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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 Sep 01 2021
Journal Name
Review Of International Geographical Education
A New Approach in Determining the Criteria of Equations for Morphometric Characteristics of River Basins - Applied Morphometric Study of The Mamaran Basin
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This study aimed at some of the criteria used to determine the form of the river basins, and exposed the need to modify some of its limitations. In which, the generalization of the elongation and roundness ratio coefficient criterion was modified, which was set in a range between (0-1). This range goes beyond determining the form of the basin, which gives it an elongated or rounded feature, and the ratio has been modified by making it more detailed and accurate in giving the basin a specific form, not only a general characteristic. So, we reached a standard for each of the basins' forms regarding the results of the elongation and circularity ratios. Thus, circular is (1-0.8), and square is (between 0.8-0.6), the blade or oval form is (0.6-0

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Publication Date
Sun Sep 06 2015
Journal Name
Baghdad Science Journal
A study of the effect of new cobalt (II) complex and cyclophosphamide drug on (GPT, ALP) activity by using in vivo system
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The present work involved a study the effect of cobalt(II) complex with formula [CoL(H2O)NO3] .4ETOH where L=Nitro [5-(P-nitro phenyl) -4-phenyl-1,2,4 traizole-3-dithiocarbamato hydrazide] aqua. (4) Ethanol and anti-cancer drug - cyclophosphamide on specific activity of two liver enzymes (GPT,ALP) by utilizing an in vivo system in female mice. On the enzymatic level an inhibition in the activity of GPT was noticed in different body organs such as liver, kidney and lung. The inhibition was noticed in both test and cyclophosphamide drug (cp). Mice were treated with three doses of cyclophosphamide (90,180, 250) ?g/ mouse for three days. The same doses were used for the cobalt (II) complex. The liver shows the highest rate of(GPT) inhibition co

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Publication Date
Mon Mar 01 2010
Journal Name
Basrah Journal Of Science
Hiding Three Images at one image by Using Wavelet Coefficients at Color Image
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Publication Date
Sun Jun 20 2021
Journal Name
Baghdad Science Journal
Wireless Propagation Multipaths using Spectral Clustering and Three-Constraint Affinity Matrix Spectral Clustering
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This study focused on spectral clustering (SC) and three-constraint affinity matrix spectral clustering (3CAM-SC) to determine the number of clusters and the membership of the clusters of the COST 2100 channel model (C2CM) multipath dataset simultaneously. Various multipath clustering approaches solve only the number of clusters without taking into consideration the membership of clusters. The problem of giving only the number of clusters is that there is no assurance that the membership of the multipath clusters is accurate even though the number of clusters is correct. SC and 3CAM-SC aimed to solve this problem by determining the membership of the clusters. The cluster and the cluster count were then computed through the cluster-wise J

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Publication Date
Wed Jan 01 2020
Journal Name
Says Rev Pharm
Healing of apical periodontitis after minimally invasive endodontics therapy using Er,Cr:YSGG laser: A prospective clinical study
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Publication Date
Sat Dec 02 2023
Journal Name
Journal Of Engineering
Reservoir Sedimentation Assessment Using Geospatial Technology: A case Study of Dukan Reservoir, Sulaimani Governorate, Kurdistan Region, Iraq
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The accumulation of sediment in reservoirs poses a major challenge that impacts the storage capacity, quality of water, and efficiency of hydroelectric power generation systems. Geospatial methods, including Geographic Information Systems (GIS) and Remote Sensing (RS), were used to assess Dukan Reservoir sediment quantities. Satellite and reservoir water level data from 2010 to 2022 were used for sedimentation assessment. The satellite data was used to analyze the water spread area, employing the Normalized Difference Water Index (NDWI) and Modified Normalized Difference Water Index (MNDWI) to enhance the water surface in the satellite imagery of Dukan Reservoir. The cone formula was employed to calculate the live storag

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Publication Date
Sun Sep 06 2015
Journal Name
Baghdad Science Journal
A theoretical Design of a cover for lowering the solar cells temperature and enhance their performance
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In this research, main types of optical coatings are presented which are used as covers for solar cells, these coatings are reflect the infrared (heat) from the solar cell to increase the efficiency of the cell (because the cell’s efficiency is inversely proportional to the heat), then the theoretical and mathematical description of these optical coatings are presented, and an optical design is designed to meet this objective, its optical transmittance was calculated using (MATLAB R2008a) and (Open Filters 1.0.2) programs

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Publication Date
Sat Dec 01 2018
Journal Name
Journal Of Economics And Administrative Sciences
The evaluation a proposed strategy for the Ministry of Planning for the years 2018-2022 .
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abstract

the research discussed a stage of strategic management. The strategic of the evaluation of the proposed strategy through feedback is to ensure that it is implemented with the least possible variation. The research aims at evaluation  a proposed strategy for the Ministry of Planning for the years 2018-2022 in line with the orientations of the state, taking into account the surrounding environmental conditions. It relies on scientific bases and steps to formulate the strategy The extent of the strategy suitability was tested through a set of statistical means and its objectivity was verified through a survey of a number of specialized experts who were selected in accordance with the principle

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Publication Date
Sun Jun 01 2025
Journal Name
Journal Of The College Of Languages
A Stylistic Study of the Concept of Love in Kahlil Gibran’s ’The Prophet’
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In his masterpiece ’The Prophet’, Kahlil Gibran presents his unwavering faith and passionate belief in the healing power of universal love that brings humans to sublime ideas and elevates their souls and behavior. The current study aims to find out the stylistic devices utilized to represent the concept of love based on the hypothesis that Gibran tends to use certain stylistic effects to convey his meaning. The study adopts Leech and Short’s (2007) framework of stylistic analysis to analyze the lexical items and figures of speech in selected extracts from the book. The findings reveal that Gibran prefers concrete nouns, dynamic verbs, and physical adjectives over abstract nouns, stative verbs, and psychological adjectives to s

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Publication Date
Wed Dec 27 2017
Journal Name
Al-khwarizmi Engineering Journal
A New Structure for Cascaded Single-Stage Distributed Amplifier Using Proposed Active Inductor Loads
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A modification to cascaded single-stage distributed amplifier (CSSDA) design by using active inductor is proposed. This modification is shown to render the amplifier suitable for high gain operation in small on-chip area. Microwave office program simulation of the Novel design approach shows that it has performance compatible with the conventional distributed amplifiers but with smaller area. The CSSDA is suitable for optical and satellite communication systems.

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