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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 Jan 01 2024
Journal Name
Medical Research Archives
Genetic Polymorphism for the Gene Encoding Endoplasmic Reticulum Aminopeptidase-1 (ERAP-1) in Iraqi Patients with Ankylosing Spondylitis
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Ankylosing spondylitis (AS) is a common, highly heritable inflammatory arthritis affecting primarily the spine and pelvis. This study was aimed to investigate the relationship between the rs27044 polymorphism in Endoplasmic reticulum aminopeptidase-1 (ERAP-1) with the susceptibility and severity of AS correlated with some biochemical markers such as hematological parameter (Erythrocytes sedimentation rate (ESR)) and immunological parameters (C-reactive protein (CRP), Human leukocyte antigen-B27 (HLA-B27), Interlukin-6 (IL-6) and Interlukin-23 (IL-23)), and oxidative stress parameters (Glutathione (GSH) and Malondialdehyde (MDA)) in a sample of Iraqi population. A total of 60 blood samples were collected from AS patients requited Rhe

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Publication Date
Sun Dec 31 2023
Journal Name
Lark
Digital and pedagogical practices of French as a foreign language in a post-COVID-19 context (The case of the University of Baghdad)
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Publication Date
Fri Jan 01 2021
Journal Name
Annals Of Pure And Applied Mathematics
Linear Regression Model Using Bayesian Approach for Iraqi Unemployment Rate
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In this paper we used frequentist and Bayesian approaches for the linear regression model to predict future observations for unemployment rates in Iraq. Parameters are estimated using the ordinary least squares method and for the Bayesian approach using the Markov Chain Monte Carlo (MCMC) method. Calculations are done using the R program. The analysis showed that the linear regression model using the Bayesian approach is better and can be used as an alternative to the frequentist approach. Two criteria, the root mean square error (RMSE) and the median absolute deviation (MAD) were used to compare the performance of the estimates. The results obtained showed that the unemployment rates will continue to increase in the next two decade

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Publication Date
Sun Jan 30 2022
Journal Name
Gsc Biological And Pharmaceutical Sciences
Comparative anatomical study for fruits of some species of Bunium L. (Umbelliferae) in Iraq
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Bunium is one of the interested genus that grow in different region of Iraq, it is within the family Umbelliferae (Apiaceae), and the species within this family have a considerable fruit characteristics. The species that were chosen in this study are: B. brachyactis (Post) H. Wolff, B. caroides (Boiss.) Hausskn. Ex Bornm., B. chaerophylloides (Regel& Schmalh.) Drude, B. rectangulum Boiss. & Hausskn., B. verruculosum C.C.Towns. and B. avromanum (Boiss.& Hausskn) Drude., the study found that the fruits of these species have 5 protrusions different in size but all have the same number of vittae, but some are semiler in size and some are not, the number of vascular element are varied between these species, anatomical charact

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Publication Date
Fri May 11 2018
Journal Name
War, Experience And Memory In Global Cultures Since 1914
The Iraqi Prose Poem as a Legacy of the Experience of the 1980s Iraq–Iran War
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The essay investigates the rise and development of the prose poem form in Iraqi poetry in the period during and after the 1980s Iraq–Iran war. The essay follows the legacy of Western experiments with form following the First World War and their impact on the development of form in Iraqi poetry culminating in the prose poem. The dominance of this form on poetic development in this period has a close relationship with the experience of warfare and the ensuing of the cultural changes in Iraq after 1980. Poets of the 1980s war used poetic form as a means of dissent. The prose poem became for them an inherently subversive form that reflected their disaffection with the political, cultural, and literary conflicts of the time. The prose poem in

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Publication Date
Sun Aug 28 2016
Journal Name
World Journal Of Pharmacy And Pharmaceutical Sciences
AN INSIGHT ON THE IDENTIFICATION OF CANCER STEM CELLS USING NOVEL IMMUNOLOGICAL AND MOLECULAR STRATEGIES
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Cancer stem cells (CSCs) are defined as a population of cells present in tumours, which can undergo self-renewal and differentiation. Identification and isolation of these CSCs using putative surface markers have been a priority of research in cancer. With this background we selected pancreatic normal and tumor cells for this study and passaged them into animal tissue culture medium. Further staining was done using alkaline phosphatase and heamatoxilin staining. Blue to purple colored zones in undifferentiated pluripotent stem cells and clear coloration in the chromatin material indicated pancreatic cells. Further studies on the cell surface marker CD 44 were done using ELISA. For this, the protein was extracted from cultivated normal and t

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Publication Date
Mon Jun 01 2009
Journal Name
Journal Of Economics And Administrative Sciences
Performance Series Performance Metrics (*) A case study in the General Company for Cotton Industries
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The problem of the research is focused on importance limited of Iraq industrial companies in application of scientific measurements of supply chains performance,  The research sought to achieve a group of goals, the most important are , identifying the strengths and weaknesses in the reality of supply chain in General Company for Cotton Industries, The data and information required are gathered from the dependence company, records through the field observations and personal interviews, the research used some quantitative indicators to measure of supply chain performance, The research reached to many conclusions , the most outstanding among them is the existence of a strong inverse correlatio

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Publication Date
Tue Jan 01 2019
Journal Name
Journal Of International Oral Health
Endothelin-1 is a surrogate biomarker link severe periodontitis and endothelial dysfunction in hypertensive patients: The potential nexus
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Aim and Objectives: The objective of this study was to illustrate the link between periodontitis (PO) and endothelial dysfunction in hypertensive patients. Materials and Methods: This cross‑sectional study involved 53 hypertensive patients with or without PO compared with 28 healthy controls. On the basis of the study protocol, the participants were divided into three groups: Group (1): 24 patients with hypertension only, Group (2): 29 patients with hypertension and PO, and Group (3): 28 healthy controls. Lipid profile, endothelin‑1 (ET‑1), and high‑sensitivity C‑reactive protein (hs‑CRP) were measured. Blood pressure and body mass index (BMI) were evaluated. Diagnostic criteria of severe PO periodontal indices including plaque

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Publication Date
Fri May 01 2020
Journal Name
Journal Of Engineering
A Study of the Hydrodynamics Behavior of Cylindrical Gas-Solid Fluidized Beds for pharmaceutical material “Paracetamol “
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The hydrodynamics behavior of gas - solid fluidized beds is complex and it should be analyzed  and understood due to its importance in the design and operating of the units. The effect of column inside diameter and static bed height on the minimum fluidization velocity, minimum bubbling velocity, fluidization index, minimum slugging velocity and slug index have been studied experimentally and theoretically for three cylindrical columns of 0.0762, 0.15 and 0.18 m inside diameters  and 0.05, 0.07 and 0.09 m static bed heights .The experimental results showed that the minimum fluidization and bubbling velocities had a direct relation with column diameter and static bed height .The minimum slugging velocity had an

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Publication Date
Wed Jan 08 2020
Journal Name
International Journal Of Advanced Science And Technology
The local stability of an eco-epidemiological model involving a harvesting on predator population
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In this paper a prey - predator model with harvesting on predator species with infectious disease in prey population only has been proposed and analyzed. Further, in this model, Holling type-IV functional response for the predation of susceptible prey and Lotka-Volterra functional response for the predation of infected prey as well as linear incidence rate for describing the transition of disease are used. Our aim is to study the effect of harvesting and disease on the dynamics of this model.

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