
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The irony pushes us to inquire about what is in the text of contradiction, irony, suspense, and other acts of paradox, as well as a departure from what is logical, or familiar, that attracts the attention of the addressee, and this is what drives us to introspect the text and interrogate it in order to get to know the intended product of the text or its real or metaphorical intent. On the other hand, the irony is more in the literary text than in the scientific texts. Therefore, critics add the word literature to it in their definition.

 As it is represented by the paradox, we will seek to study the paradox of the title and the problematic that it may pose as the beginning of the text, and i

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