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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
Sun Jan 01 2017
Journal Name
The Iraqi Journal Of Agricultural Science 48 (5), 1197-1205‏
Sex identification of date palm by using dna molecular markers
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Publication Date
Mon Mar 08 2021
Journal Name
Baghdad Science Journal
state selection of ammonia molecular beam using tapered ring focuser
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I've made extensive studies on the distribution of the electric field stable heterogeneous within intensive that contain metal rings with slope diagonal positive to a site halfway to be in its maximum value, followed by decline negative and equally to the other end of the concentrated distributed by electric stable thanking sequentially and have focused empirical studies in the pastthe molecules that you focused Pantqaúha during passage

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Publication Date
Wed Jan 01 2025
Journal Name
Aip Conference Proceedings
Comparative analysis of parameter estimation methods for Meixner process using wavelet packet transform
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The current research creates an overall relative analysis concerning the estimation of Meixner process parameters via the wavelet packet transform. Of noteworthy presentation relevance, it compares the moment method and the wavelet packet estimator for the four parameters of the Meixner process. In this paper, the research focuses on finding the best threshold value using the square root log and modified square root log methods with the wavelet packets in the presence of noise to enhance the efficiency and effectiveness of the denoising process for the financial asset market signal. In this regard, a simulation study compares the performance of moment estimation and wavelet packets for different sample sizes. The results show that wavelet p

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Publication Date
Wed Aug 01 2018
Journal Name
Journal Of Economics And Administrative Sciences
The Impact of Using the international standard for Training (ISO-10015) to Improve the Quality of the Control Activity – A Survey Study at the Federal Board of Supreme Audit.
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The great  importance of training made it as an investment for the organization, and assert the Quality of performance which support it by prepare the employee to the Current and future Jobs . The Research problem a rounded about How to measure the impact of training based on (ISO 10015) and its effect on the Quality of performance , How to evaluation the results of training to attained the training goals . The Research aims to find out the effects of application of international standard guidelines (ISO 10015) to attained the quality of audit work achieved in the Federal Board of Supreme Audit. The Research sought to achieve a number of objectives cognitive and applied on the basis of four key assumptions, and other su

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Publication Date
Tue Nov 01 2022
Journal Name
Journal Of Engineering
Comparative Study on the Hardness of Mechroha Water Springs
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The vacancy of natural resources is undoubtedly limited by time. The sustainable development principle recommends modern technology for its protection and renewal. This project conducted analyses on two underground water sources in the north of Algeria (Mechroha Province). Besides, the use of the hardness factor and the adoption of the titration method, which is  the determining the concentration of an unknown solution using a known solution concentration, have permitted the characterization of the examples taken and to verify their conformity to the standard required, the results found showed HT=6.66 French degrees (oF) ) for Ain Guilloume water spring in comparison to Ain Messai water spring H

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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
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
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
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
Tue Jun 01 2021
Journal Name
Journal Of Planner And Development
Case studies on urban agriculture as a planning strategy for achieving sustainability in cities
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 Urban agriculture is one of the important urban uses of land in cities since the inception of cities and civilizations, but the great expansion of cities in the world during the twentieth century and the beginning of the twentieth century and the increase in the number of urban residents compared to the rural population has led to a decline in this use in favor of other uses.

 This decline in agricultural and green land areas in cities has negatively affected the environment, natural life and biological diversity in cities in addition to the great impact on the climate and the increase in temperatures and the negative impact on the economic side, since urban agriculture is an important pillar of the economy, especially

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