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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
Thu Jan 01 2015
Journal Name
Journal Of Natural Sciences Research
Isolation and Characterization of Lignin from Iraqi Date Palm Phoenix Dactylifera L. Frond Bases as a Good and Cheap Source of Lignin‏
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Publication Date
Thu Mar 31 2022
Journal Name
Journal Of The College Of Education For Women
The Impact of a Counseling Program with a Cognitive Reconstruction Method on the Development of the Psychological Hardness among Middle School Students
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The current research aims to determine the impact of the cognitive reconstruction program on the development of psychological hardness among middle school students through the experimental verification of three hypotheses. The research sample consisted of (16) out of (450) students selected from Ibn Rushud preparatory school- Al-Rusafa 2. These participants have been randomly distributed into two equal groups. The researcher has used the method of cognitive reconstruction with the experimental group, whereas with the controlling group, he used nothing. The researcher has further used the scale of psychological hardness of Kobassa with the participants; the scale has been built in a way that suits the sample of the study, which consisted

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Publication Date
Tue Feb 02 2010
Journal Name
Advances In Software Engineering
A Strategy for Automatic Quality Signing and Verification Processes for Hardware and Software Testing
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We propose a novel strategy to optimize the test suite required for testing both hardware and software in a production line. Here, the strategy is based on two processes: Quality Signing Process and Quality Verification Process, respectively. Unlike earlier work, the proposed strategy is based on integration of black box and white box techniques in order to derive an optimum test suite during the Quality Signing Process. In this case, the generated optimal test suite significantly improves the Quality Verification Process. Considering both processes, the novelty of the proposed strategy is the fact that the optimization and reduction of test suite is performed by selecting only mutant killing test cases from cumulating t-way test ca

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Publication Date
Thu Jul 09 2020
Journal Name
Agrosystems, Geosciences & Environment
Yield and quality of three potato cultivars under series of nitrogen rates
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Undesirable growth of potato (Solanum tuberosum L.) crop under an excessive N fertilizer application is the main obstacle presently. This research was conducted to investigate the response of different potato cultivars; Russet Burbank, Shepody, and Superior, and its qualitative characteristics under a series of N rates. Six rates of N fertilization (0–280 kg ha−1) were applied on 11 sites in a randomized complete block design, with four replications. Sites with ≥30 g kg−1 of soil organic matter (OM) produced total tuber yield, marketable yield, and tuber weight per plant 39.5, 45.2, and 54.9%, respectively, higher than sites with ≤30 g kg−1 of OM. Tubers specific gravity increased by 0.18% in the sites with ≥30 g kg−1 of OM.

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Publication Date
Tue Jun 11 2019
Journal Name
Al-kindy College Medical Journal
Evaluation of Application of Nutritional Status Assessment for Children Under 5 years by Using IMCI Program in a Sample of Primary Health Care Centers in Baghdad City
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Background: World Health Organization (WHO) and United Nation International Children Fund (UNICEF) developed a strategy known as Integrated Management of Childhood Illness (IMCI); which aims to reduce less than five years children morbidity and mortality in developing countries.

Objective: To assess the completion of the IMCI format status in primary health care centers, Baghdad.

Methods:  A cross sectional study with analytic element was conducted during the period from 15th  of January till 15th  May 2016 in selected Primary health centers in Baghdad, Iraq. The sample consists of form of child files less than 2 months and form from 2

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Publication Date
Thu Nov 01 2018
Journal Name
Journal Of Economics And Administrative Sciences
Analysis of the relationship between the prices of wheat and rice importer in Iraq and crude oil prices and the exchange rate using the ARDL model
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Since the beginning of 21st century, the prices of Agricultural crops have increased. This Increases is accompanied with that increases of crude oil prices and fluctuation of a dollar exchange rate as a dominant currency used in the global trade. The paper aimed to analysis the short run and long run cointegration relationships between prices of some of Agricultural crops imported by Iraq such as wheat and rice crops and both the crude oil prices and the Iraq dinar exchange rate a gained America dollar using ARDL model. The results show the long run equilibrium between they three variable throng the error correction mechanizem. The results also show the significant and economically sound effects of cru

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Publication Date
Wed Mar 29 2017
Journal Name
Iraqi Journal Of Pharmaceutical Sciences ( P-issn 1683 - 3597 E-issn 2521 - 3512)
Validity of Generalized Standard Addition Method for a Mixture of Amino Acid Analysis
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A Modified version of the Generlized standard addition method ( GSAM) was developed. This modified version was used for the quantitative determination of arginine   (Arg) and glycine ( Gly) in arginine  acetyl salicylate – glycine complex . According to this method two linear equations were solved to obtain the amounts of (Arg) and (Gly). The first equation was obtained by spectrophotometic measurement of the total absorbance of (Arg) and (Gly) colored complex with ninhydrin . The second equation was obtained by measuring the total acid consumed by total amino groups of (Arg) and ( Gly). The titration was carried out in non- aqueous media using perchloric acid in glacial acetic acid as a titrant. The developed metho

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Publication Date
Fri Jun 01 2018
Journal Name
Journal Of Engineering
Direct Contact Membrane Distillation for Separation of Hcl From A Mixture of Acids
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HCl is separated from HCl –H2SOsolution by membrane distillation process(MD). The flat –sheet membranes made from polyvinylidene fluoride (PVDF) and polypropylene (pp.). Plate and frame these types of membrane where used in the process. The feed is a mixture of HCl and H2SO4 acids compositions depended on metals treated object.HCl concentration increased in the permeate during the process but sulfuric acid increased gradually in the feed .During the concentration of solution acids concentrations in the feed at the beginning were 50 g/dm3 of sulfuric acid and 50 g/dm3 of hydrochloric acid at 333K feed temperature the permeate flux was 71 dm

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Publication Date
Sun Sep 01 2019
Journal Name
Baghdad Science Journal
The Effect of MHD on a Longitudinal Flow of a Fractional Maxwell Fluid between Two Coaxial Cylinders
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      In this paper fractional Maxwell fluid equation has been solved. The solution is in the Mettag-Leffler form. For  the corresponding solutions for ordinary Maxwell fluid are obtained as limiting case of general solutions. Finally, the effects of different parameters on the velocity and shear stress profile are analyzed through plotting the velocity and shear stress profile.

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Publication Date
Fri Dec 30 2011
Journal Name
Al-kindy College Medical Journal
The Role of the Use of Low Molecular Weight Heparin in the Prevention of Deep Venous Thrombosis after Total Knee Arthroplasty
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Background A prospective clinical study was
performed to compare the efficacy of the use of lowmolecular-
weight heparin group (enoxparin group)
with control group in the prevention of deep-vein
thrombosis after total knee arthroplasty.
Aim of the study: to assess the prevalence of DVT
after total knee arthroplasty and evaluate the
importance of the use of low molecular weight
heparin in the prevention of this DVT.
Methods Thirty-three patients undergoing total
knee arthroplasty were randomly divided into two
groups. One group consisted of 12 patients who
received no prophylaxis with an anticoagulant (the
control group), other group consisted of 21 patients
who received the low-molecular-weight h

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