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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 Mar 24 2020
Journal Name
Mintage Journal Of Pharmaceutical & Medical Sciences
CD44 AS A TUMOR MARKER DIAGNOSTIC, THE ROLE IN CANCER PROGRESSION
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Publication Date
Wed Aug 01 2018
Journal Name
Journal Of Economics And Administrative Sciences
Analysis of the Current Financial Crisis : Causes and Solutions (Iraqi crisis a model , based on the public budget for the fiscal year 2016)
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The research aims to analysis of the current financial crisis in Iraq through knowing its causes and then propose some solutions that help in remedy the crisis and that on the level of expenditures and revenues, and has been relying on the Federal general budget law of the Republic of Iraq for the fiscal year 2016 to obtain the necessary data in respect of the current expenditures and revenues which necessary to achieve the objective of the research , and through the research results has been reached to a set of conclusions which the most important of them that causes of the current financial crisis in Iraq , mainly belonging to increased expenditures and especially the current ones and the lack of revenues , especially non-oil o

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Publication Date
Wed Feb 01 2017
Journal Name
International Journal Of Science And Research (ijsr)
A Comparative Study between Computer Textbooks Content in the Secondary Stage and Computer Textbooks Content in the University Stage in Colleges of Education at Baghdad University
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Record, verify, and showcase your peer review contributions in a format you can include in job and funding applications (without breaking reviewer anonymity).

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Publication Date
Thu Sep 01 2022
Journal Name
Brazilian Journal Of Chemical Engineering
A computational study on the potential application of Ca12O12 cluster for sensing of fungicide molecule
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Density functional theory calculations are employed to investigate the impact of edifenphos molecule on the reactivity and electronic sensitivity of pure calcium oxide (CaO) nanocluster. The strong adsorption of edifenphos molecule on CaO nanocluster occurs by the sulfur head of the adsorbate, and the amount of the energy of this adsorption is around − 84.40 kcal/mol. The adsorption of edifenphos molecules results in a decrease in the values of Eg of CaO from 4.67 to 3.56 eV, as well as an increase in the electrical conductance. Moreover, the work function of CaO nanocluster is significantly affected, which changes the current of the field emission electron. Eventually, the recovery time is calculated around 99 ms at ambient temperature f

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Publication Date
Sun Aug 01 2021
Journal Name
Journal Of Engineering
Practical comparation of the accuracy and speed of YOLO, SSD and Faster RCNN for drone detection
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Convolutional Neural Networks (CNN) have high performance in the fields of object recognition and classification. The strength of CNNs comes from the fact that they are able to extract information from raw-pixel content and learn features automatically. Feature extraction and classification algorithms can be either hand-crafted or Deep Learning (DL) based. DL detection approaches can be either two stages (region proposal approaches) detector or a single stage (non-region proposal approach) detector. Region proposal-based techniques include R-CNN, Fast RCNN, and Faster RCNN. Non-region proposal-based techniques include Single Shot Detector (SSD) and You Only Look Once (YOLO). We are going to compare the speed and accuracy of Faster RCNN,

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Publication Date
Fri Mar 01 2024
Journal Name
Baghdad Science Journal
Deep Learning Techniques in the Cancer-Related Medical Domain: A Transfer Deep Learning Ensemble Model for Lung Cancer Prediction
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Problem: Cancer is regarded as one of the world's deadliest diseases. Machine learning and its new branch (deep learning) algorithms can facilitate the way of dealing with cancer, especially in the field of cancer prevention and detection. Traditional ways of analyzing cancer data have their limits, and cancer data is growing quickly. This makes it possible for deep learning to move forward with its powerful abilities to analyze and process cancer data. Aims: In the current study, a deep-learning medical support system for the prediction of lung cancer is presented. Methods: The study uses three different deep learning models (EfficientNetB3, ResNet50 and ResNet101) with the transfer learning concept. The three models are trained using a

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Publication Date
Sat Sep 30 2017
Journal Name
College Of Islamic Sciences
The ignorant poem and the body language: (The sieve of the Sikkhar sieve is a model)
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This study is marked by: The ignorant poem and body language
 Its main objective is to reveal the manifestations of this language in the text mentioned, and accordingly, the sieve poem has been read semantic (semantic) and hermeneutic, revealing the poet's ability to employ symbols and signals (body language) in the poem chosen for this purpose; The existence of such language in pre-Islamic poetry. After a long reflection and reading, the signs and symbols of the physical movement of the body, and its feminine and aesthetic manifestations were identified, and this was achieved through the use of modern critical methodologies that directly affect this language. The study consisted of an introduction and three topics, followed by t

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Publication Date
Thu Oct 25 2018
Journal Name
Al–bahith Al–a'alami
War Reporters In Iraqi Satellite Channels And Its Role In Increasing Understanding Of The Audience Of The News .: Field Study For The Reporters And The Audiences In Baghdad For The Period From 1/07/2014 Till – 1/11/2014
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The importance of media coverage in the war remains dependent on many indicators for its success, the most important is to have qualified reporters who carry the war news professionally. The idea of this research is to determine the role played by war correspondents working on Iraqi satellite channels during the war against ISIS.
The researcher has chosen ( 40 ) reporters those who was able to contact them and prepared a questionnaire for them to study their situations. Also, he chose an intentional sample from Baghdad audience on condition they should be informed by the performance of the reporters in the satellite channels applying the hypotheses of the theory of depending upon media.
The most important results reached by the re

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Publication Date
Mon Feb 14 2022
Journal Name
Journal Of Educational And Psychological Researches
The Reality of Adapting Curricula and Educational Programs for Pupils with Visual Handicapped from Their Teachers’ Perspectives
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The current study aims to identify the level of adaptation of the curriculum for visually handicapped pupils from the point of view of their teachers as well as to identify the level of adaptation of the educational programs offered to visually handicapped pupils from the point of view of their teachers. In order to achieve the goals of the research, the researcher developed two tools to measure the adaptation of curricula and educational programs for pupils with visual handicapped from the point of view of teachers. The sample included (60) teachers from Al Noor Institute for Blinders in Baghdad, the two tools were applied to them, and then the Reliability and Validity coefficients were extracted. The results sh

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Publication Date
Fri Mar 31 2017
Journal Name
Al-khwarizmi Engineering Journal
Design of Nonlinear PID Neural Controller for the Speed Control of a Permanent Magnet DC Motor Model based on Optimization Algorithm
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In this paper, the speed control of the real DC motor is experimentally investigated using nonlinear PID neural network controller. As a simple and fast tuning algorithm, two optimization techniques are used; trial and error method and particle swarm optimization PSO algorithm in order to tune the nonlinear PID neural controller's parameters and to find best speed response of the DC motor. To save time in the real system, a Matlab simulation package is used to carry out these algorithms to tune and find the best values of the nonlinear PID parameters. Then these parameters are used in the designed real time nonlinear PID controller system based on LabVIEW package. Simulation and experimental results are compared with each other and showe

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