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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
Mon Jun 10 2019
Journal Name
Al-kindy College Medical Journal
Knowledge and Attitudes Regarding Health Education among Sample of Iraqi Patients Attending Primary Health Care Centers
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Background: Health education was put as one of the components of primary health care elements and was recognized as a fundamental tool to the attainment of health for all

Objective: To evaluate the Knowledge, attitude regarding health education & to find out if there is any association between the gathered data and certain variables (age, gender, educational level, occupation). Methods: A Cross-sectional study done at Al Mustansyryia Primary Health Care Center from the 1st of January to 1st of May 2016. All patients attending the Primary Health Care Centers who were above 18 years of age and willing to participate in the research (303) were included in t

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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)
Effects of Allopurinol on Ketone Body Metabolism and Tissue Lipid Peroxidation in Alloxan Diabetes in Rats
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The aim of the present study is to investigate whether or not xanthine oxidase (XO)–derived reactive oxygen species (ROS) may play a role in the pathogenesis of alloxan (ALX)–induced diabetes in rats using the specific XO inhibitor and hydroxyl radical scavenger, allopurinol

The involvement of oxidative stress in ALX – diabetes was assessed by the measurement of plasma and various tissues lipid peroxides levels ( using thiobarbituric acid ( TBA ) reactive substances ). Furthermore, the ability of allopurinol to influence these and other biochemical parameters, including plasma and urine ketones levels were also investigated in diabetic rats.

Rats were divided into four groups: control, untreated diabe

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Publication Date
Sat Jan 01 2022
Journal Name
Geotechnical Engineering And Sustainable Construction
Stability and Seismic Performance of Tall Steel Structures with Hybrid Energy Absorbers Including P-Delta Effect
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Publication Date
Tue Jan 01 2019
Journal Name
Plant Archives
Effect of organic fertilizer sources and application methods on qualitativeand quantitativeapricot (Prunus armeniaca L.) fruit characteristics
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Publication Date
Thu Jun 15 2023
Journal Name
Journal Of Baghdad College Of Dentistry
Effects of vitamin D deficiency on bone and root re-sorption post-orthodontic retention in rats
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Background: Orthodontic therapy often causes external root resorption. Serum vitamin D (VD) level is important for tooth mineralization and bone remodeling. This study aimed to test the impact of vitamin D (VD) supplements on bone and root remodelling in a vitamin D (VD) deficient rat model following orthodontic retention. Methods and Material: 30 male Wistar rats were divided into three groups: a control group of 10 rats and two experimental groups of 10 rats each with vitamin D deficiency (VDD) induced by a VD-free diet for 21 days. And a third group with VD supplementAll groups received orthodontic active treatment using a modified orthodontic appliance that applied 50 gm of force for 14 days to move the maxillary right first mol

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Publication Date
Wed Jun 01 2022
Journal Name
Journal Of The College Of Languages (jcl)
Technique and music of letter poetry in Nali’s poetry: هونەر و مۆسیقای «پیتەشیعر» له شیعری نالیدا
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Musicality is a fundamental feature of poetry that takes the interest of scholars and critics. Most poets rely on a variety of literary devices and techniques to bring music to their work like rhymes - words that appear at the end of lines in poetry - and on arranging words techniques in such a way to create a pseudo melody, which is achieved primarily by patterning (or repeating) certain sounds. Such a poetic rhetorical and verbal enhancer’s aspect represented ever since the beginning of the classical poetry has been manifested more evidently in Nali’s poetry. His poetry is marked with particular letters that have played a substantial role in the rhyming that rings like cymbals or jingle like internal elevated rhymes. Within a descr

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Publication Date
Tue Dec 11 2018
Journal Name
Iraqi National Journal Of Nursing Specialties
Impact of Health Educational Program Upon Nurses' Knowledge Towards Postoperative Wounds Care In Mosul Teaching Hospitals
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Objectives: The study aimed to assess the needs of nurses' knowledge toward post operative wound care and to constructed health educational program upon nurses who are working in surgical wards, to determine the relation between nurses' knowledge and their demographical characteristic which includes ( age, gender, level of education, number of years experience in the surgical wards, years of experience in nursing service, and number of attending an educational sessions), and to identify the impact of the health educational program on their knowledge through perform post-test every two months after imp

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Publication Date
Sat Mar 01 2008
Journal Name
Iraqi Journal Of Physics
Effect of Nd-YAG, XeCl, and Nitrogen Laser Radiation on Human Aorta , and Some Arterial Tissues
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The effect of laser radiation on human aorta, coronary, and pulmonary arteries, and pulmonary veins has been investigated. Xenon-Chloride (eximer), Nitrogen, and Nd-YAG pulsed lasers of wavelengths 308, 337, and 1060 nm respectively were used. Their effects on fresh postmortem tissues, normal and diseased, was studied. The diameter and depth of ablation of the exposed tissues, in air, were measured as a function of many factors related to the type of laser and nature of the tissue. The effect of properties of the applied lasers, such as average power density and deposited energy density, on the exposed tissue surface were studied. The increase of these two parameters cause an increase in the depth and diameter of ablation. However the di

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Publication Date
Wed Jun 15 2022
Journal Name
International Journal Of Agriculture Environment And Food Sciences
Functional and numerical response of Hippodamia variegata (Goeze) (Coleoptera: Coccinellidae) on Macrosiphum rosae (L.) (Hemiptera: Aphididae)
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In this study, functional and numerical response tests, which are important components in the selection of biological control agent, were carried out. In functional response trials, the amount of food consumed, attack rate (a) and handling time (Th) were calculated for each developmental period, depending on the number of preys given after 24 hours. The obtained results were evaluated with the Holling. In numerical response experiments, the development of the predator insect was examined depending on the number of preys given in certain numbers (5, 10, 20, 40 and 80) and the data were recorded. This phase of the trials continued until the individuals died. At this stage of the trials, the reproductive response of the p

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Publication Date
Mon Jul 10 2023
Journal Name
Journal Of Engineering
Removal of Hexavalent Chromium from Aqueous Solutions by Adsorption on Thermally Modified and Non-Modified Eggshells
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Removal of heavy metals from waste water has received a great deal of attention. The compare Cr
(VI) adsorption characteristics removing from wastewater by using thermally modified and non-modified
eggshells were examined

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