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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
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
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 2018
Journal Name
African Journal Of Hospitality, Tourism And Leisure
An analytical study of the strategic flexibility variation as a function of the dynamic capabilities based on supply chain management (Case study: The General Petroleum Products Distribution Company in Baghdad)
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Publication Date
Mon Aug 31 2020
Journal Name
Bmc Oral Health
The success of using 2% lidocaine in pain removal during extraction of mandibular premolars: a prospective clinical study
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Abstract<sec><title>Background

The purpose of this study was to evaluate the anesthetic effectiveness of a buccal infiltration technique combined with local massage (using 2% lidocaine) in the extraction of mandibular premolars to be utilized as an alternative to the conventional inferior alveolar nerve block.

Methods

Patients eligible included any subject with a clinical indication for tooth extraction of the mandibular 1st or 2nd premolars. All patients were anesthetized buccally by local infiltration technique followed by an external pressure applied for 1 min directly over the injection area. In each case, another local

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Publication Date
Thu Dec 01 2022
Journal Name
Baghdad Science Journal
Molecular Characterization of Potential Crop Pathogens Associated with Weeds as Endophytes in Uniilorin Plantations, Nigeria
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Crop diseases are usually caused by inoculum of pathogens which might exist on alternate hosts or weeds as endophytes. These endophytes, cum pathogens, usually confer some beneficial attributes to these weeds or alternate hosts from protection against herbivores, disease resistance, stress tolerance to secondary metabolites production. This study was therefore carried out to isolate potential crop pathogens which exist as endophytes on weed species in the University of Ilorin plantations. Green asymptomatic leaves were collected from 10 weed species across the plantations, and processed for their endophytic fungi isolation. Isolates were purified into pure cultures and used for molecular identification using the internal transcribed spac

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Publication Date
Thu Aug 08 2019
Journal Name
Iop Conference Series: Materials Science And Engineering
A Study of poly4-oxo-4-(4-sulfamoylphenylamino) but-2-enoic acid as a good anti – Corrosion of 316L stainless steel in 0.2M hydrochloric acid solution.
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Publication Date
Sun Dec 31 2023
Journal Name
Lark
Digital and pedagogical practices of French as a foreign language in a post-COVID-19 context (The case of the University of Baghdad)
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Publication Date
Fri Jan 01 2021
Journal Name
Annals Of Pure And Applied Mathematics
Linear Regression Model Using Bayesian Approach for Iraqi Unemployment Rate
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In this paper we used frequentist and Bayesian approaches for the linear regression model to predict future observations for unemployment rates in Iraq. Parameters are estimated using the ordinary least squares method and for the Bayesian approach using the Markov Chain Monte Carlo (MCMC) method. Calculations are done using the R program. The analysis showed that the linear regression model using the Bayesian approach is better and can be used as an alternative to the frequentist approach. Two criteria, the root mean square error (RMSE) and the median absolute deviation (MAD) were used to compare the performance of the estimates. The results obtained showed that the unemployment rates will continue to increase in the next two decade

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Publication Date
Fri May 11 2018
Journal Name
War, Experience And Memory In Global Cultures Since 1914
The Iraqi Prose Poem as a Legacy of the Experience of the 1980s Iraq–Iran War
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The essay investigates the rise and development of the prose poem form in Iraqi poetry in the period during and after the 1980s Iraq–Iran war. The essay follows the legacy of Western experiments with form following the First World War and their impact on the development of form in Iraqi poetry culminating in the prose poem. The dominance of this form on poetic development in this period has a close relationship with the experience of warfare and the ensuing of the cultural changes in Iraq after 1980. Poets of the 1980s war used poetic form as a means of dissent. The prose poem became for them an inherently subversive form that reflected their disaffection with the political, cultural, and literary conflicts of the time. The prose poem in

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