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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
Tue Aug 01 2023
Journal Name
Advances In Mechanical Engineering
Using a spherical inverted pendulum and statokinesigram for modeling and evaluating quiet standing posture
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This paper proposes a new approach to model and analyze erect posture, based on a spherical inverted pendulum which is used to mimic the body posture. The pendulum oscillates in two directions, [Formula: see text] and [Formula: see text], from which the mathematical model was derived and two torque components in oscillation directions were introduced. They are estimated using stabilometric data acquired by a foot pressure mapping system. The model was quantitatively investigated using data from 19 participants, who were first were classified into three groups, according to the foot arch-index. Stabilometric data were then collected and fed into the model to estimate the torque’s components. The components were statistically proce

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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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Publication Date
Tue Dec 05 2023
Journal Name
Baghdad Science Journal
A Novel System for Confidential Medical Data Storage Using Chaskey Encryption and Blockchain Technology
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Secure storage of confidential medical information is critical to healthcare organizations seeking to protect patient's privacy and comply with regulatory requirements. This paper presents a new scheme for secure storage of medical data using Chaskey cryptography and blockchain technology. The system uses Chaskey encryption to ensure integrity and confidentiality of medical data, blockchain technology to provide a scalable and decentralized storage solution. The system also uses Bflow segmentation and vertical segmentation technologies to enhance scalability and manage the stored data. In addition, the system uses smart contracts to enforce access control policies and other security measures. The description of the system detailing and p

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Publication Date
Tue May 01 2018
Journal Name
Journal Of Engineering
Power System Stabilizer PSS4B Model for Iraqi National Grid using PSS/E Software
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To damp the low-frequency oscillations which occurred due to the disturbances in the electrical power system, the generators are equipped with Power System Stabilizer (PSS) that provide supplementary feedback stabilizing signals. The low-frequency oscillations in power system are classified as local mode oscillations, intra-area mode oscillation, and interarea mode oscillations. Double input multiband Power system stabilizers (PSSs) were used to damp out low-frequency oscillations in power system. Among dual-input PSSs, PSS4B offers superior transient performance. Power system simulator for engineering (PSS/E) software was adopted to test and evaluate the dynamic performance of PSS4B model on Iraqi national grid. The res

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Publication Date
Sun Mar 01 2015
Journal Name
Journal Of Engineering
Multi-Sites Multi-Variables Forecasting Model for Hydrological Data using Genetic Algorithm Modeling
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A two time step stochastic multi-variables multi-sites hydrological data forecasting model was developed and verified using a case study. The philosophy of this model is to use the cross-variables correlations, cross-sites correlations and the two steps time lag correlations simultaneously, for estimating the parameters of the model which then are modified using the mutation process of the genetic algorithm optimization model. The objective function that to be minimized is the Akiake test value. The case study is of four variables and three sites. The variables are the monthly air temperature, humidity, precipitation, and evaporation; the sites are Sulaimania, Chwarta, and Penjwin, which are located north Iraq. The model performance was

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Publication Date
Tue May 01 2018
Journal Name
Journal Of Engineering
Power System Stabilizer PSS4B Model for Iraqi National Grid using PSS/E Software
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To damp the low-frequency oscillations which occurred due to the disturbances in the electrical power system, the generators are equipped with Power System Stabilizer (PSS) that provide supplementary feedback stabilizing signals. The low-frequency oscillations in power system are classified as local mode oscillations, intra-area mode oscillation, and interarea mode oscillations. Double input multiband Power system stabilizers (PSSs) were used to damp out low-frequency oscillations in power system. Among dual-input PSSs, PSS4B offers superior transient performance. Power system simulator for engineering (PSS/E) software was adopted to test and evaluate the dynamic performance of PSS4B model on Iraqi national grid. The results showed

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Publication Date
Wed Jun 21 2023
Journal Name
Journal Of Electrochemical Science And Engineering
Phenol removal by electro-Fenton process using a 3D electrode with iron foam as particles and carbon fibre modified with graphene
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The 3D electro-Fenton technique is, due to its high efficiency, one of the technologies suggested to eliminate organic pollutants in wastewater. The type of particle electrode used in the 3D electro-Fenton process is one of the most crucial variables because of its effect on the formation of reactive species and the source of iron ions. The electrolytic cell in the current study consisted of graphite as an anode, carbon fiber (CF) modified with graphene as a cathode, and iron foam particles as a third electrode. A response surface methodology (RSM) approach was used to optimize the 3D electro-Fenton process. The RSM results revealed that the quadratic model has a high R2 of 99.05 %. At 4 g L-1 iron foam particles, time of 5 h, and

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Publication Date
Wed Aug 01 2018
Journal Name
Engineering And Technology Journal
A Proposed Method for the Sound Recognition Process
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Publication Date
Sun Dec 16 2018
Journal Name
Al-academy
Scenography Features in the Iraqi Contemporary Theatre Show (Macbeth Play, by Salah Al-Qasab- A Model)
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Societies developed throughout history with the development of life technology, that ideas presented by the contemporary art have been crystallized. The development included all the artistic fields such as the dramatic arts which depend on many effects and elements that led to the completion of the structure of the theater show. Scenography is considered one of the most important elements that the theatre show depends on such as the decoration, lighting, sound effects, costumes and accessories. The research addressed the following question: what are the characteristics and traits of scenography in the theatre show?
The research importance has become clear because it sheds lights on the characteristics of scenography in the Iraqi thea

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Publication Date
Tue Oct 22 2024
Journal Name
Iraqi Statisticians Journal
Inferential Methods for the Dagum Regression Model
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The Dagum Regression Model, introduced to address limitations in traditional econometric models, provides enhanced flexibility for analyzing data characterized by heavy tails and asymmetry, which is common in income and wealth distributions. This paper develops and applies the Dagum model, demonstrating its advantages over other distributions such as the Log-Normal and Gamma distributions. The model's parameters are estimated using Maximum Likelihood Estimation (MLE) and the Method of Moments (MoM). A simulation study evaluates both methods' performance across various sample sizes, showing that MoM tends to offer more robust and precise estimates, particularly in small samples. These findings provide valuable insights into the ana

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