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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 Jun 01 2007
Journal Name
Journal Of The College Of Languages (jcl)
Old Age as a Motif In the Poetry of W.B. Yeats (1865-1939)
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In 1908 , the American poet Ezra Pound (1885-1972) , the central figure in the modern movement who was the driving force behind several movements , notably Imagism and Vorticism , met the Irish poet W. B. Yeats in London . Pound was employed as his secretary and the two soon became close friends . He found Yeats a realist, symbolist and a metaphysical poet with an uncanny power over words and regarded him the greatest living poet .The poetical style and the occult beliefs of the Irish poet drew the attention of the American Imagist .During the war, Pound and Yeats lived together at Stone Cottage in Sussex studying Japanese literature .Speaking of Yeats , T. S. Eliot described him as "one of those few whose history is the history of their

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Publication Date
Mon Jan 01 2024
Journal Name
Journal Of Engineering
Evaluating the Moisture Susceptibility of Asphalt Mixtures Containing Aluminum Dross as a Filler
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One of the most essential components of asphalt pavements is the filler. It serves two purposes. First, this fine-grained material (diameter less than 0.075 mm) improves the cohesiveness of aggregate with bitumen. Second, produce a dense mixture by filling the voids between the particles. Aluminum dross (AD), which is a by-product of aluminum re-melting, is formed all over the world. This material causes damage to humans and the environment; stockpiling AD in landfills is not the best solution. This research studies the possibility of replacing part of the conventional filler with aluminum dross. Three percent of dross was used, 10, 20, and 30% by filler weight. The MarshallMix design method was adopted to obtain the op

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Publication Date
Mon Mar 08 2021
Journal Name
Baghdad Science Journal
a study of the womens collages in usa
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The study aims to identify the colleges women in the USA where he was browsing the Internet for five universities and sixty-two women's college located these colleges in 25 states only three general and other civil 51% supported by the churches and religious associations of various began its founding in Alqrnn eighteenth and continued in the nineteenth and twentieth and to provide an opportunity for women to complete higher education, while most men's colleges opened their doors to the admission of women and turned it on coeducation

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Publication Date
Sat Sep 30 2017
Journal Name
College Of Islamic Sciences
Semantic Exchange A study of rooting the term
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The term "semantic exchange" was popularized in Arabic, especially in derivatives, grammatical structures, etc., but it came under different names or terms, including deviation, deviation, transition, displacement, tooth breach, replacement, attention, etc. In the rooting of this term through its study in language and terminology, and among linguists, grammar and others, we have reached a number of results, including The existence of a harmonization between the lexical and idiomatic meaning of the term exchange, and the phenomenon of semantic exchange is a form of expansion in language, and that the first language scientists They had turned to this And studied under Cairo for different names, as noted above.

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Publication Date
Mon Jan 01 2024
Journal Name
Medical Research Archives
Genetic Polymorphism for the Gene Encoding Endoplasmic Reticulum Aminopeptidase-1 (ERAP-1) in Iraqi Patients with Ankylosing Spondylitis
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Ankylosing spondylitis (AS) is a common, highly heritable inflammatory arthritis affecting primarily the spine and pelvis. This study was aimed to investigate the relationship between the rs27044 polymorphism in Endoplasmic reticulum aminopeptidase-1 (ERAP-1) with the susceptibility and severity of AS correlated with some biochemical markers such as hematological parameter (Erythrocytes sedimentation rate (ESR)) and immunological parameters (C-reactive protein (CRP), Human leukocyte antigen-B27 (HLA-B27), Interlukin-6 (IL-6) and Interlukin-23 (IL-23)), and oxidative stress parameters (Glutathione (GSH) and Malondialdehyde (MDA)) in a sample of Iraqi population. A total of 60 blood samples were collected from AS patients requited Rhe

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Publication Date
Sun Mar 07 2010
Journal Name
Baghdad Science Journal
Serum ceruloplasmin ,copper and iron levels as a risk factors for coronary heart diseases(CHD)
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Ceruloplasmin (Cp) is one of the acute phase protein, in this review ,we studied the level of ceruloplasmin with copper (Cu) and iron in 90 patients with coronary heart diseas ( those patients are divided into three groups, whom are stable angina , unstable angina and myocardial infarction compared with 30 healthy volunteers) and the roles of them as diagnostic and prognostic tools.The diagnosis was attend by a clinical examination carried out by the consult medical staff in Ibn AL-Nafis hospital. The result: ceruloplasmin recorded a significantly(p<0.05)higher level in all patient groups compared with the control, so this result supports the hypothesis that a high serum ceruloplasmin level is a risk factor for coronary heart di

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Publication Date
Sat Nov 01 2025
Journal Name
Construction And Building Materials
Polyalphaolefin as a potential modifying agent for hard asphalt cement: Physical, rheological, and chemical characterization
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Hard-grade asphalt binders like AC20-30 typically exhibit excessive stiffness, reduced penetration, and compromised workability, necessitating modification before use in paving applications. This study evaluates the efficacy of regular polyalphaolefin (PAO), a synthetic olefin-based lubricant, as a performance-enhancing modifying agent for such binders. AC20-30 was blended with PAO at dosages ranging from 2 wt.% to 10 wt.%, and the modified binders were characterized via penetration, ductility, softening point, and rotational viscosity measurements, alongside advanced rheological and chemical-morphological analyses. Incorporating PAO in AC20-30 asphalt progressively reduced the binder stiffness and enhanced its flexibility, with all modifie

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Publication Date
Mon Aug 17 2020
Journal Name
Biochemical And Cellular Archives
SERUM FERRITIN AS A BIOMARKER FOR THYROID GLAND (HYPO AND HYPER) THYRODISM WITH METABOLIC SYNDROME
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Publication Date
Wed May 10 2023
Journal Name
Journal Of Engineering
DOUBLE DIFFUSIVE FREE CONVECTION IN A PACKED BED SQUARE ENCLOSURE BY USING LOCAL THERMAL NON-EQUILIBRIUM (LTNE) MODEL
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In the present study, free convection heat and mass transfer of fluid in a square packed bed enclosure is numerically investigated. For the considered geometrical shape, the left vertical wall of enclosure was assumed to be kept at high temperature and concentration while the opposite wall was kept at low temperature and concentration with insulating both the top and bottom walls of enclosure. The Brinkman– Forchheimer extended Darcy model was used to solve the momentum equations, while the energy equations for fluid and solid phases were solved by using the local thermal non-equilibrium (LTNE) model.Computations are performed for a range of the Darcy number from 10-5 to 10-1, the porosity from 0.5 to 0.9, and buoyancy ratio from -15 t

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Publication Date
Sun Jun 01 2014
Journal Name
Baghdad Science Journal
Are obese women potential for inflammatory process? A pilot study
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This study was designed to look for certain biochemical markers(serum uric acid and serum peroxynitrite) in women presented with obesity and to compare the level of these markers with non-obese women. A total number of 63 women were recruited from outpatients and private clinics to admit in this study. The patients were grouped into non obese women (Group I) and obese women (Group II). The anthropometric and blood pressure were determined and venous blood was obtained from each patient for determination of C-reactive protein, uric acid and peroxynitrite. The results showed that there were no significant differences in age or in concomitant or associated diseases in both groups except rheumatoid arthritis which account 80% of group I and 25%

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