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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
Sun Jun 02 2013
Journal Name
Baghdad Science Journal
Taxonomical and Comparative morphological study for two wild species of the genus Chaenorhinum (D.C.) Reichb. (Scrophulariaceae) in Iraq.
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Comparative morphological study has been treated for two species of the genus Chaenorhinum (D.C.) Richb., These species were: 1. Chaenorhinum calycinum 2. Chaenorhinum rubrifolium (Robill. & cast. Ex Lam. & DC.) Fourr. The genus belong to the family Scorphulariaceae. Morphological characters has been studies for: root, stem, leaves, flowers (calyx, corolla, androcium including filaments and anthers, gynocium including ovary, style and stigma), fruits and seeds also has been characterized. Key for there two species presented using some quantitative characters. Other characters like shape of fruits and seeds were used too, and they were of a useful taxonomic value

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Publication Date
Sun Jan 14 2018
Journal Name
Journal Of Engineering
The effect of Laser Shock Peening on Fatigue Life Using Pure Water and Hydrofluoric Acid As a Confining Layer of Al – Alloy 7075-T6
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Laser shock peening (LSP) is deemed as a deep-rooted technology for stimulating compressive residual stresses below the surface of metallic elements. As a result, fatigue lifespan is improved, and the substance properties become further resistant to wear and corrosion. The LSP provides more unfailing surface treatment and a potential decrease in microstructural damage. Laser shock peening is a well-organized method measured up to the mechanical shoot peening. This kind of surface handling can be fulfilled via an intense laser pulse focused on a substantial surface in extremely shorter intervals. In this work, Hydrofluoric Acid (HF) and pure water as a coating layer were utilized as a new technique to improve the properti

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Publication Date
Thu Feb 01 2018
Journal Name
Journal Of Economics And Administrative Sciences
Evaluation of Common Stocks Using The Fama-French Five Factor Model An Applied Study in The Iraq Stock Exchange
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     The process of stocks evaluating considered as a one of challenges for the financial analysis, since the evaluating focuses on define the current value for the cash flows which the shareholders expected to have. Due to the importance of this subject, the current research aims to choose Fama & French five factors Model to evaluate the common stocks to define the Model accuracy in Fama& French for 2014. It has been used factors of volume, book value to market value, Profitability and investment, in addition to Beta coefficient which used in capital assets pricing Model as a scale for Fama & French five factors Model. The research sample included 11 banks listed in Iraq stock market which have me

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Publication Date
Fri Jan 23 2026
Journal Name
Revista Iberoamericana De Psicología Del Ejercicio Y El Deporte, Issn 1886-8576, Vol. 17, Nº. 6, 2022, Págs. 408-412
A Comparative Study In (resilience And Immunity) Psychological And The Level Of Skillful Performance In Some Ball Skills In Rhythmic Gymnastics Between Students Of The Second And Third Stages
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Autorías: Nuha Mohsin Dhahi, Muhammad Hamza Shihab. Localización: Revista iberoamericana de psicología del ejercicio y el deporte. Nº. 6, 2022. Artículo de Revista en Dialnet.

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Publication Date
Thu Nov 01 2018
Journal Name
Computers & Fluids
Assessing moment-based boundary conditions for the lattice Boltzmann equation: A study of dipole-wall collisions
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Publication Date
Wed Nov 01 2017
Journal Name
Journal Of Economics And Administrative Sciences
Nonparametric statistical study for the crime motives on a sample of inmates in Khartoum State prisons
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The aim of the research was to investigate the use of non-parametric tests in the analysis of the questionnaire and how to choose the appropriate test for testing the hypothesis of the study of crime motives in Khartoum State. The data were collected through the primary sources by designing a questionnaire and distributed to a sample of inmates in Khartoum state; the data were analysis by SPSS program using the analytical statistical method through using some of the suitable non-parametric tests for each case. The most important results of the research were: there was significant relationship between the type of crime and the age group therefore, we found that the age group (20-29) was the most frequent crime particularly, the fi

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Publication Date
Wed Dec 15 2021
Journal Name
Nasaq
A Corpus-Based Approach to the Study of Vocabulary in English Textbooks for Iraqi Intermediate Schools
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Learning the vocabulary of a language has great impact on acquiring that language. Many scholars in the field of language learning emphasize the importance of vocabulary as part of the learner's communicative competence, considering it the heart of language. One of the best methods of learning vocabulary is to focus on those words of high frequency. The present article is a corpus based approach to the study of vocabulary whereby the research data are analyzed quantitatively using the software program "AntWordprofiler". This program analyses new input research data in terms of already stored reliable corpora. The aim of this article is to find out whether the vocabularies used in the English textbook for Intermediate Schools in Iraq are con

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Publication Date
Fri Nov 01 2013
Journal Name
American Journal Of Dermatology And Venereology
Topical Adapalene 0.1% Gel versus Topical Combination of (Tretinoin 0.025% and Erythromycin 4%) Gel in Treatment of AcneVulgaris (A Split Face Comparative Study)
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HR Al-Hamamy, AA Noaimi, HA Salman, NAA Jabbar, American Journal of Dermatology and Venereology, 2013

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Publication Date
Fri Jan 23 2026
Journal Name
Journal Of Baghdad College Of Dentistry
Caries severity in relation to oral health knowledge and behavior of third and fifth year dental students / University of Baghdad (A comparative study)
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Background: Tooth wear is one of the most common problems in the older dentate population which results from the interaction of three processes (attrition, abrasion and erosion) and it affects all societies, different age groups, and all cultures. This study was achieved to evaluate the prevalence and distribution of tooth wear among institutionalized residents in Baghdad city\ Iraq. Subjects and Methods: This survey was accomplished on four private and one governmental institution in Baghdad city. One-hundred twenty three (61 males, 62 females) aged 50-89 years were participated in this study. The diagnosis and recording of tooth wear were according to criteria of Smith and Knight. Results: The prevalence of tooth wear was 100% with a mean

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Publication Date
Sat Jan 02 2021
Journal Name
Journal Of The College Of Languages (jcl)
The comparative method in Maupassant’s (A woman’s Life): Le système comparatif dans Une vie de Maupassant
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The comparative method plays a major role in Maupassant’s novel (A woman’s Life).This is due to a good theme choice and smooth writing style characterized by simplicity, spontaneity and brevity.

The author uses the comparative method in the introduction of his novel where he compares the monastery’s closed world to the open world of the countryside of La Normandie, which represents the dream life of the heroine Jeanne.

The present paper is an attempt to answer the question regarding the importance of applying the comparative method in the novel (A Woman’s Life) by Maupassant. The paper stresses the fact that the novelist employs the comparative method in his book for certain features .One of these features is the

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