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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
Sun Jul 02 2006
Journal Name
Journal Of The Faculty Of Medicine Baghdad
a placebo control study of the effect of nigella sativa fixed oil on the healing rate of recurrent aphthous ulceration
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Publication Date
Tue Dec 01 2020
Journal Name
Journal Of Economics And Administrative Sciences
The Impact of Envy on Workplace Stress A field Study of Faculty Staff at the Technical College of Management-Baghdad
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The research aims to measure the impact of envy on job stress because the topic of envy represents a negative emotion that exists at all organizational levels, which may cause stress in the work environment.

The Research problem is represented by the lack of perception of most of the faculty staff on the negative effects of envy on their well-being in the Technical College of Management - Baghdad, and what is the impact level of envy on their job stress.

To achieve this, the scale of envy was based on two dimensions (being envied, Envying others), While the job stress scale was based on seven dimensions (workload, conflict role, Family factors, work environment, work relationships

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Publication Date
Thu Mar 30 2017
Journal Name
Iraqi Journal Of Pharmaceutical Sciences ( P-issn 1683 - 3597 E-issn 2521 - 3512)
Effect of COX-2 Inhibitors Selectivity on Lipid Profile in Hyperlipidemic and Normolipidemic Type 2 Diabetics
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Development of NSAIDS based on inhibiting cyclooxygenase activity. However, the different physiological consequences arrised by appearance of new drugs with different selectivity to COX-2 enzyme upon their administration with their relevant affects on some cardiovascular risk factors. To study the potential effects of relatively  diclofenac and highly specific  celecoxib COX-2 inhibitors on lipid profile and serum C-reactive protein in type 2 diabetes, whom have hyperlipidemia to be compared by their effects with normolipidemic patients. A total number of 34 type 2 diabetics (14 normolipidemics and 20 hyperlipidemics) treated with either diclofenac 100mg/day or celecoxib 200mg/day for eight weeks. Analysis  of results indi

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Publication Date
Sat Jan 27 2024
Journal Name
History Of Medicine
Developing and Validating a Spectrophotometric Method for Estimating Antifungal (Nystatin) in its Pure Form Pharmaceutical Formulation Using Tetrachloro-1,4 benzoquinone
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The UV−VIS absorption spectroscopy technique was used to study the formation of a new complex of charge transfer (CT) between bioactive organic molecules as (Nystatin) containing both a π-electrons from a conjugated system and lone-pair of electrons (amine) with Tetrachloro-1,4 benzoquinone (TCBQ) as a π-acceptor in which the transferred electron goes into its vacant anti-bonding molecular orbitals. The Tyrian purple-colored complex formed was quantitatively measured at 544 nm. This complex shows obeying Beer's law within the concentration range of (10-90) μg.ml-1The stoichiometry of the formed complex between the (Nys.) and (TCBQ) was found 1:2 as evaluated by continuous variation (Job's method) and mole ratio method The value of mola

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Publication Date
Tue Jul 09 2024
Journal Name
Diagnostics
A Novel Hybrid Machine Learning-Based System Using Deep Learning Techniques and Meta-Heuristic Algorithms for Various Medical Datatypes Classification
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Medicine is one of the fields where the advancement of computer science is making significant progress. Some diseases require an immediate diagnosis in order to improve patient outcomes. The usage of computers in medicine improves precision and accelerates data processing and diagnosis. In order to categorize biological images, hybrid machine learning, a combination of various deep learning approaches, was utilized, and a meta-heuristic algorithm was provided in this research. In addition, two different medical datasets were introduced, one covering the magnetic resonance imaging (MRI) of brain tumors and the other dealing with chest X-rays (CXRs) of COVID-19. These datasets were introduced to the combination network that contained deep lea

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Publication Date
Sat Jul 21 2018
Journal Name
The American Society For Virology's 38th Annual Meeting Will Be Held At The University Of Minnesota In Minneapolis, Mn
Comparative Study of different Predators’ effect on Chlorovirus Amplification Foraging on Zoochlorellae-Containing Paramecia?
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Publication Date
Sun Dec 01 2013
Journal Name
Baghdad Science Journal
Assessment of Inflammasome Activity in Type 2 Diabetes Mellitus and Simple Obesity: Comparative Study
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Inflammasome is a multiprotein oligomer complex which is the precursor procaspase-1 and is a component of the innate immune system so that this study aimed to determine the serum levels of interleukin-1? and 18 in patients with T2D and simple obesity in an attempt to clarify the role of inflammasome in these disorders.Twenty five known cases of T2D, twenty four patients with simple obesity and twenty healthy subjects were randomly recruited from AL-Kindy Teaching Hospital in Baghdad to enroll in this study. All the data about the demographic characteristics and anthropometric measurements were determined in all patients, also the C-reactive protein and serum interleukin (IL)-1? and IL-18 levels were obtained from each patient. The results s

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Publication Date
Sat Jan 09 2016
Journal Name
World Journal Of Experimental Biosciences
Comparative study of oral bacterial composition and neutrophil count between smokers and non-smokers
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Publication Date
Mon Feb 01 2021
Journal Name
Indonesian Journal Of Electrical Engineering And Computer Science
Comparative study of logistic regression and artificial neural networks on predicting breast cancer cytology
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<p>Currently, breast cancer is one of the most common cancers and a main reason of women death worldwide particularly in<strong> </strong>developing countries such as Iraq. our work aims to predict the type of tumor whether benign or malignant through models that were built using logistic regression and neural networks and we hope it will help doctors in detecting the type of breast tumor. Four models were set using binary logistic regression and two different types of artificial neural networks namely multilayer perceptron MLP and radial basis function RBF. Evaluation of validated and trained models was done using several performance metrics like accuracy, sensitivity, specificity, and AUC (area under receiver ope

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Publication Date
Mon Oct 07 2019
Journal Name
Journal Of Global Pharma Technology
Contribution of Equilibrium Variables with the High Spike Accuracy of the Position Diagonal Center (4) in the National Volleyball Team Players
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What is important about this study is whether there is a relationship between the ability to balance and beating overwhelming for the Iraqi national team volleyball? The study aims to identify the percentage of the equilibrium contribution and its variables with the accuracy of the skill of beating the high spike Diagonal center (4) in the players. In the national volleyball team season (2016-2017), the researchers used the descriptive approach in the style of associative relationships to suit the problem of research. The research community included all the players specialized in the high beating of the Iraqi national team applicants in the ball The researchers concluded that the equilibrium variables contributed accurately and quickly to t

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