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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
Fri Mar 21 2025
Journal Name
Iklil For Human Studies
Review Article A Feminist Gothic in the American Literary Fiction
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Teresa Fitzpatrick presents a connection between oppressed women and the plant of Wisteria in gothic fiction in her article “Wisteria: A Female Eco-Gothic Metaphor in American Fiction Through the Ages.” The connection between women and nature is common in literature as women are usually compared to the beauty or ferocity of flowers, rivers, or natural phenomena in general. The connection extends to the architecture and sort of plants that appear in gothic literature. Gothic novels have routinely been connected to the secrets and life stories of women who cannot have the liberty to live or share them outside their homes. A fearful house with a prisoned person, ghost, or a secret is mostly normally found in gothic writing. Women have exce

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Publication Date
Sat Sep 24 2022
Journal Name
Arab World English Journal
Conflict in Atwood’s The Handmaid’s Tale: A Critical Discourse Approach
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Conflict is a common but complicated phenomenon. It has been extensively researched in many domains, including philosophy, sociology, psychology, and linguistics. Using the Critical Discourse Approach, this study examines the issue of self-society conflict in The Handmaid’s Tale. The significance of this work lies in the identification and explanation of the discursive strategies that force the ideological polarization of the positively portrayed self versus the negatively portrayed other. The purpose of this study is to answer two questions: what are the discursive strategies used in The Handmaid’s Tale to create a positive or negative representation, and how are these strategies implemented? Five extracts from The Handmaid’s

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Publication Date
Sat Sep 01 2007
Journal Name
Al-khwarizmi Engineering Journal
A Fully Computerized Method to Backup the Router Configuration File
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This paper presents a fully computerized method to backup the router configuration file. The method consists of a friendly graphical interface programmed by Java programming language.

    The proposed method is compared with the two existing methods, namely: TFTP server method and Copy/Paste method. The comparison reveals that the proposed method has many advantages over the existing ones. The proposed method has been implemented on Cisco routers (series 2500, 2600 and 2800).

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Publication Date
Tue May 01 2018
Journal Name
Journal Of Physics: Conference Series
Evaluation of the Epoxy/Antimony Trioxide Nanocomposites as Flame Retardant
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Publication Date
Wed Jan 01 2025
Journal Name
Rsc Advances
Development of a multi-source blue light irradiation platform for photometric quantification of ascorbic acid <i>via</i> continuous absorbance quenching of the ferric–thiocyanate complex
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Diagram of CFIA system: (A) Fe 3+ line; (B) SCN line; (C) A.A carrier; (D) sample valve; (E) mixing/reaction coil quenched by A.A; (F) blue LED detector.

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Publication Date
Wed Jan 02 2019
Journal Name
Journal Of Educational And Psychological Researches
An Instructional Design According to the Active Learning Model and Its Effect on Students' Achievement in Chemistry for Fifth Intermediate Stage
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The objective of the research is to identify the effect of an instructional design according to the active learning modelsالباحثين in the achievement of the students of the fifth grade, the instructional design was constructed according to the active learning models for the design of education. The research experience was applied for a full academic year (the first & the second term of 2017-2018). The sample consisted of 58 students, 28 students for the experimental group and 30 students for the control group. The experimental design was adopted with partial and post-test, the final achievement test consisted of (50) objectives and essays items on two terms, the validity of the test was verified by the adoption of the Kudoric

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Publication Date
Sat Jul 01 2023
Journal Name
Journal Of Engineering
Comparative Reliability Analysis between Horizontal-Vertical-Diagonal Code and Code with Crosstalk Avoidance and Error Correction for NoC Interconnects
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Ensuring reliable data transmission in Network on Chip (NoC) is one of the most challenging tasks, especially in noisy environments. As crosstalk, interference, and radiation were increased with manufacturers' increasing tendency to reduce the area, increase the frequencies, and reduce the voltages.  So many Error Control Codes (ECC) were proposed with different error detection and correction capacities and various degrees of complexity. Code with Crosstalk Avoidance and Error Correction (CCAEC) for network-on-chip interconnects uses simple parity check bits as the main technique to get high error correction capacity. Per this work, this coding scheme corrects up to 12 random errors, representing a high correction capac

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Publication Date
Sun Sep 03 2023
Journal Name
Al-mansour Journal
Biometrics Systems Challenges in a Post-COVID-19 Pandemic World: A review
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One of the most serious health disasters in recent memory is the COVID-19 epidemic. Several restriction rules have been forced to reduce the virus spreading. Masks that are properly fitted can help prevent the virus from spreading from the person wearing the mask to others. Masks alone will not protect against COVID-19; they must be used in conjunction with physical separation and avoidance of direct contact. The fast spread of this disease, as well as the growing usage of prevention methods, underscore the critical need for a shift in biometrics-based authentication schemes. Biometrics systems are affected differently depending on whether are used as one of the preventive techniques based on COVID-19 pandemic rules. This study provides an

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Publication Date
Sat Oct 01 2022
Journal Name
Al–bahith Al–a'alami
ADVERTISING CAMPAIGNS IN TV CHANNELS : (A Research Drawn from A Master Thesis)
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Television culture has become the most dangerous of our time. It manipulates with minds and hearts together; and forms consciousness. It transforms societies into actual forces rejecting certain principles by guiding the media landscape through visible connotations acceptable to the public; or provokes the citizen against elements that put a burden on the viewer or the public in order to create a positive reaction to the subject of combating terrorism by combining these ads in line with what the public wants of security and tranquility and a decent living after suffering from terrorism in the past years.

Therefore, this research deals with television advertisements as one of the most important fo

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Publication Date
Wed Jan 30 2019
Journal Name
Journal Of Accounting And Financial Studies ( Jafs )
The Effect of The Tax Core Competencies in The Tax Settlement: An Empirical Study of The General Commission for Taxes
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This Study Sought to Determine The Relationship and Impact Between The Tax Core Capabilities and Tax Settlement The Study Took Place in The Tax Administration, and Based The Problem Was to Two Hypotheses As Solutions Initial Mocked Content to Explain The Relationship Between The Phenomena, and to Test The Validity of Assumptions And Due To The Fact That The General Authority for Taxes is The Body for The Advancement of The Collection Tax In Iraq Random Sample Was Selected to Represent The Population of The Study, Since The Sample Included 22 Individuals Representing 70% of The Total Community to Study, Represented by The Director General, Agents and Directors of Departments and Branch Managers Managers Working in The General Authority fo

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