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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 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
Fri Jul 01 2016
Journal Name
Journal Of Engineering
Study the Properties of Sodium Silicate Composite as a Barrier Separating Between the Internal Oil Distillation Towers and Chemical Fumes of Crude Oil
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The study of surface hardness, wear resistance, adhesion strength, electrochemical corrosion resistance and thermal conductivity of coatings composed from sodium silicate was prepared using graphite micro-size particles and carbon nano particles as fillers respectively of concentration of (1-5%), for the purpose of covering and protecting the oil distillation towers. The results showed that the sodium silicate coating reinforced with carbon nano-powder has higher resistance to stitches, mechanical wear, adhesive and thermal conductivity than graphite/sodium silicate composite especially when the ratio 5% and 1%, the electrochemical corrosion test confirmed that the coating process of stainless steel 304 lead to increasin

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Publication Date
Sun Feb 10 2019
Journal Name
Journal Of The College Of Education For Women
Social Medical Care for the Deformed Children: A Field Study in Baghdad City
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The Child is the first sedum for the human society performing, and we deal in our
research to explain the nature of the mutual relations in between the form and the medicine
social caring foundation. So the motherhood and the childhood nowadays become the most
dedicated in the researchers works, whom interesting in the social affairs, and that whom
work in the medicine field as scientists.
So the child is the future man and must be in wright body construction that need to great
care and interest to make him wright mind through capability of performing anything support
to him.
In our research we deal with the main factors in which lead to infect the child by the
creative malfunction, like the environmental and m

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Publication Date
Mon Feb 04 2019
Journal Name
Journal Of The College Of Education For Women
Popular naming for goods and materials in the Iraqi slang "A Semantic Study"
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The current research is concerned with the prices of Goods and materials in the Iraqi slang a descriptive, lexicographic , and semantic study expressing the meanings of these names and their positions , as well as expressing the imaginations of Human mind , the popular mind in describing these goods with evaluating them besides the semantic of each word accordingly
The current research is divided into two parts , the first part is consisted of Vocalizations" words" That are arisen through cognitive naming that concentrate on the mental imaginations for the most important and sensitive such as colors , taste , shapes and forms impacts of Goods and materials according to users' ' taste for those words , on other hand, the second part of

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Publication Date
Mon Jan 02 2017
Journal Name
Journal Of Educational And Psychological Researches
Toward a theoretical model of the terrorist personality and differentiation from psychopathic personality
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The current theoretical research targeted to construct a model of terrorist personality and its differentiation from psychopathic personality . Several assumptions or theories of perspectives of psychopathic personality have been compared with the terrorist personality studies that concerned . The suggested theoretical  model is interrupting the terrorist personality . The conclusions , discussions are mentioned. Finally, recommendation is suggested .

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Publication Date
Mon May 01 2017
Journal Name
The Journal Of Immunology
Resveratrol improves a murine model of asthma through alterations in the gut microbiome
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Abstract<p>Asthma is a condition characterized by bronchial spasms, inflammation, and mucous hypersecretion which leads to difficulties in respiration. Asthmatic patients are usually presented with recurrent attacks of coughing, wheezing, and shortness of breath which could be life-threatening. More than three million cases of asthma in the United States are diagnosed annually. Resveratrol, a polyphenolic stilbene, is known to be useful in controlling asthmatic attacks via different molecular mechanisms within the lung epithelium and infiltrating immune cells. However, few studies mentioned the effect of resveratrol on the microbiome in ovalbumin-induced asthma mouse model. In this study, we ind</p> ... Show More
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Publication Date
Thu Oct 01 2020
Journal Name
Journal Of Engineering
Developing a Model to Estimate the Productivity of Ready Mixed Concrete Batch Plant
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Productivity estimating of ready mixed concrete batch plant is an essential tool for the successful completion of the construction process. It is defined as the output of the system per unit of time. Usually, the actual productivity values of construction equipment in the site are not consistent with the nominal ones. Therefore, it is necessary to make a comprehensive evaluation of the nominal productivity of equipment concerning the effected factors and then re-evaluate them according to the actual values.

In this paper, the forecasting system was employed is an Artificial Intelligence technique (AI). It is represented by Artificial Neural Network (ANN) to establish the predicted model to estimate wet ready mixe

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Publication Date
Wed Jul 01 2015
Journal Name
Political Sciences Journal
The concept of ethnicity in contemporary American political thought Jerry Mueller, a model ...
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الخلاصة

تشير نظريات علم اجتماع المعرفة الى ان ظهور مفهوم معين او سقوطه لايتم بمحض الصدفة، بل نتيجة تفاعل مجموعة من العوامل الثقافية والسياسية وحتى الاقتصادية ومن هنا فأن ظهور مفهوم الاثنية كان محصلة عوامل كثيرة خصوصاً بعد ان اصبح موضوع الاثنية في العقود الاخيرة من القرن الماضي وبداية القرن الواحد والعشرين محور نقاش رئيس في ميدان البحث الاجتماعي والسياسي، ليس في

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Publication Date
Wed Mar 10 2021
Journal Name
Baghdad Science Journal
On The Dynamical Behavior of a Prey-Predator Model With The Effect of Periodic Forcing
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The dynamical behavior of a two-dimensional continuous time dynamical system describing by a prey predator model is investigated. By means of constructing suitable Lyapunov functional, sufficient condition is derived for the global asymptotic stability of the positive equilibrium of the system. The Hopf bifurcation analysis is carried out. The numerical simulations are used to study the effect of periodic forcing in two different parameters. The results of simulations show that the model under the effects of periodic forcing in two different parameters, with or without phase difference, could exhibit chaotic dynamics for realistic and biologically feasible parametric values.

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Publication Date
Mon Feb 19 2018
Journal Name
Al-academy
The preoccupation of mental image in the designs of internal spaces (cinema) is a model
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The design studies, especially in their contemporary stages, have not been isolated from the subjects that underpin advanced ideas in the field of technical treatments that enrich and improve the social life of users through those technological innovations that have enhanced and changed life styles, Especially in the field of general institutional techniques, including cinemas, as the ideal places for people and visitors to this space, which can contribute to the promotion of cultural, social and technical aspects within this millennium. DONC as reflected on the positive communication and communication between the intellectual and cognitive develop individuals, including cultural and technical side of the individual. The first chapter co

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