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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 May 24 2026
Journal Name
Al–bahith Al–a'alami
THE IMPACT OF ENTERTAINMENT PROGRAMS IN ARAB SATELLITE CHANNELS ON THE SOCIAL BEHAVIOR OF IRAQI YOUTH (Field study)
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Our research is based on the fact that the reflection of entertainment programs in Arab satellite channels on the social behavior of Iraqi youth … a field analysis of the Arab ldol program) and that its importance is the entertainment programs and their reflection on social behavior، which occupies
large areas of time from Satellite channels in the form of various episodes and each episode contains several categories، or in the form of templates and forms of various goals and contents، but the problem of
research boils down to (how far iraqi youth follow the entertainment programs in Arab satellite channels and what are the motives for watching the Program Arab ldol )) by For Iraqi youth and what are the positive and negative

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Publication Date
Wed Feb 15 2017
Journal Name
كلية بغداد للعلوم الاقتصادية الجامعة
Competitiveness of business organizations according to the role of knowledge management and customer orientation: a comparative survey study in Iraqi business organizations
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The research aims to reach a set of objectives concerning creation a clear vision about conceptual, philosophical and practical dimension of relations, and effects between knowledge management, costumer orientation and competitiveness to construct a framework of a pragmatic model as a solution to research problem and its questions which the main one is about the role of knowledge management and costumer orientation in competitiveness of business organizations. To achieving this goal, it was necessary to make, in priory, a review and discussion to the theoretical dimension of research variables to have a clear vision about constructing hypostatical research model implying a set of hypotheses which, by proving them in companies studied, repr

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Publication Date
Wed Jan 01 2025
Journal Name
Lecture Notes In Networks And Systems
The Impact of AI-Based Pronunciation and Dialogue Apps on English Language Acquisition: A Comparative Phonetic Study of ELSA Speak and Mondly
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Publication Date
Tue Apr 01 2025
Journal Name
Journal Of Economics And Administrative Sciences
Spatial Quantile Autoregressive Model: A Review
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This paper is specifically a detailed review of the Spatial Quantile Autoregressive (SARQR) model that refers to the incorporation of quantile regression models into spatial autoregressive models to facilitate an improved analysis of the characteristics of spatially dependent data. The relevance of SARQR is emphasized in most applications, including but not limited to the fields that might need the study of spatial variation and dependencies. In particular, it looks at literature dated from 1971 and 2024 and shows the extent to which SARQR had already been applied previously in other disciplines such as economics, real estate, environmental science, and epidemiology. Accordingly, evidence indicates SARQR has numerous benefits compar

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Publication Date
Tue Apr 01 2025
Journal Name
Journal Of Economics And Administrative Sciences
Spatial Quantile Autoregressive Model: A Review
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This paper is specifically a detailed review of the Spatial Quantile Autoregressive (SARQR) model that refers to the incorporation of quantile regression models into spatial autoregressive models to facilitate an improved analysis of the characteristics of spatially dependent data. The relevance of SARQR is emphasized in most applications, including but not limited to the fields that might need the study of spatial variation and dependencies. In particular, it looks at literature dated from 1971 and 2024 and shows the extent to which SARQR had already been applied previously in other disciplines such as economics, real estate, environmental science, and epidemiology. Accordingly, evidence indicates SARQR has numerous benefits compar

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Publication Date
Wed Feb 01 2023
Journal Name
Periodicals Of Engineering And Natural Sciences (pen)
Bitcoin Prediction with a hybrid model
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In recent years, Bitcoin has become the most widely used blockchain platform in business and finance. The goal of this work is to find a viable prediction model that incorporates and perhaps improves on a combination of available models. Among the techniques utilized in this paper are exponential smoothing, ARIMA, artificial neural networks (ANNs) models, and prediction combination models. The study's most obvious discovery is that artificial intelligence models improve the results of compound prediction models. The second key discovery was that a strong combination forecasting model that responds to the multiple fluctuations that occur in the bitcoin time series and Error improvement should be used. Based on the results, the prediction acc

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Publication Date
Tue Feb 28 2023
Journal Name
Periodicals Of Engineering And Natural Sciences (pen)
Bitcoin Prediction with a hybrid model
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. In recent years, Bitcoin has become the most widely used blockchain platform in business and finance. The goal of this work is to find a viable prediction model that incorporates and perhaps improves on a combination of available models. Among the techniques utilized in this paper are exponential smoothing, ARIMA, artificial neural networks (ANNs) models, and prediction combination models. The study's most obvious discovery is that artificial intelligence models improve the results of compound prediction models. The second key discovery was that a strong combination forecasting model that responds to the multiple fluctuations that occur in the bitcoin time series and Error improvement should be used. Based on the results, the prediction a

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Publication Date
Tue Nov 19 2024
Journal Name
Review Of Clinical Pharmacology And Pharmacokinetics - International Edition
Clinical use of tumor necrosis factor-alpha inhibitors in Iraq: a review of their documented efficacy, safety, and associated genetics
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This comprehensive review examines the efficacy and safety of tumor necrosis factor-alpha (TNF-α) inhibitors in treating various autoimmune diseases, and focuses on their application in Iraqi patients. Elevated TNF-α levels are linked to autoimmune disorders, leading to the development of anti-TNF-α therapies such as infliximab, etanercept, adalimumab, certolizumab pegol, and golimumab, which have gained FDA approval for conditions like psoriasis, in¬flammatory bowel disease, ankylosing spondylitis, and rheumatoid arthritis. While these therapies demonstrate sig¬nificant therapeutic benefits, including improved quality of life and disease management, they also carry risks, such as increased susceptibility to infections and pote

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Publication Date
Sun Dec 01 2019
Journal Name
2019 First International Conference Of Computer And Applied Sciences (cas)
A Comparison for Some of the estimation methods of the Parallel Stress-Strength model In the case of Inverse Rayleigh Distribution
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Publication Date
Tue Aug 15 2023
Journal Name
Journal Of Current Researches On Social Sciences
An Examination of Discourse Investigation of Fallacies in Religious Texts: Islam as a Case Study
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BN RASHİD, 2023

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