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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 Jan 30 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
Sat Jul 01 2023
Journal Name
Journal Of Engineering
Using of Constructed Wetlands in The Treatment of Wastewater: A Review for Operation and Performance: Review for Using of Constructed Wetlands in The Treatment of Wastewater: Operation and Performance
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Wastewater recycling for non-potable uses has gained significant attention to mitigate the high pressure on freshwater resources. This requires using a sustainable technique to treat natural municipal wastewater as an alternative to conventional methods, especially in arid and semi-arid rural areas. One of the promising techniques applied to satisfy the objective of wastewater reuse is the constructed wetlands (CWs) which have been used extensively in most countries worldwide through the last decades. The present study introduces a significant review of the definition, classification, and components of CWs, identifying the mechanisms controlling the removal process within such units. Vertical, horizontal, and hybrid CWs

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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 30 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 Dec 18 2021
Journal Name
Egyptian Journal Of Chemistry
Coumarin based-histone deactylace HADC inhibitors
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Coumarins have been recognized as anticancer competitors. HDACis are one of the interesting issues in the field of antitumor research. In order to achieve an increased anticancer efficacy, a series of hybrid compounds bearing coumarin scaffolds have been designed and synthesized as novel HDACis, In this review we present a series of novel HDAC inhibitors comprising coumarin as a core e of cap group of HDAC inhibitors that have been designed, synthesized and assessed for their enzyme inhibitory activity as well as antiproliferative activity. Most of them exhibited potent HDAC inhibitory activity and significant cytotoxicity

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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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Publication Date
Sun Nov 01 2015
Journal Name
Journal Of Cosmetics, Dermatological Sciences And Applications
A Comparative Study of Topical Azailic Acid Cream 20% and Active Lotion Containing Triethyl Citrate and Ethyl Linoleate in the Treatment of Mild to Moderate Acne Vulgaris
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HR Al-Hamamy, AA Noaimi, IA Al-Turfy, AI Rajab, Journal of Cosmetics, Dermatological Sciences and Applications, 2015

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Publication Date
Fri Jan 01 2021
Journal Name
Aip Conference Proceedings
Plasma levels and diagnostic utility of MMP-2 and TIMP-2 in the diagnosis of Iraqi women with breast tumor: A comparative study with Ca 15-3
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Publication Date
Fri Jan 01 2021
Journal Name
Aip Conference Proceedings
Plasma levels and diagnostic utility of MMP-2 and TIMP-2 in the diagnosis of Iraqi women with breast tumor: A comparative study with Ca 15-3
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Publication Date
Tue Dec 01 2020
Journal Name
Journal Of Economics And Administrative Sciences
The effect of the Iraqi dinar exchange rate on inflation and economic growth using the joint integration methodology "a standard study"
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The exchange rate is of great importance at the global and local levels alike, as this importance increases with the increasing rates of development of economic relations between countries of the world due to openness and integration into the global economy, expressed by the expansion of the volume of trade and financial relations between countries. The Central Bank of Iraq has set the need to stabilize this price as a goal to reduce inflation rates and reduce them to the internationally accepted rates by using the foreign currency sale window to achieve a balance between the forces of supply and demand for foreign currency and to preserve the value of the Iraqi dinar. The research concluded that the central bank was It has a maj

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