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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 Feb 05 2014
Journal Name
Baghdad Science Journal
Study of Plasma Metanephrine Level As Biochemical Parameter in Pregnant Women with Preeclampsia
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Pregnancy- including hypertension(PIH), also known as preeclampsia, is one of the major causes of maternal and fetal death. This study was carried out on 30 pregnant women with preeclampsia and 30 healthy pregnant women as control ranging in age mean ±SD (28.84±3.55) years , BMI (76.80±9.78) Kg/m2 and gestation age(30.82±0.75)week. The aim of this research was studied the plasma Metanephrine level and other biochemical parameters such as Hemoglobin(Hb), serum Protein, S. Albumin, Globulin, Albumin/Globulin ratio (Alb/Glu. ratio), S.Glutamate Pyruvate aminotransferase (GPT), S.Glutamate Oxaloacetate aminotransferase(GOT). The obtained results have been compared with 30 healthy pregnant women as control group. The result showed that ther

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Publication Date
Sun Jun 01 2014
Journal Name
Baghdad Science Journal
Study of Plasma Metanephrine Level As Biochemical Parameter in Pregnant Women with Preeclampsia
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Pregnancy- including hypertension(PIH), also known as preeclampsia, is one of the major causes of maternal and fetal death. This study was carried out on 30 pregnant women with preeclampsia and 30 healthy pregnant women as control ranging in age mean ±SD (28.84±3.55) years , BMI (76.80±9.78) Kg/m2 and gestation age(30.82±0.75)week. The aim of this research was studied the plasma Metanephrine level and other biochemical parameters such as Hemoglobin(Hb), serum Protein, S. Albumin, Globulin, Albumin/Globulin ratio (Alb/Glu. ratio), S.Glutamate Pyruvate aminotransferase (GPT), S.Glutamate Oxaloacetate aminotransferase(GOT). The obtained results have been compared with 30 healthy pregnant women as control group. The result showed

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Publication Date
Tue Aug 01 2023
Journal Name
Physics Of Atomic Nuclei
Electroexcitation Form Factors for Positive- and Negative-Parity States in Some Si Isotopes Using Truncated Large-Scale Shell Model With Skyrme–Hartree–Fock Method
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Publication Date
Sat Jun 01 2013
Journal Name
Int. J. Nanoelectronics And Materials
The response of a window glass to the frequencies of sound
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Publication Date
Mon Mar 13 2017
Journal Name
Journal Of Baghdad College Of Dentistry
Periodontal Health Status and Assessment of Osteocalcin levels in Saliva of Diabetic Patients and Systemically Healthy Persons (Comparative study)
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ABSTRACT Background: Diabetes and periodontitis are complicated prolonged disorders through a recognized two-way association. There is elongated-conventional mark that hyperglycaemia in diabetes is affected on immune-inflammatory response and disturb the action of osteoclast and in balance bone turnover, which might rise the person vulnerability to the progress of prolonged periodontitis. Osteocalcin is one of the greatest plentiful matrix proteins originate in bones and produced absolutely there. Small osteocalcin crumbles are noticed in regions of bone remodeling and are in fact degradation products of the bone matrix, that is released outside cells into the Gingival Crevicular Fluid (GCF) and saliva after destruction of periodontal tissu

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Publication Date
Mon Nov 24 2025
Journal Name
Journal Of Baghdad College Of Dentistry
Regulation of HbA1c of uncontrolled diabetic type II obese and normal weight patients by oral hygiene performance (Comparative study)
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Background: The association between periodontal diseases incidence and development and the metabolic diseases as Diabetes Mellitus and Obesity are recently have attract great deal of researchers attention and investigation. The periodontal health proved to reduce the systemic inflammatory reactions and positively improve the glycemic control of diabetes Type2 patients. The aim of the study was to investigate the influence of oral hygiene control on the glycemic control of obese and normal weight moderately controlled Diabetic Type 2 patients, in addition to study the association of obesity with the gingival inflammation. Materials and Methods: Cross sectional study of three months duration. Included 30 moderately controlled diabetic type2 p

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Publication Date
Thu Feb 07 2019
Journal Name
Iraqi Journal Of Laser
Evaluation of 532 nm Q-Switched Nd:YAG Laser and Acid Etching of Class V Composite Restoration: Comparative Histological Study
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Laser etching may be an alternative to acid etching of enamel and dentin. Several characteristics of irradiated dental hard tissues have been considered advantageous, microscopically rough surfaces without demineralization, open dentinal tubules without smear layer production and dentin surface sterilization. The aim of this study is to determine and compare histology the microleakage in class V cavity restored with a light cured composite after conditioning the samples(tooth surface) with 1-acid etching, 2-Q-switched Nd:YAG Laser etching and finally 3- acid and laser etching. Materials and methods: Twenty four non carious human extracted teeth were used in this study. The samples were equally grouped into four groups of six teeth each.

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Publication Date
Fri Mar 01 2019
Journal Name
Journal Of Accounting And Financial Studies ( Jafs )
Formulate a strategy to manage tax compliance risks: An applied research in the General commission for Taxes
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  This research discussed and analyzed the formulation of a strategy to manage tax compliance risks, as an applied research in the General commission for Taxes. The questionnaire was used as a research tool to identify the factors that stimulate or retard the research sample from being compliant. The K-means clustering method was also used to enable the classification of the research sample's views into four behaviors, some of these views pose tax-compliance risks. The research concluded that risk management is a continuous process and that all departments of the General commission for Taxes are responsible for its implementation to enable them to deal with the behavior of the taxpayer towards tax compliance. And it recommended

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Publication Date
Sat May 01 2010
Journal Name
College Of Education Journal, Al-mustansiriyah University
Artin Characters for the Special Linear Group SL(2,p) where p is a prime number  19
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Publication Date
Sun Feb 01 2015
Journal Name
Journal Of Economics And Administrative Sciences
Use of model sales man fuzzy multi-objective linear for speed up and rationing in the transport mechanism used in the General Company for grain Processing
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     Applications of quantitative methods, which had been explicit attention during previous period (the last two centuries) is the method of application sales man or traveling salesman method. According to this interest by the actual need for a lot of the production sectors and companies that distribute their products, whether locally made or the imported for customers or other industry sectors where most of the productive sectors and companies distributed always aspired to (increase profits, imports, the production quantity, quantity of exports. etc. ...) this is the part of the other hand, want to behave during the process of distribution routes that achieve the best or the least or most appropriate.

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