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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
Thu Sep 01 2016
Journal Name
Journal Of Engineering
Effect of Using Porcelanite as Partial Replacement of Fine Aggregate on Roller Compacted Concrete with Different Curing Methods
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Roller-Compacted Concrete is a no-slump concrete, with no reinforcing steel, no forms, no finishing and wet enough to support compaction by vibratory rollers. Due to the effect of curing on properties and durability of concrete, the main purpose of this research is to study the effect of various curing methods (air curing, 7 days water curing, and permanent water curing) and porcelanite (local material used as an Internal Curing agent) with different replacement percentages of fine aggregate (volumetric replacement) on some properties of Roller-Compacted Concrete and to explore the possibility of introducing practical Roller-Compacted Concrete for road pavement with minimum requirement of curing. Specimens were sawed fro

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Publication Date
Wed Nov 26 2025
Journal Name
Webology
Is the Stealth Marketing an Element of Promotion Mix? A Review of the Techniques
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Stealth marketing is considered as one of the contemporary issues that researchers have begun to explore as a current understanding. It is the marketing approach used by organizations to promote their products and services to the public in implicit and indirect manner. In this article, the concept of stealth marketing will be discussed throw its advantages and disadvantages. In addition, the different techniques of stealth marketing have been discussed including: viral marketing, celebrity marketing, brand pushers, bait-and-tease marketing, video games marketing, and marketing in music. Furthermore, a new technique of marketing entitled “Marketing through social responsibility” has been added and discussed according to the themes in the

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Publication Date
Thu Jan 20 2011
Journal Name
Journal Of Planner And Development
Architectural void is a revolution in the formation of the facades of digital architecture
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Architecture has evolved through the ages as forms, relationships, materials and mechanisms according to the data of each era and up to the era of digital technology, where the change in proportions and aesthetic dimensions of contemporary architectural formation due to the capabilities of digitization has created innovative plastic properties using the void formation in the facades and the introduction of void as a formative and aesthetic element, which led to The emergence of new creative concepts and ideas that contradict traditional ideas and are consistent with the spirit of the times, led to a revolution in the world of architectural form at the level of (architectural ideas and the generation of shapes, materials and construction

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Publication Date
Mon Feb 01 2016
Journal Name
Al-academy
Building the foundations of a formal system of the laptop table: حنان غازي صالح
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The study of the laptop computer table is one of the important studies at the present time due to the importance of electronic computers that are used in work sites and homes for very long hours, so one of the most important basics of caring for the comfort of the user lies in the design of the laptop table in different shapes and sizes and multiple functions in addition to calculating the measurements of the human body and the extent Its compatibility with the design and measurements of laptop computer tables by taking into account the calculations and measurements of the dimensions of the user's body of all ages and their consistency and use with the general measurements of the tables and the importance of research comes through the es

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Publication Date
Sat Jan 01 2022
Journal Name
Aip Conference Proceedings
Study of ground properties of oxygen isotopes using Cosh potential
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Publication Date
Tue Oct 25 2022
Journal Name
Vi. International Scientific Congress Of Pure, Applied And Technological Sciences
Study the effect of adding alcoholic and aqueous extract of turmeric to processed chees as natural antioxidant and in improving its physicochemical properties
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Publication Date
Mon Mar 15 2021
Journal Name
Al-academy
Study of the participation of Saudi women in official visual arts exhibitions "Contemporary Saudi Art Exhibition as an Example": حنان بنت سعود الهزاع
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This research studies the Saudi women participation in the visual arts, presents descriptive and analytical overview on their artworks and assess development through their participation in the said exhibition, frequency of participation, and aims to understand the most important stages and changes of the subjects addressed, artistic styles and the factors affecting these results in view of female artist's attitude pertaining to several aspects such as administrative organization, judging committees etc.

Interviews were held with a sample of female artists, 17 artists from different regions and generations out of 182 participants and reviewed relevant exhibition literature during the period 1979-2018. The research problem is to id

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Publication Date
Sat Jul 05 2025
Journal Name
Journal Of Machine And Computing
Cyber Neutrosophic Model for Secure and Uncertainty Aware Evaluation in Indoor Design Projects
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To perform a secure evaluation of Indoor Design data, the research introduces a Cyber-Neutrosophic Model, which utilizes AES-256 encryption, Role-Based Access Control, and real-time anomaly detection. It measures the percentage of unpredictability, insecurity, and variance present within model features. Also, it provides reliable data security. Similar features have been identified between the final results of the study, corresponding to the Cyber-Neutrosophic Model analysis, and the cybersecurity layer helped mitigate attacks. It is worth noting that Anomaly Detection successfully achieved response times of less than 2.5 seconds, demonstrating that the model can maintain its integrity while providing privacy. Using neutrosophic sim

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Publication Date
Mon Dec 03 2018
Journal Name
Association Of Arab Universities Journal Of Engineering Sciences
Condition assessment and rehabilitation for trunk sewer deterioration based on Semi-Markov model
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An accurate assessment of the pipes’ conditions is required for effective management of the trunk sewers. In this paper the semi-Markov model was developed and tested using the sewer dataset from the Zublin trunk sewer in Baghdad, Iraq, in order to evaluate the future performance of the sewer. For the development of this model the cumulative waiting time distribution of sewers was used in each condition that was derived directly from the sewer condition class and age data. Results showed that the semi-Markov model was inconsistent with the data by adopting ( 2 test) and also, showed that the error in prediction is due to lack of data on the sewer waiting times at each condition state which can be solved by using successive conditi

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Publication Date
Mon Oct 28 2019
Journal Name
Journal Of Mechanics Of Continua And Mathematical Sciences
Heuristic Initialization And Similarity Integration Based Model for Improving Extractive Multi-Document Summarization
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