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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 Feb 28 2021
Journal Name
Journal Of Electrochemical Science And Technology
Simultaneous Removal of Cadmium and Copper from a Binary Solution by Cathodic Deposition Using a Spiral-Wound Woven Wire Meshes Packed Bed Rotating Cylinder Electrode
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Publication Date
Wed Jan 01 2025
Journal Name
Aip Conference Proceedings
Determination of cefotaxime-sodium at nanoscale level by a microflow injection cell via measuring turbidity using five irradiation sources (WSLEDs) with a single solar cell
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This work presents a completely new develop an analyzer, named NAG-5SX1-1D-SSP, that is simple, accurate, reproducible, and affordable for the determination of cefotaxime sodium (CFS) in both pure and pharmaceutical drugs. The analyzer was designed according to flow injection analysis, and conducted to turbidimetric measurements. Ammonium cerium nitrate was utilized as a precipitating agent. After optimizing the conditions, the analysis system exhibited a linear range of 0.008-27 mmol. L-1 (n=29), with a limit of detection of 439.3 ng/sample, a limit of quantification of 0.4805 mg/sample, and a correlation coefficient of 0.9988. The repeatability of the responses was assessed by performing six successive injections of CFS at concentra

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Publication Date
Mon Jan 01 2024
Journal Name
Lecture Notes In Mechanical Engineering
Development and Validation of a Free Piston Engine Linear Generator Simulation Model Including Cycle-To-Cycle Variation and Ignition Timing Sub-Models
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Publication Date
Fri May 16 2025
Journal Name
Asean Journal Of Science And Engineering
Enhancing Predictive Maintenance in Energy Systems Using a Hybrid Kolmogorov-Arnold Network (KAN) with Short-Time Fourier Transform (STFT) Framework for Rotating Machinery
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This study proposes a hybrid predictive maintenance framework that integrates the Kolmogorov-Arnold Network (KAN) with Short-Time Fourier Transform (STFT) for intelligent fault diagnosis in industrial rotating machinery. The method is designed to address challenges posed by non-linear and non-stationary vibration signals under varying operational conditions. Experimental validation using the FALEX multispecimen test bench demonstrated a high classification accuracy of 97.5%, outperforming traditional models such as SVM, Random Forest, and XGBoost. The approach maintained robust performance across dynamic load scenarios and noisy environments, with precision and recall exceeding 95%. Key contributions include a hardware-accelerated K

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Publication Date
Thu Jan 16 2020
Journal Name
Journal Of Accounting And Financial Studies ( Jafs )
Suggested Model for activating the roleof the regulators for the auditing professionin achieving quality audit: دراسة تطبيقية في الشركة العامة للصناعات النسيجية- واسط
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The modern business environment Witness tremendous.These developments result from globalization of markets and economic and technological openness. Those developments resulting a heightened competition between economic units and higher the costs of their products and lower their functional characteristics. They do not take into account the response to the requirements of customers. This matter commit it to search for scientific methods to help it to cope with the happening changes and improve its competitive position, The current study acquired its importance by providing significance through by applicable integrated framework to reduce the costs of products. This reduction should be without compromising their quality by using the integr

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Publication Date
Sat Oct 01 2016
Journal Name
Journal Of Economics And Administrative Sciences
Harnessing Innovative Solutions for Achieving Continuous Quality Improvement Requirements in Water Treatment Plants: A Case Study of Continuous Quality Improvement in Baghdad Water Authority.
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Abstract

This Research aims for harnessing critical and innovative thinking approaches besides innovative problem solving tools in pursuing continual quality improvement initiatives for the benefit of achieving operations results effectively in water treatment plants in Baghdad Water Authority. Case study has been used in fulfilling this research in the sadr city water treatment plant, which was chosen as a study sample as it facilitates describing and analyzing its current operational situation, collecting and analyzing its own data, in order to get its own desired improvement opportunity be done. Many statistical means and visual thinking promoting methods has been used to fulfill research task.

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Publication Date
Sun Jun 05 2016
Journal Name
Baghdad Science Journal
Kinetic Model for Solute Diffusion in Liquid Membrane Systems
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In this study, a mathematical model for the kinetics of solute transport in liquid membrane systems (LMSs) has been formulated. This model merged the mechanisms of consecutive and reversible processes with a “semi-derived” diffusion expression, resulting in equations that describe solute concentrations in the three sections (donor, acceptor and membrane). These equations have been refined into linear forms, which are satisfying in the special conditions for simplification obtaining the important kinetic constants of the process experimentally.

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Publication Date
Sat Jan 01 2022
Journal Name
Journal Of Cybersecurity And Information Management
Machine Learning-based Information Security Model for Botnet Detection
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Botnet detection develops a challenging problem in numerous fields such as order, cybersecurity, law, finance, healthcare, and so on. The botnet signifies the group of co-operated Internet connected devices controlled by cyber criminals for starting co-ordinated attacks and applying various malicious events. While the botnet is seamlessly dynamic with developing counter-measures projected by both network and host-based detection techniques, the convention techniques are failed to attain sufficient safety to botnet threats. Thus, machine learning approaches are established for detecting and classifying botnets for cybersecurity. This article presents a novel dragonfly algorithm with multi-class support vector machines enabled botnet

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Publication Date
Thu Jun 29 2023
Journal Name
Wasit Journal For Pure Sciences
Suitable Methods for Solving COVID-19 Model in Iraq
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Because the Coronavirus epidemic spread in Iraq, the COVID-19 epidemic of people quarantined due to infection is our application in this work. The numerical simulation methods used in this research are more suitable than other analytical and numerical methods because they solve random systems. Since the Covid-19 epidemic system has random variables coefficients, these methods are used. Suitable numerical simulation methods have been applied to solve the COVID-19 epidemic model in Iraq. The analytical results of the Variation iteration method (VIM) are executed to compare the results. One numerical method which is the Finite difference method (FD) has been used to solve the Coronavirus model and for comparison purposes. The numerical simulat

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Publication Date
Mon Apr 25 2022
Journal Name
Knowledge And Information Systems
Unsupervised model for aspect categorization and implicit aspect extraction
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People’s ability to quickly convey their thoughts, or opinions, on various services or items has improved as Web 2.0 has evolved. This is to look at the public perceptions expressed in the reviews. Aspect-based sentiment analysis (ABSA) deemed to receive a set of texts (e.g., product reviews or online reviews) and identify the opinion-target (aspect) within each review. Contemporary aspect-based sentiment analysis systems, like the aspect categorization, rely predominantly on lexicon-based, or manually labelled seeds that is being incorporated into the topic models. And using either handcrafted rules or pre-labelled clues for performing implicit aspect detection. These constraints are restricted to a particular domain or language which is

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