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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 Aug 08 2025
Journal Name
Journal Of Baghdad College Of Dentistry
An Evaluation of the Efficacy of Different Gingival Retraction Materials on the Gingival Tissue Displacement (A Comparative In Vivo Study)
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Background: An accurate adaptation of the crown to the finish line is essential to minimize cement dissolution and to preserve periodontium in fixed partial denture cases. An accurate adaptation of crown is possible only when preparation details are captured adequately in the impression and transferred to cast. For these reasons, gingival displacement is necessary to capture subgingival preparation details.The aim of the present study is to measure in vivo the horizontal displacement of the gingival sulcus obtained by using three new cordless retraction materials (Magic Foam Cord®, Racegel and Astringent Retraction Paste) in comparison to medicated retraction cord. Materials and method: Thirty-two patients requiring porcelain fused to me

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Publication Date
Sun Mar 05 2017
Journal Name
Baghdad Science Journal
Study a concentration of Uranium for samples of soil from Falluja City using PM-355
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In this study a concentration of uranium was measured for twenty two samples of soil distributed in many regions (algolan, almoalmeen, alaskary and nasal streets) from Falluja Cityin AL-Anbar Governorate in addition to other region (alandlos street) as a back ground on the Falluja City that there is no military operations happened on it. The uranium concentrations in soil samples measured by using fission tracks registration in (PM-355) track detector that caused by the bombardment of (U) with thermal neutrons from (241Am-Be) neutron source that has flux of (5×103n cm-2 s-1). The concentrations values were calculated by a comparison with standard samples. The results shows that the uranium concentrations algolan street varies from(1.

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Publication Date
Sun Nov 01 2015
Journal Name
Iosr Journal Of Dental And Medical Sciences (iosr-jdms)
Acanthosis Nigricans as a Cause of Facial M Elanosis (Clinical Andhistopathological Study
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PKE Sharquie MD, PDPAA Noaimi MD, DDV, FDSM Al-Ogaily MD, IOSR Journal of Dental and Medical Sciences (IOSR-JDMS), 2015

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Publication Date
Mon Feb 01 2021
Journal Name
Journal Of Engineering
Electrical Conductivity as a General Predictor of Multiple Parameters in Tigris River Based on Statistical Regression Model
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Surface water samples from different locations within Tigris River's boundaries in Baghdad city have been analyzed for drinking purposes. Correlation coefficients among different parameters were determined. An attempt has been made to develop linear regression equations to predict the concentration of water quality constituents having significant correlation coefficients with electrical conductivity (EC). This study aims to find five regression models produced and validated using electrical conductivity as a predictor to predict total hardness (TH), calcium (Ca), chloride (Cl), sulfate (SO4), and total dissolved solids (TDS). The five models showed good/excellent prediction ability of the parameters mentioned

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Publication Date
Mon Feb 01 2021
Journal Name
Https://www.researchgate.net/journal/university-of-baghdad-engineering-journal-1726-4073
Electrical Conductivity as a General Predictor of Multiple Parameters in Tigris River Based on Statistical Regression Model
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Surface water samples from different locations within Tigris River's boundaries in Baghdad city have been analyzed for drinking purposes. Correlation coefficients among different parameters were determined. An attempt has been made to develop linear regression equations to predict the concentration of water quality constituents having significant correlation coefficients with electrical conductivity (EC). This study aims to find five regression models produced and validated using electrical conductivity as a predictor to predict total hardness (TH), calcium (Ca), chloride (Cl), sulfate (SO4), and total dissolved solids (TDS). The five models showed good/excellent prediction ability of the parameters mentioned above, which is a very

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Publication Date
Fri Mar 31 2017
Journal Name
Iraqi Journal Of Pharmaceutical Sciences ( P-issn 1683 - 3597 E-issn 2521 - 3512)
A Modified Organic Method for Preparation of Ibuprofen Microcapsules As a Sustained Release Solid Dosage Form
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ABSTRACT:
Microencapsulation is used to modify and retard drug release as well as to overcome the unpleasant effect
(gastrointestinal disturbances) which are associated with repeated and overdose of ibuprofen per day.
So that, a newly developed method of microencapsulation was utilized (a modified organic method) through a
modification of aqueous colloidal polymer dispersion method using ethylcellulose and sodium alginate coating materials to
prepare a sustained release ibuprofen microcapsules.
The effect of core : wall ratio on the percent yield and encapsulation efficiency of prepared microcapsules was low, whereas
, the release of drug from prepared microcapsules was affected by core: wall ratio ,proportion of coa

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Publication Date
Mon Feb 04 2019
Journal Name
Journal Of The College Of Education For Women
THE PORTRAIT OF THE ARTIST AS A ROBOT: A LITERARY LOOK AT E-POETRY
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This study examines the validity of e-poetry as an acceptable literary genre. The
thematic, stylistic and esthetic features of a selected number of e-poems produced by
poetry generators are analyzed for this purpose. The e-poems are then compared with a
number of works written by Dada poets in order to establish the literary merit of the
former.

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Publication Date
Fri Mar 31 2023
Journal Name
Iraqi Geological Journal
History Matching of Reservoir Simulation Model: a Case Study from the Mishrif Reservoir, Buzurgan Oilfield, Iraq
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In petroleum reservoir engineering, history matching refers to the calibration process in which a reservoir simulation model is validated through matching simulation outputs with the measurement of observed data. A traditional history matching technique is performed manually by engineering in which the most uncertain observed parameters are changed until a satisfactory match is obtained between the generated model and historical information. This study focuses on step by step and trial and error history matching of the Mishrif reservoir to constrain the appropriate simulated model. Up to 1 January 2021, Buzurgan Oilfield, which has eighty-five producers and sixteen injectors and has been under production for 45 years when it started

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Publication Date
Sun Aug 30 2020
Journal Name
Journal Of Economics And Administrative Sciences
Relational leadership and its effect on organizational energy (A comparative study in the Rafidain and Rashid banks)
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This research aims to test the relationship between "relational leadership as an independent variable and organizational energy as a dependent variable. The current research variables are among the recent and important variables for the development of organizations, and for the purpose of explaining the relationship and influence between the variables, a set of goals has been formulated, including providing the interested and scientific and theoretical information explaining the nature of the variables The research, and the extent to which its causes are reflected in the research sample to increase the interest of the research organization’s organization and make it more appropriate to the required performance in light of a cha

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Publication Date
Fri Mar 26 2021
Journal Name
Chemical Papers
DFT, anticancer, antioxidant and molecular docking investigations of some ternary Ni(II) complexes with 2‑[(E)‑[4‑(dimethylamino) phenyl]methyleneamino]phenol
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The biological activities of some ternary nickel complexes with a Schiff base obtained from 4-dimethylaminobenzaldehyde and 2-aminophenol have been reported. The Schiff base ( HL1) acts as a primary ligand whereas, anthranilic acid ( HL2), 2-nitroaniline ( HL3), alanine ( HL4) and histidine ( HL5) act as secondary ligand or co-ligand. The anticancer activity of these compounds was studied against human colon carcinoma (HCT-116), human hepatocellular liver carcinoma (HEPG-2) and human breast carcinoma (MCF-7) cell lines. As per the results, the compounds were active against the cell lines. The antioxidant activity of the same compounds was evaluated using DPPH (1,1-diphenyl-2-picryl-hydrazyl) radical scavenging and compared with ascorbic aci

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