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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
Wed Jun 01 2011
Journal Name
Journal Of Economics And Administrative Sciences
The role of the cognitive peak and its implications for achieving outstanding performanceAnalytical study of the views of a sample of the staff of the University of Baghdad
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        Knowledge represents the foundation stone for the work of all organizations, are working who leads the thinking of individuals is the ability that leads to behavior based on rationality, it is the work that creates value to the organization and thus gain access to performance winning where that knowledge is a new type of capital based on the thought and experience and is the so-called intellectual capital, which is renewable and is constantly evolving. The study sought to explain the role of the climax  knowledge in achieving the highest levels of performance Organizational and then access to the performance winning in educational organizations the study sample, was found to be a co

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Publication Date
Fri Feb 01 2019
Journal Name
Journal Of Economics And Administrative Sciences
Comparison of Some Methods for Estimating the Scheff'e Model of the Mixture
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Because of the experience of the mixture problem of high correlation and the existence of linear MultiCollinearity between the explanatory variables, because of the constraint of the unit and the interactions between them in the model, which increases the existence of links between the explanatory variables and this is illustrated by the variance inflation vector (VIF), L-Pseudo component to reduce the bond between the components of the mixture.

    To estimate the parameters of the mixture model, we used in our research the use of methods that increase bias and reduce variance, such as the Ridge Regression Method and the Least Absolute Shrinkage and Selection Operator (LASSO) method a

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Publication Date
Tue Sep 10 2019
Journal Name
Periodicals Of Engineering And Natural Sciences (pen)
A classification model on tumor cancer disease based mutual information and firefly algorithm
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Publication Date
Wed Jun 01 2016
Journal Name
Journal Of Engineering
A Novel Analytical Model to Design Piezoelectric Patches Used to Repair Cracked Beams
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In this paper, an analytical solution describing the deflection of a cracked beam repaired with piezoelectric patch is introduced. The solution is derived using perturbation method. A novel analytical model to calculate the proper dimensions of piezoelectric patches used to repair cracked beams is also introduced. This model shows that the thickness of the piezoelectric patch depends mainly on the thickness of the cracked beam, the electro-mechanical properties of the patch material, the applied load and the crack location. Furthermore, the model shows that the length of the piezoelectric patches depends on the thickness of the patch as well as it depends on the length of the cracked beam and the crack depth. The additio

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Publication Date
Sat Jul 01 2023
Journal Name
Journal Of Engineering
Toward Improving BIM Acceptance in FM: A Conceptual Model Integrating TTF and TAM
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Substantial research has been performed on Building Information Modeling (BIM) in various topics, for instance, the use and benefit of BIM in design, construction, sustainable environment building, and Facility assets over the past several years. Although there are various studies on these topics, Building Information Modeling (BIM) awareness through facilities management is still relatively poor. The researcher's interest is increased in BIM study is based heavily upon the perception that it can facilitate the exchange and reuse of information during various project phases. This property and others can be used in the Iraqi Construction industry to motivate the government to eliminate the change resistance to use innovat

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Publication Date
Sat Jun 04 2022
Journal Name
Al–bahith Al–a'alami
paratexte in specialized literary journals : AL ADEEB AL IRAQI magazine is a model
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Post-structural critical studies highlighted the importance of studying the texts surrounding the text as an important part in the process of receiving and understanding texts, and although this topic was dealt with by the ancient Arabs and Europeans, interest in it appeared clearly after the appearance of Gerard Genet's book (SEUILS), which separated it Text Thresholds. Or what he called paratexte, and dealt with them with interest as he reads them on books. With the development of semiotic studies, interest in paratexte studies began in a broader way and in various literary and non-literary texts, including journalistic texts. And since specialized magazines are one of the press releases that enjoy their privacy in terms of topics and

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Publication Date
Wed Jun 01 2016
Journal Name
Journal Of Engineering
A Novel Analytical Model to Design Piezoelectric Patches Used to Repair Cracked Beams
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In this paper, an analytical solution describing the deflection of a cracked beam repaired with piezoelectric patch is introduced. The solution is derived using perturbation method. A novel analytical model to calculate the proper dimensions of piezoelectric patches used to repair cracked beams is also introduced. This model shows that the thickness of the piezoelectric patch depends mainly on the thickness of the cracked beam, the electro-mechanical properties of the patch material, the applied load and the crack location. Furthermore, the model shows that the length of the piezoelectric patches depends on the thickness of the patch as well as it depends on the length of the cracked beam and the crack depth. The additional flexibil

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Publication Date
Wed Aug 28 2024
Journal Name
Mesopotamian Journal Of Cybersecurity
A Novel Anomaly Intrusion Detection Method based on RNA Encoding and ResNet50 Model
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Cybersecurity refers to the actions that are used by people and companies to protect themselves and their information from cyber threats. Different security methods have been proposed for detecting network abnormal behavior, but some effective attacks are still a major concern in the computer community. Many security gaps, like Denial of Service, spam, phishing, and other types of attacks, are reported daily, and the attack numbers are growing. Intrusion detection is a security protection method that is used to detect and report any abnormal traffic automatically that may affect network security, such as internal attacks, external attacks, and maloperations. This paper proposed an anomaly intrusion detection system method based on a

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Publication Date
Wed Aug 28 2024
Journal Name
Mesopotamian Journal Of Cybersecurity
A Novel Anomaly Intrusion Detection Method based on RNA Encoding and ResNet50 Model
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Cybersecurity refers to the actions that are used by people and companies to protect themselves and their information from cyber threats. Different security methods have been proposed for detecting network abnormal behavior, but some effective attacks are still a major concern in the computer community. Many security gaps, like Denial of Service, spam, phishing, and other types of attacks, are reported daily, and the attack numbers are growing. Intrusion detection is a security protection method that is used to detect and report any abnormal traffic automatically that may affect network security, such as internal attacks, external attacks, and maloperations. This paper proposed an anomaly intrusion detection system method based on a

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Publication Date
Wed Jun 15 2022
Journal Name
Journal Of Sensors
A Modern Approach towards an Industry 4.0 Model: From Driving Technologies to Management
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Every so often, a confluence of novel technologies emerges that radically transforms every aspect of the industry, the global economy, and finally, the way we live. These sharp leaps of human ingenuity are known as industrial revolutions, and we are currently in the midst of the fourth such revolution, coined Industry 4.0 by the World Economic Forum. Building on their guideline set of technologies that encompass Industry 4.0, we present a full set of pillar technologies on which Industry 4.0 project portfolio management rests as well as the foundation technologies that support these pillars. A complete model of an Industry 4.0 factory which relies on these pillar technologies is presented. The full set of pillars encompasses cyberph

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