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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
Tue Feb 01 2022
Journal Name
Macromolecular Symposia
Synthesis of 5‐Fluorouracil–Naproxen Conjugates as a Mutual Prodrug for Targeting Cancer Tissues
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Abstract<p>A new 5‐fluorouracil–naproxen conjugate is synthesized as a mutual prodrug for targeting cancer tissues. The structure of the target compound and their intermediate are characterized by their melting point, IR, <sup>1</sup>H NMR, <sup>13</sup>C NMR, and elemental microanalysis. The cytotoxic activity is preliminarily evaluated using nonsmall lung cancer CRL‐2049, human breast cancer CAL‐51, and one type of normal cell line; rat embryo fibroblast cell line. The synthesized compound shows a good cytotoxic effect at the cancer cell and no significant effect at rat embryo fibroblast cell line.</p>
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Publication Date
Fri Sep 02 2022
Journal Name
Military Medical Science Letters
SOLID LIPID NANOPARTICLES AS A PROMISING APPROACH FOR DELIVERY OF ANTICANCER AGENTS: REVIEW ARTICLE
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Cancer disease has a complicated pathophysiology and is one of the major causes of death and morbidity. Classical cancer therapies include chemotherapy, radiation therapy, and immunotherapy. A typical treatment is chemotherapy, which delivers cytotoxic medications to patients to suppress the uncontrolled growth of cancerous cells. Conventional oral medication has a number of drawbacks, including a lack of selectivity, cytotoxicity, and multi-drug resistance, all of which offer significant obstacles to effective cancer treatment. Multidrug resistance (MDR) remains a major challenge for effective cancer chemotherapeutic interventions. The advent of nanotechnology approach has developed the field of tumor diagnosis and treatment. Cancer nanote

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Publication Date
Wed Jul 01 2020
Journal Name
Iop Conference Series: Materials Science And Engineering
Automation in architecture and its effect on the regeneration of traditional buildings: Al-Shawi House as a case study
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Abstract<p>The increased applications of technology in the field of architecture, especially digital technology and aspects of automation, have made a major impact on various aspects of local architecture, especially the traditional ones. As these technologies have succeeded in integrating many technological applications in many traditional and heritage buildings and taking them to more complex uses. And included in it characteristics that were not contained, therefore the research problem was concentrated in the absence of a holistic view of the role of the aspects of automation as a technological and design effect and its mutual effects on traditional buildings (especially the traditional Bagh</p> ... Show More
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Publication Date
Wed Dec 04 2013
Journal Name
Proceedings Of Nuclei Of Seyfert Galaxies And Qsos - Central Engine &amp; Conditions Of Star Formation — Pos(seyfert 2012)
Are Narrow Line Seyfert 1 galaxies a special class of Active Galactic Nuclei?
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No. Due to their apparently extreme optical to X-ray properties, Narrow Line Seyfert 1s (NLSy1s) have been considered a special class of active galactic nuclei (AGN). Here, we summarize observational results from different groups to conclude that none of the characteristics that are typically used to define the NLSy1s as a distinct group – from the, nowadays called, Broad Line Seyfert 1s (BLSy1s) – is unique, nor ubiquitous of these particular sources, but shared by the whole Type 1 AGN. Historically, the NLSy1s have been distinguished from the BLSy1s by the narrow width of the broad Hb emission line. The upper limit on the full width at half maximum of this line is 2000kms−1 for NLSy1s, while in BLSy1s it can be of several thousands

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Publication Date
Fri Jun 01 2012
Journal Name
Journal Of Economics And Administrative Sciences
Handling a problem of transport solid waste in Baghdad City to Healthy landfill sites using transportation Model
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 A problem of solid waste became in the present day common global problem among all countries, whether developing or developed countries, and can say that no country in the world today is immuning from this dilemma which must find appropriate solutions. The problem has reached a stage that can not ignore or delay, but has became a daily problem occupies the minds of ecologists, economists and politicians took occupies center front in the lists of  priorities for the countries in terms of finding solutions to the rapid scientific and radical them. and that transport costs constitute an important component of total costs borne by the municipal districts in the process of disposal of solid waste, so any improvement in the

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Publication Date
Wed Oct 09 2019
Journal Name
Journal Of The College Of Education For Women
Silence as a Means of Communication in Harold Pinter’s The Caretaker
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Harold Pinter’s The Caretaker(1959) clearly portrays a lack of communication among the characters of the play which refers to the condition of modern man. This failure of communication led Harold Pinter to use a lot of pauses and silences in all the plays he wrote instead of words. Samuel Beckett preceded Pinter in doing so in his plays and one way to express the bewilderment of modern man during the 20th century is through the use of no language in the dramatic works. Language is no more important to modern man; instead, he uses silence to express his feelings. Silence is more powerful than the words themselves. That’s why long and short pauses can be seen throughout all Pinter’s plays.

In this play, th

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Publication Date
Tue Mar 15 2022
Journal Name
Al-academy
the indication of the scene as a symbolic system in the Iraqi theatrical
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The theatrical view reflects various connotations and intellectual and aesthetic implications, as the view includes a symbolic geometric, architectural and archetypal connotation suggestive of reality and nature, as theatrical art is the woman that reflects reality, specifically the significance of the theatrical view that reveals to us the philosophical, aesthetic and cognitive dimensions of theatrical trends, so the research came with the methodological framework, which It included the research problem (what is the significance of the scene as a symbolic system in the Iraqi theatrical performance), the importance of the research and the need for it, the research objective, the limits of the research and the most important terms.
A

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Publication Date
Wed Apr 01 2015
Journal Name
Ibn Al-haitham Journal For Pure And Applied Science
Security For Three -Tired Web Application
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Web application protection lies on two levels: the first is the responsibility of the server management, and the second is the responsibility of the programmer of the site (this is the scope of the research). This research suggests developing a secure web application site based on three-tier architecture (client, server, and database). The security of this system described as follows: using multilevel access by authorization, which means allowing access to pages depending on authorized level; password encrypted using Message Digest Five (MD5) and salt. Secure Socket Layer (SSL) protocol authentication used. Writing PHP code according to set of rules to hide source code to ensure that it cannot be stolen, verification of input before it is s

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Publication Date
Fri Nov 20 2020
Journal Name
Solid State Technology
Comparative Study for Bi-Clustering Algorithms: Historical and Methodological Notes
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Publication Date
Sat Oct 01 2016
Journal Name
Journal Of Economics And Administrative Sciences
Practice of Continuous Auditing in accordance with Technology Acceptance Model: An analytical study of a sample of the Iraqi auditing Offices
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Abstract

This paper discusses the essence of the developmental process in auditing firms and offices at the world today. This process is focused on how to adopt the audit concepts which is based on Information and Communication Technology (ICT), including the Continuous Auditing (CA) in particular. The purpose of this paper is to design a practical model for the adoption of CA and its requirements according to the Technology Acceptance Model (TAM). This model will serve as a road map for manage the change and development in the Iraqi auditing firms and offices. The paper uses the analytical approach in reaching to the target results. We design the logical and systematic relations between the nine variable

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