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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 01 2023
Journal Name
Baghdad Science Journal
Synthesis, Theoretical Study, and Biological Evaluation of Some Metal Ions with Ligand "Methyl -6-[2-(4-Hydroxyphenyl) -2-((1-Phenylethylidene) Amino) Acetamido] -2,2-Dimethyl-5—Oxo-1-Thia-4-Azabicyclo [3.2.0] Heptane-3-Carboxyylate
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Schiff base (methyl 6-(2- (4-hydroxyphenyl) -2- (1-phenyl ethyl ideneamino) acetamido) -3, 3-dimethyl-7-oxo-4-thia-1-azabicyclo[3.2.0] heptane-2-carboxylate)Co(II), Ni(II), Cu (II), Zn (II), and Hg(II)] ions were employed to make certain complexes. Metal analysis M percent, elemental chemical analysis (C.H.N.S), and other standard physico-chemical methods were used. Magnetic susceptibility, conductometric measurements, FT-IR and UV-visible Spectra were used to identified. Theoretical treatment of the generated complexes in the gas phase was performed using the (hyperchem-8.07) program for molecular mechanics and semi-empirical computations. The (PM3) approach was used to determine the heat of formation (ΔH˚f), binding energy (ΔEb), an

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Publication Date
Mon Jul 01 2019
Journal Name
Iop Conference Series: Materials Science And Engineering
Study of different geostatistical methods to model formation porosity (Cast study of Zubair formation in Luhais oil field)
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Abstract<p>This study is concerned with making comparison in using different geostatistical methods for porosity distribution of upper shale member - Zubair formation in Luhais oil field which was chosen to study.</p><p>Kriging, Gaussian random function simulation and sequential Gaussian simulation geostatistical methods were adopted in this study. After preparing all needed data which are contour map, well heads of 12 wells, well tops and porosity from CPI log. Petrel software 2009 was used for porosity distribution of mentioned formation in methods that are showed above. Comparisons were made among these three methods in order to choose the best one, the comparing cri</p> ... Show More
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Publication Date
Sun Mar 06 2016
Journal Name
Basic Education
Synthesis, spectroscopic and biological studies of some lanthanide (ш) nitrate complexes with 1, 1--bis (orthoamino phenyl thio) - methane.
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Publication Date
Wed Nov 01 2017
Journal Name
Journal Of Economics And Administrative Sciences
Building marketing culture and reflection on the mental image Search for a pilot sample of managers in the General Company for Vegetable Oil Industry
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          The subject of marketing culture and mental image is one of the important topics in the field of management. There is no study that combines these two variables. The research is important because of the increasing importance of the subject. The future direction of the company in question will support the company's economic and marketing responsibilities. And reflect the company's mental image, as a culture that contributes to changing the reality of the organization investigated by polling the views of a sample of managers in the General Company for Vegetable Oil Industry, which (30) out of the (65) individual, and There are two hypotheses of research: There is a significant

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Publication Date
Thu Jun 29 2023
Journal Name
Iraqi Journal Of Chemical And Petroleum Engineering
Comparative Study between Different Oil Production Enhancement Scenarios in an Iraqi Tight Oil Reservoir
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This paper presents a comparative study between different oil production enhancement scenarios in the Saadi tight oil reservoir located in the Halfaya Iraqi oil field. The reservoir exhibits poor petrophysical characteristics, including medium pore size, low permeability (reaching zero in some areas), and high porosity of up to 25%. Previous stimulation techniques such as acid fracturing and matrix acidizing have yielded low oil production in this reservoir. Therefore, the feasibility of hydraulic fracturing stimulation and/or horizontal well drilling scenarios was assessed to increase the production rate. While horizontal drilling and hydraulic fracturing can improve well performance, they come with high costs, often accounting for up t

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Publication Date
Wed Dec 12 2018
Journal Name
Iraqi National Journal Of Nursing Specialties
Relationship between General and Spinal Anesthesia and Its Impact upon Breast Feeding: Comparative Study
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Objective: To identified the relationship between general and spinal Anesthesia upon breastfeeding and (demographic &reproductive) : Comparative Study. Methodology: The present study employs a descriptive comparative design held at the labor and delivery room , operational room for cesarean section and maternity word in maternity department at Al Emamain Al Kadhamain Medical City in Baghdad city. Data collection was initiated on 2nd January to end of March /2014. Purposive sample consisted of (150) mother and her neonate, The study sample divided into three groups:(50) under general anesthesia , (50) under

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Publication Date
Mon Oct 02 2023
Journal Name
Journal Of Engineering
Comparative Study between Recycled Fine and Coarse Aggregate Used in Roller Compacted Concrete Pavement
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To decrease the impact on the environment of building waste, the recycled aggregate may be used in various sustainable engineering applications, such as roller compacted concrete pavement (RCCP). This research examined how using recycled aggregate as a partial replacement for natural aggregate as coarse or fine affected the mechanical properties of roller-compacted concrete pavement. The recycled aggregate was crushed and sieved to coarse and fine aggregate before being used in the roller-compacted concrete pavement. Compressive strength, splitting tensile strength, and flexural strength were all evaluated after the samples were prepared at 28 and 90 days of curing. According to the study's findings, the partial replacem

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Publication Date
Mon Dec 30 2024
Journal Name
Gsc Biological And Pharmaceutical Sciences
Taxonomic study of a cultivated plant of genus Zanthoxylum l. 1753 (Rutaceae) in Iraq
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Zanthoxylum L. 1753 belongs to the family Rutaceae. The plant, with its forest green color and with its distinctive fragrance attracted the attention of the study, specially it was an exotic to the environment of Iraq. Zanthoxylum is an exotic plant produced to Iraq and planted in gardens as an ever-green aromatic plant named (BUKHUR HINDI), as it is known among sellers and farmers in Iraq, because of the aromatic smell that emanated from the leaves and resembles Indian incense. The plant adapted to environmental conditions and succeeded in growing and blooming. It was examined and diagnosed for the first time in Iraq as Zanthoxylum beechyanum K. Koch. (Chinese pepper tree). Morphological characteristics and anatomical characteristi

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Publication Date
Thu Dec 30 2021
Journal Name
Al-kindy College Medical Journal
Impact of different sources of noise exposure on hearing impairment: A cross- sectional study
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Background: Mental health is integrated into PHC as a strategy of WHO to fill the gap in mental health treatment. Part of this strategy needs a level of task shifting so that mental health care is provided by different level of PHC workers and not only specialists such as psychiatrists and psychologists.

Objectives: To assess the knowledge and attitudes of family doctors regarding the provision of psychological health in PHCC and if there is an association between the certificates of these family doctors and their Knowledge and attitudes to psychological health.

Subjects and Methods:  A cross-sectional descriptive study with analytic elements was conducted in 8 famil

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Publication Date
Mon Nov 24 2025
Journal Name
Journal Of Baghdad College Of Dentistry
Effect of systemic administration of Simvastatin on dental implant stability: A random clinical study
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Background: the primary objective for many researches carried out in dental implantology was to reduce the period needed for functional implant loading, simvastatin (cholesterol lowering medication) had many pleiotropic effects, one of which was increasing bone density around titanium implants (1) and subsequently establishing faster osseointegrated dental implants (2,3). This study aims to reduce the period of time needed to establish secondary stability of dental implant measured in ISQ (Implant Stability Quotient) by investigating the effect of orally administered simvastatin on bone. Materials and methods: simvastatin tablets (40mg/day for three months) were administered orally for 11 healthy women aged (40-51) years old who received 1

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