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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 Jul 01 2022
Journal Name
Nternational Journal Of Special Education
Comparative Study between a Combination of Plants Extracts and Drugs on Thyroid Hormones and Lipid Profile in Experimental Animals
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The thyroid gland is a vital part of the overall endocrine system, which is regulated some of body function as oxygen use, basal metabolic rate, growth, cellular metabolism and development This study shed light on a number of extracts that have been shown to have beneficial effects on the thyroid and its function, as well as the various factors linked to thyroid dysfunction. The experiment was conducted to determine the effect of a mixture of two extracts of "Fucus vesiculosus (150 mg/ kg) with Coleus forskohlii (1000 mg/ kg) and Rosmarinus officinalis (220 mg/ kg) with Camellia sinensis (1.25 mg/ kg)" on thyroid hormones as well as lipids profile and tested the effectiveness of two drugs one of them stimulates the hormones of the thyroid (

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Publication Date
Thu Jun 26 2025
Journal Name
Journal Of Baghdad College Of Dentistry
An Assessment of Salivary Leptin and Resistin Levels in Type Two Diabetic Patients with Chronic Periodontitis (A Comparative Study)
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Background: Type 2 diabetes mellitusand chronic periodontitis hold a close relationship that has been the focus of many researches. Currently there is an appreciation to the role of adipose tissue-derived substances "the adipokines" in immune-inflammatory responses; also, there is an interest in using the simple non-invasive saliva in diagnosing and linking oral and general health problems. The current study aims to determine the periodontal health status in the chronic periodontitis patients with and without poorly or well controlled type 2 diabetes mellitus, measure the salivary levels of two adipokines "leptin and resistin", pH and flow rate and then correlate between these clinical periodontal, biochemical and physical parameters in eac

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Publication Date
Thu Jun 26 2025
Journal Name
Journal Of Baghdad College Of Dentistry
Periodontal health status of heavy and light smokers and its correlation with salivary superoxide dismutase enzyme (A comparative study)
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Background: Periodontal disease is a chronic bacterial infection that affects the gingiva and bone supporting the teeth. Smoking, which is an important risk factor for periodontitis, induce oxidative stress in the body and cause an imbalance between reactive oxygen species (ROS) and antioxidants, such as superoxide dismutase (SOD). This study aimed to evaluate the influence of smoking on periodontal health status by estimating the levels of salivary SOD level in non-smokers (controls) and light and heavy smokers and to test the correlation between the SOD enzyme level and the clinical periodontal parameters in each group. Materials and Methods: The study sample consisted of 75 male, with age ranged from 35 to 50 years. Clinically, the perio

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Publication Date
Sun Jan 01 2023
Journal Name
Communications In Mathematical Biology And Neuroscience
The dynamics of a delayed ecological model with predator refuge and cannibalism
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This study has contributed to understanding a delayed prey-predator system involving cannibalism. The system is assumed to use the Holling type II functional response to describe the consuming process and incorporates the predator’s refuge against the cannibalism process. The characteristics of the solution are discussed. All potential equilibrium points have been identified. All equilibrium points’ local stability analyses for all time delay values are investigated. The system exhibits a Hopf bifurcation at the coexistence equilibrium, which is further demonstrated. The center manifold and normal form theorems for functional differential equations are then used to establish the direction of Hopf bifurcation and the stability of the per

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Publication Date
Thu Oct 06 2022
Journal Name
Advances In Systems Science And Applications
Stability and Bifurcation of a Delay Cancer Model in the Polluted Environment
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It is well known that the spread of cancer or tumor growth increases in polluted environments. In this paper, the dynamic behavior of the cancer model in the polluted environment is studied taking into consideration the delay in clearance of the environment from their contamination. The set of differential equations that simulates this epidemic model is formulated. The existence, uniqueness, and the bound of the solution are discussed. The local and global stability conditions of disease-free and endemic equilibrium points are investigated. The occurrence of the Hopf bifurcation around the endemic equilibrium point is proved. The stability and direction of the periodic dynamics are studied. Finally, the paper is ended with a numerical simul

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Publication Date
Sun Dec 16 2018
Journal Name
Al-academy
Philosophy of Precognitive Dream in the American Film (Minority Report - a Model)
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When we talk about the foresight in films, it is necessary to talk about dreams because foresight represents one of its distinct types. The Precognitive vision has become a possible material in dealing with as subjects in the film industry that adopt these ideas with their philosophical and scientific orientations, because they represent the imagination that predictors are specialized with. It can be invested through the introduction of a vision of another kind to achieve its goals and ambitions in the film industry and in particular the huge institutions of production as in Hollywood. The cinema works in the light of those concepts of production which found the prognostic dream (the foresight) as a distinctive genre in its films,
Th

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Publication Date
Fri Dec 31 2021
Journal Name
Iraqi Journal Of Market Research And Consumer Protection
GEOMETRY OPTIMIZATION OF COUPLING ALLIN -METFORMIN USING DFT/B3LYP MOLECULAR MODELLING TECHNIQUE: GEOMETRY OPTIMIZATION OF COUPLING ALLIN -METFORMIN USING DFT/B3LYP MOLECULAR MODELLING TECHNIQUE
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This researchpaper includes the incorporation of Alliin at various energy levels and angles 

With Metformin using Gaussian 09 and Gaussian view 06. Two computers were used in this work. Samples were generated to draw, integrate, simulate and measure the value of the potential energy surface by means of which the lowest energy value was (-1227.408au). The best correlation compound was achieved between Alliin and Metformin through the low energy values where the best place for metformin to b

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Publication Date
Mon Oct 01 2018
Journal Name
Journal Of Economics And Administrative Sciences
A comparative study of the role of monetary policies in achieving economic growth in some oil and non-oil countries during the period 1990-2017
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The research problem was to identify the impact of monetary policies on economic growth in the oil and non-oil countries. The researcher chose the Republic of Iraq as an example for the oil countries and the Arab Republic of Egypt as an example for the non-oil countries to hold a comparison on the impact of monetary policies.

The research found that the monetary policies and their tools in the Iraqi economy affect the rate of GDP growth by 73%, which shows the strong impact of monetary policies on the economic growth in the Iraqi economy as an example of an oil state. GDP growth rate of 61%, indicating the impact of monetary policies on economic growth in the

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Publication Date
Fri Nov 20 2020
Journal Name
Solid State Technology
Comparative Study for Bi-Clustering Algorithms: Historical and Methodological Notes
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Publication Date
Wed Jun 15 2022
Journal Name
Linguistics And Translation Studies
Metaphor as a method of forming the lexical meaning of a word (on the material of Russian and Arabic languages)
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The article aims to consider the concept of language metaphor in Russian and Arabic languages and the problem of metaphor functioning in language, since it is one of the most important figurative components of the structural organization of the text and an important means of reflecting the national culture of each people. and often in revealing the image of a metaphor one can feel the full flexibility of the language and its beauty.

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