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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
Sat Apr 01 2023
Journal Name
Baghdad Science Journal
Honeyword Generation Using a Proposed Discrete Salp Swarm Algorithm
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Honeywords are fake passwords that serve as an accompaniment to the real password, which is called a “sugarword.” The honeyword system is an effective password cracking detection system designed to easily detect password cracking in order to improve the security of hashed passwords. For every user, the password file of the honeyword system will have one real hashed password accompanied by numerous fake hashed passwords. If an intruder steals the password file from the system and successfully cracks the passwords while attempting to log in to users’ accounts, the honeyword system will detect this attempt through the honeychecker. A honeychecker is an auxiliary server that distinguishes the real password from the fake passwords and t

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Publication Date
Tue Aug 01 2023
Journal Name
Journal Of Engineering
Risk Response in Construction Project: A Review Study
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Construction projects are characterized as projects with multi phases and activities, complex, unique, and have many different parties and stakeholders. Risks could appear at one or more of the construction project stages and may affect the achievement of project objectives. Therefore, one of the key elements in the planning phase of any project is the risk management process (RMP). This study attempts to understand the terminology of risk in general, risk management, and response to risk in particular. This study is mainly a review of thirty-eight studies that have been published between 1997 and 2020 that demonstrate the importance of the crucial phase of risk response from the risk management process and its impact on

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Publication Date
Fri Jun 30 2023
Journal Name
Samarra Journal Of Pure And Applied Science
Preclinical Oral Histology Research: A Retrospective Review Study
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A retrospective study is conducted to identify factors that improve prospective animal studies; contribute to the optimization of animal protection from all unnecessary and preventable damage. Preclinical oral histology research from 2010-2020 is evaluated and 64 studies were reviewed relating to two interventions: bone trauma and surgical incision. The harm-benefit analysis is featured in this study through the application of the recent form of Bateson's Cube. Depending on its three axes, we can assess animal suffering, the likelihood of benefit, and the importance of research. The total number of animals used in the research is 2685. Rats, 51.6%, and rabbits, 48.4%, are the most commonly used animals. Research related to bone healing acco

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Publication Date
Sat Apr 01 2017
Journal Name
Al–bahith Al–a'alami
Quranic Words Referring to Lies A Media Study
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This research aims to invest qur›anic words referring to lie in media language. The researcher has chosen a set of qur›anic words functioning as «lie».
It is an attempt to review the media language which is used to make use of repetition of terms and templated which make it weak and ineffective language. The use of qur›anic texts and terms according to the semantic field for each topic will give this media language an opportunity for growth, development and stability.
This researcher identifies a number of words to study them in the light of their lexical meaning using the Dictionary of Language Standards by Ibn Fares as it focuses on the general meaning of the root language. He also uses the Dictionary of the Basis of Rhe

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Publication Date
Mon Jul 25 2022
Journal Name
Studies In Pragmatics And Discourse Analysis
Negation in American Discourse: A Socio-Cognitive Study
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The present study cognitive aims to investigate the negation phenomenon in American political discourse under Critical Discourse Analysis (CDA) principles. The research sample includes two speeches given by Clinton and Trump in their election campaigns in 2016. Since the nature of the study follows the social-cognitive approach, the researcher adopted two models of analysis to achieve the study’s objectives: First, the theoretical framework of MST (developed by Fauconnier (1994), Fauconnier and Sweetser (1996) to examine meaning construction resulting from building different levels of negative mental spaces by two different genders the selected speeches. Second, pragmatic model to examine the role of gender from the functional per

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Publication Date
Mon Mar 08 2021
Journal Name
Baghdad Science Journal
A study copepoda invertebrates ecology in lower Zab
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The samples were collected monthly crustaceans Mjmafah foot of two stations in tributary Zab down and two others in the Tigris River for one year with effect from November 2001 until October 2002 recorded during the study period the current 41 units taxonomic and were higher density of Mjmafah foot Guy Tigris River before the mouth of the tributary

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Publication Date
Thu Jun 18 2020
Journal Name
Rimak International Journal Of Humanities And Social Sciences
STRESS IN ENGLISH AND ARABIC: A CONTRASTIVE STUDY
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DBN Rashid, Rimak International Journal of Humanities and Social Sciences, 2020

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Publication Date
Thu Jun 01 2006
Journal Name
Journal Of The College Of Languages (jcl)
Demonstratives in English and Arabic : A Contrastive Study
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This paper studies the demonstratives as deictic expressions in Standard Arabic and English by outlining their phonological, syntactic and semantic properties in the two languages. On the basis of the outcome of this outline, a contrastive study of the linguistic properties of this group of deictic expressions in the two languages is conducted next. The aim is to find out what generalizations could be made from the results of this contrastive study.

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Publication Date
Mon Mar 01 2021
Journal Name
Journal Of Professional Nursing
Incivility among nursing faculty: A multi-country study
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Publication Date
Thu Mar 30 2017
Journal Name
Iraqi Journal Of Pharmaceutical Sciences ( P-issn 1683 - 3597 E-issn 2521 - 3512)
Single Dose Antibiotic Prophylaxis in Outpatient Oral Surgery Comparative Study
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         It is clear that correct application of antibiotic prophylaxis can reduce the incidence of infection  resulting from the bacterial  inoculation in a variety of clinical situations; it cannot   prevent  all  infections  any  more  than it  can   eliminate  all  established infections. Optimum  antibiotic   prophylaxis  depends on:  rational  selection  of the drug(s),  adequate  concentrations  of the  drug  in  the  tissues that  are at risk, and attention to  timing  of  administration.  Moreover,  the  risk  of

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