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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
Fri Dec 31 2021
Journal Name
International Journal Of Intelligent Engineering And Systems
Airborne Computer System Based Collision-Free Flight Path Finding Strategy Design for Drone Model
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Publication Date
Mon Oct 01 2018
Journal Name
Journal Of Engineering
Mathematical Model for BOD in Waste Water Discharges from Al Dora Refinery in Baghdad
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This research consists of two parts, the first part concern with analyzing the collected data of BOD and COD values in discharge waste water from Al-Dora refinery during 2010 to find the relationship between these two variables The results indicates that there is a high correlation between BOD and COD when using a natural logarithm model (0.86 ln(COD)) with correlation coefficient of 0.98. This relationship is useful in predicting the BOD value using the COD value. The second part includes analyzing collected data from the same site in order to find a relationsip between BOD and other parameters COD, Phenol(phe), Temperature(T), Oil, Sulphat(SO4),pH and Total dissolved solids( TDS) discharged from the refinery. The results indicated that th

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Publication Date
Thu Apr 01 2021
Journal Name
Indonesian Journal Of Electrical Engineering And Computer Science
Pushing towards ehealth for iraqi hypertensives: an integrated class association rules into SECI model
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<span lang="EN-GB">This paper highlights the barriers that have led to a delay in the implementation of E-Health services in Iraq. A new framework is proposed to improve the E-Health sector using a SECI model which describes how explicit and tacit knowledge is generated, transferred, and recreated in organizations through main stages (socialization, externalization, combination and internalization). Class association rules (CARs) is integrated to mine the SECI model by extracting related rules which correspond to the medical advice. The proposed framework (SECICAR) can be done through a web portal to assemble healthcare professionals, patients in one environment. SECICAR will be applied to the hypertension community to show th

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Publication Date
Mon Jun 09 2025
Journal Name
Intelligent Decision Technologies
Safety assessment model for DoS attacks detection in wireless communication and network OS environments
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Wireless networks and communications have witnessed tremendous development and growth in recent periods and up until now, as there is a group of diverse networks such as the well-known wireless communication networks and others that are not linked to an infrastructure such as telephone networks, sensors and wireless networks, especially in important applications that work to send and receive important data and information in relatively unsafe environments, cybersecurity technologies pose an important challenge in protecting unsafe networks in terms of their impact on reducing crime. Detecting hacking in electronic networks and penetration testing. Therefore, these environments must be monitored and protected from hacking and malicio

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Publication Date
Thu May 18 2023
Journal Name
Journal Of Engineering
Genetic Algorithm Optimization Model for Central Marches Restoration Flows with Different Water Quality Scenarios
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A Genetic Algorithm optimization model is used in this study to find the optimum flow values of the Tigris river branches near Ammara city, which their water is to be used for central marshes restoration after mixing in Maissan River. These tributaries are Al-Areed, AlBittera and Al-Majar Al-Kabeer Rivers. The aim of this model is to enhance the water quality in Maissan River, hence provide acceptable water quality for marsh restoration. The model is applied for different water quality change scenarios ,i.e. , 10%,20% increase in EC,TDS and BOD. The model output are the optimum flow values for the three rivers while, the input data are monthly flows(1994-2011),monthly water requirements and water quality parameters (EC, TDS, BOD, DO and

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Publication Date
Fri Jan 01 2016
Journal Name
Journal Of College Of Education
Some of the Probability Characteristics Functions of the Solution of a System of Random Linear Inequalities
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Publication Date
Thu Jan 01 2009
Journal Name
Bayt Alhekma
COMPARATIVE ANALYSIS OF RUSSIAN AND ARABIC PHRASEOLOGICAL UNITS (TURNS)
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Abstract The study aimed at reviewing translation theories proposed to address problems in translation studies. To the end, translation theories and their applications were reviewed in different studies with a focus on issues such as critical discourse analysis, cultural specific items and collocation translation.

Publication Date
Sat Feb 09 2019
Journal Name
Journal Of The College Of Education For Women
Learning for Scientific Culture by Using Interactive Whiteboard According to the Faculty of the University of Baghdad Viewpoint
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The progress of science in all its branches and levels made great civilized changes of
our societies in the present day, it's a result of the huge amount of knowledge, the increase of
number of students, and the increase of community awareness proportion of the importance of
education in schools and universities, it became necessary for us as educators to look at
science from another point of view based on the idea of scientific development of curricula
and teaching methods and means of education, and for the studying class environment as a
whole, by computer and internet use in education to the emergence of the term education
technology, which relies on the use of modern technology to provide educational content to<

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Publication Date
Sat May 01 2021
Journal Name
Journal Of Physics: Conference Series
The Bifurcation Analysis of Food Web Prey- Predator Model with Toxin
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Abstract<p>Local and global bifurcations of food web model consists of immature and mature preys, first predator, and second predator with the current of toxicity and harvesting was studied. It is shown that a trans-critical bifurcation occurs at the equilibrium point <italic>E</italic> <sub>0</sub>, and it revealed the existence of saddle-node bifurcation occurred at equilibrium points <italic>E</italic> <sub>1</sub>, <italic>E</italic> <sub>2</sub> and <italic>E</italic> <sub>3</sub>. At any point, the occurrence of bifurcation of the pitch for</p> ... Show More
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Publication Date
Fri Feb 12 2016
Journal Name
International Journal Of Applied Mathematical Research
The dynamics of nutrient, toxic phytoplankton, nontoxic phytoplankton and zooplankton model
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<p>The objective of this paper is to study the dynamical behavior of an aquatic food web system. A mathematical model that includes nutrients, phytoplankton and zooplankton is proposed and analyzed. It is assumed that, the phytoplankton divided into two compartments namely toxic phytoplankton which produces a toxic substance as a defensive strategy against predation by zooplankton, and a nontoxic phytoplankton. All the feeding processes in this food web are formulating according to the Lotka-Volterra functional response. This model is represented mathematically by the set of nonlinear differential equations. The existence, uniqueness and boundedness of the solution of this model are investigated. The local and global stability

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