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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 Jan 11 2018
Journal Name
Al-khwarizmi Engineering Journal
Control on a 2-D Wing Flutter Using an Adaptive Nonlinear Neural Controller
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An adaptive nonlinear neural controller to reduce the nonlinear flutter in 2-D wing is proposed in the paper. The nonlinearities in the system come from the quasi steady aerodynamic model and torsional spring in pitch direction. Time domain simulations are used to examine the dynamic aero elastic instabilities of the system (e.g. the onset of flutter and limit cycle oscillation, LCO). The structure of the controller consists of two models :the modified Elman neural network (MENN) and the feed forward multi-layer Perceptron (MLP). The MENN model is trained with off-line and on-line stages to guarantee that the outputs of the model accurately represent the plunge and pitch motion of the wing and this neural model acts as the identifier. Th

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Publication Date
Fri Nov 21 2025
Journal Name
Journal Of Advances In Information Technology
Towards Accurate SDG Research Categorization: A Hybrid Deep Learning Approach Using Scopus Metadata
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The complexity and variety of language included in policy and academic documents make the automatic classification of research papers based on the United Nations Sustainable Development Goals (SDGs) somewhat difficult. Using both pre-trained and contextual word embeddings to increase semantic understanding, this study presents a complete deep learning pipeline combining Bidirectional Long Short-Term Memory (BiLSTM) and Convolutional Neural Network (CNN) architectures which aims primarily to improve the comprehensibility and accuracy of SDG text classification, thereby enabling more effective policy monitoring and research evaluation. Successful document representation via Global Vector (GloVe), Bidirectional Encoder Representations from Tra

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Publication Date
Wed Feb 06 2013
Journal Name
Eng. & Tech. Journal
A proposal to detect computer worms (malicious codes) using data mining classification algorithms
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Malicious software (malware) performs a malicious function that compromising a computer system’s security. Many methods have been developed to improve the security of the computer system resources, among them the use of firewall, encryption, and Intrusion Detection System (IDS). IDS can detect newly unrecognized attack attempt and raising an early alarm to inform the system about this suspicious intrusion attempt. This paper proposed a hybrid IDS for detection intrusion, especially malware, with considering network packet and host features. The hybrid IDS designed using Data Mining (DM) classification methods that for its ability to detect new, previously unseen intrusions accurately and automatically. It uses both anomaly and misuse dete

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Publication Date
Mon Aug 29 2022
Journal Name
Eurasian Chem. Commun.
Removing some alizarin dyes from an aqueous solution using a polyacrylic acid hydrogel
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The present work utilizes polyacrylic acid beads (PAA) to remove Alizarin yellow R (AYR)] and Alizarin Red S (ARS) from its solution. The isotherms of adsorption were investigated and the factors that impact them, such as temperature, ionic strength effect, shaking effect, and wet PAA. The isotherms of adsorption of (ARS) were found obeys the Freundlich equation. The isotherms of adsorption of (AYR) were found obeys the Langmuir equation. At various temperatures, the adsorption process on (PAA) was investigated. According to our data, there is a positive correlation between the (ARS and AYR) adsorption on the PAA and temperature (Endothermic process). The computation of the thermodynamic functions (ΔH, ΔG, and ΔS) is based on the foregoi

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Publication Date
Mon Jan 01 2024
Journal Name
Journal Of Industrial And Engineering Chemistry
Petroleum refinery wastewater treatment using a novel combined electro-Fenton and photocatalytic process
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Publication Date
Fri Jan 20 2023
Journal Name
Ibn Al-haitham Journal For Pure And Applied Sciences
A Review Article: Green Synthesis by using Different Plants to preparation Oxide Nanoparticles
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Green nanotechnology is a thrilling and rising place of technology and generation that bracesthe ideas of inexperienced chemistry with ability advantages for sustainability, protection, andthe general protection from the race human. The inexperienced chemistry method introduces aproper technique for the production, processing, and alertness of much less dangerous chemicalsubstances to lessen threats to human fitness and the environment. The technique calls for inintensity expertise of the uncooked materials, particularly in phrases in their creation intonanomaterials and the resultant bioactivities that pose very few dangerous outcomes for peopleand the environment. In the twenty-first century, nanotechnology has become a systematic

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Publication Date
Thu Oct 01 2009
Journal Name
Journal Of The College Of Languages (jcl)
A RAISIN IN THE SUN: the dream of RECOGNITION
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Lorraine Hansberry’s A Raisin in the Sun (1959) appeared at the beginning of renewed political activity on the part of the blacks; it is a pamphlet about the dream of recognition of black people and the confusion of purposes and means to reach such recognition. It embodies ideas that have been uncommon on the Broadway stage in any period. Situations such as a black family moving into an all-white neighborhood were not familiar before this time; they were just beginning to emerge. In depicting this so realistically, Hansberry depends more on her personal experience as an African American embittered by social prejudices and discrimination. 

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Publication Date
Sun Jun 30 2019
Journal Name
Journal Of Accounting And Financial Studies ( Jafs )
The impact of strategic planning for electronic services to developing cash bank deposits: An Applied research for a sample of Iraqi private banks
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               The bank deposits is fuel banking activity and raw material products for the commercial bank and the basis of its activity and its lifetime So the bank, which seeks to continue the successful development of the volume of cash deposits has translated the work of the bank to meet the needs of different sectors by providing the necessary funding, and from this point of view was the research problem a lack of interest departments of banking services to commercial banks as a means for the development of electronic cash deposits have, and which represents the basis for the supplier commercial bank fund.

 

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Publication Date
Sat Aug 31 2024
Journal Name
International Journal Of Intelligent Engineering And Systems
Credit Card Fraud Detection Using an Autoencoder Model with New Loss Function
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Publication Date
Sun Feb 24 2019
Journal Name
Iraqi Journal Of Physics
High spatial resolution digital elevation model (DEM) production using different interpolations techniques
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DEMs, thus, simply regular grids of elevation measurements over the land surface.The aim of the present work is to produce high resolution DEM for certain investigated region (i.e. Baghdad University Campus\ college of science). The easting and northing of 90 locations, including the ground-base and buildings of the studied area, have been obtained by field survey using global positioning system (GPS). The image of the investigated area has been extracted from Quick-Bird satellite sensor (with spatial resolution of 0.6 m). It has been geo-referenced and rectified  using 1st order polynomial transformation. many interpolation methods have been used to estimate the elevation such as ordinary Kriging, inverse distance weight

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