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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
Sat Jul 30 2022
Journal Name
Global Academic Journal Of Linguistics And Literature
A Critical Stylistic Analysis of Transcultural Identity in Lyer’s The Global Soul (2001) Using the Tool of Negation
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This study is intended to examine the concept of transcultural identity in the travel book The Global Soul: Jet Lag, Shopping Malls, and the Search for Home by (Iyer, 2001). Jeffries’ model of critical stylistics (2010) (henceforth, CS) has been selected to analyze the book. To be more specific, Negation is selected to analyze the concept under study. As such, the study aims at finding out how Negation is used to portray ideological meanings representing the concept of transcultural identity in one non-fictional travel book; and finding out the ideologies related to the concept analyzed. The analysis of the data shows that Negation is a suitable analytical tool to reach the ideational meaning of the text towards the concept of tra

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Publication Date
Mon Mar 01 2010
Journal Name
Journal Of Economics And Administrative Sciences
Pais estimator for the reliability function of the Pareto model of Type I failure
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In this paper an estimator of reliability function for the pareto dist. Of the first kind has been derived and then a simulation approach by Monte-Calro method was made to compare the Bayers estimator of reliability function and the maximum likelihood estimator for this function. It has been found that the Bayes. estimator was better than maximum likelihood estimator for all sample sizes using Integral mean square error(IMSE).

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Publication Date
Sat Jul 01 2017
Journal Name
Journal Of Biological Chemistry
Functional and phylogenetic evidence of a bacterial origin for the first enzyme in sphingolipid biosynthesis in a phylum of eukaryotic protozoan parasites
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Publication Date
Sun Jan 01 2023
Journal Name
Chemical Engineering And Processing - Process Intensification
Optimization of a combined electrocoagulation-electro-oxidation process for the treatment of Al-Basra Majnoon Oil field wastewater: Adopting a new strategy
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Publication Date
Sun Jan 01 2023
Journal Name
Chemical Engineering And Processing - Process Intensification
Optimization of a combined electrocoagulation-electro-oxidation process for the treatment of Al-Basra Majnoon Oil field wastewater: Adopting a new strategy
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The performance of a synergistic combination of electrocoagulation (EC) and electro-oxidation (EO) for oilfield wastewater treatment has been studied. The effect of operative variables such as current density, pH, and electrolyte concentration on the reduction of chemical oxygen demand (COD) was studied and optimized based on Response Surface Methodology (RSM). The results showed that the current density had the highest impact on the COD removal with a contribution of 64.07% while pH, NaCl addition and other interactions affects account for only 34.67%. The optimized operating parameters were a current density of 26.77 mA/cm2 and a pH of 7.6 with no addition of NaCl which results in a COD removal efficiency of 93.43% and a specific energy c

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Publication Date
Sat Jun 01 2024
Journal Name
Civil And Environmental Engineering
Constructing a Corrected Stations Network Using Some Geomatic Techniques
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Abstract<p>The major objective of this study is to establish a network of Ground Control Points-GCPs which can use it as a reference for any engineering project. Total Station (type: Nikon Nivo 5.C), Optical Level and Garmin Navigator GPS were used to perform traversing. Traversing measurement was achieved by using nine points covered the selected area irregularly. Near Civil Engineering Department at Baghdad University Al-jadiriya, an attempt has been made to assess the accuracy of GPS by comparing the data obtained from the Total Station. The average error of this method is 3.326 m with the highest coefficient of determination (R<sup>2</sup>) is 0.077 m observed in Northing. While in</p> ... Show More
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Publication Date
Wed Jul 29 2020
Journal Name
Iraqi Journal Of Science
Fractal Image Compression Using Block Indexing Technique: A Review
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Fractal image compression depends on representing an image using affine transformations. The main concern for researches in the discipline of fractal image compression (FIC) algorithm is to decrease encoding time needed to compress image data. The basic technique is that each portion of the image is similar to other portions of the same image. In this process, there are many models that were developed. The presence of fractals was initially noticed and handled using Iterated Function System (IFS); that is used for encoding images. In this paper, a review of fractal image compression is discussed with its variants along with other techniques. A summarized review of contributions is achieved to determine the fulfillment of fractal ima

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Publication Date
Sat Jan 01 2022
Journal Name
Proceedings Of International Conference On Computing And Communication Networks
Speech Age Estimation Using a Ranking Convolutional Neural Network
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Publication Date
Sat Jan 01 2022
Journal Name
Proceedings Of International Conference On Computing And Communication Networks
Speech Gender Recognition Using a Multilayer Feature Extraction Method
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Publication Date
Sun Jul 01 2018
Journal Name
International Journal Of Civil Engineering And Technology (ijciet)
A Proposed Hybird Text Cryptographic Method Using Circular Queue
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The sensitive and important data are increased in the last decades rapidly, since the tremendous updating of networking infrastructure and communications. to secure this data becomes necessary with increasing volume of it, to satisfy securing for data, using different cipher techniques and methods to ensure goals of security that are integrity, confidentiality, and availability. This paper presented a proposed hybrid text cryptography method to encrypt a sensitive data by using different encryption algorithms such as: Caesar, Vigenère, Affine, and multiplicative. Using this hybrid text cryptography method aims to make the encryption process more secure and effective. The hybrid text cryptography method depends on circular queue. Using circ

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