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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
Mon Jul 10 2023
Journal Name
Journal Of Engineering
Rhythm As Creative System In Houses Architecture Comparative Application Study Between Heritage And Contemporary Houses
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Rhythm is considered one of the creative concepts in the recent architectural thought; it has emerged clearly as a mean of creating the highest levels of creativity in architecture, especially in contemporary architectural movements. The importance of rhythm has  emerged, especially, when the architecture , its beginnings concentrated on the principle of the links with poetic structures. Many architectural studies deal with concept of rhythm in architecture with different ways various according to the trend of each study, this show the importance of studying the concept of rhythm in the architectural field in general. This study try to focus on the utilization of rhythm as creative system in architecture of heritage and contemporary

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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
Mon Jan 01 2018
Journal Name
Journal Of The College Of Languages (jcl)
‘There is no place like home’: A Comparative Study of the Meaning of Home in The Wonderful Wizard of Oz and Peter and Wendy
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The Wonderful Wizard of Oz and Peter and Wendy present universal ideas that exist in all times, despite being written in the beginning of the 20th century. Among the most significant ones is the concept of “home”. The article discusses the essentiality of the idea of “home” where the identity of an individual shapes, and where one’s spiritual, psychological, and physical being develop. It also studies the attitudes of each protagonist towards the concept of ‘home’ based on their understanding of it and according to their gender differences. The characters in both stories tread on the path of perplexity between leaving their homes and returning to them. Peter’s world is the world of imagination while Doro

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Publication Date
Wed Dec 14 2016
Journal Name
Journal Of Baghdad College Of Dentistry
Comparative Evaluation of the Effect of Different Universal Adhesives and Bonding Techniques on the Marginal Gap of Class I Composite Restoration (A SEM Study)
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Background: With the increase in composite material use in posterior teeth, the concerns about the polymerization shrinkage has increased with the concerns about the formation of marginal gaps in the oral cavity environment. New generation of adhesives called universal adhesive have been introduced to the market in order to reduce the technique sensitive bonding procedures to give the advantage of using the bonding system in any etching protocol without compromising the bonding strength. The aim of the study was to study marginal adaptation of two universal adhesives (Single bondâ„¢ Universal and Prime and Bond elect) using 3 etching techniques under thermal cycling aging. Materials and Methods: Forty-eight sound maxillary first premola

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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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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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