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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 Mar 07 2010
Journal Name
Baghdad Science Journal
A systematical study about the genus Lycopus L. (Labiatae) in Iraq
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The study included gross morphology and pollen of plants – which collected during field trips , and dry ones for most specimen preserved with the Iraqi herbaria – related to the genus Lycopus L. , and to identify the unidentified species and rectify the error there in , so according to that the species L. europaeus L. only were specified for the genus . Through this work the varity L. europaeus var. glabrescens Schmidely were found at the first time , and suggested to record anew for Iraq . Pollen were of medium size, and had an ellipsoid shape in the equatorial view , and hexagonal in the polar view. The ecological and soil quality where these genus plants grows were specified , and were geographically distribut

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Publication Date
Thu Dec 24 2020
Journal Name
Advances In Civil Engineering
Analytical study on torsional behavior of concrete beams strengthened with fiber reinforced polymer laminates using softened truss model
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This study aimed at evaluating the torsional capacity of reinforced concrete (RC) beams externally wrapped with fiber reinforced polymer (FRP) materials. An analytical model was described and used as a new computational procedure based on the softened truss model (STM) to predict the torsional behavior of RC beams strengthened with FRP. The proposed analytical model was validated with the existing experimental data for rectangular sections strengthened with FRP materials and considering torque-twist relationship and crack pattern at failure. The confined concrete behavior, in the case of FRP wrapping, was considered in the constitutive laws of concrete in the model. Then, an efficient algorithm was developed in MATLAB environment t

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Publication Date
Fri Jun 15 2018
Journal Name
Journal Of Baghdad College Of Dentistry
Periodontal health status of patients with Maxillary Chronic Rhinosinusitis (Part 1: Clinical study)
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Background: Periodontal diseases (PD) are inflammatory conditions of the tissues supporting the teeth, most often gingivitis and periodontitis. Maxillary chronic rhinosinusitis (MCRS) is the inflammation of the maxillary sinuses which is last for at least 12 consecutive weeks duration. Aims of study: Distribution of periodontal diseases among patients with Maxillary chronic rhinosinusitis according to gender and age. Materials and methods: Males and females subjects (25-45 years), divided into two groups; 150 patients suffer from MCRS and 130 subjects without MCRS. Clinical periodontal parameters; Plaque Index (PL.I), Gingival Index (G.I), Probing Pocket Depth (PPD), Clinical Attachment Level (CAL) and Bleeding On Probing (BOP) recorded f

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Publication Date
Fri Nov 01 2019
Journal Name
Journal Of Global Pharma Technology
Synthesis and Phase Transition Study of New Mesogence Derived from 1, 4-Phenylenediamine
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This work include synthesized and characterization the compound [I] by reaction 1,4-phenylenediamine with chloro acetic acid then this compound reaction with methanol in present sulfuric acid to synthesized ester compound [II] after that reaction with hydrazine hydrate to synthesized acide hydrazide [III] and the later compound reaction with substituted acetophenone[IV]n to synthesized substituted acetophenone hydrazones[V-XI]. In addition synthesized4-formylpyrazole derivatives [XIIXVIII] via cyclisation substituted acetophenone hydrazones [V-XI] with Vilsmeier-Haack reagent DMF/POCl3. The compounds characterized by melting points, FTIR, 1HNMR and mass spectroscopy. The mesomorphic behavior studied by using polarized optical microscopy and

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Publication Date
Fri Mar 29 2024
Journal Name
Molecular Biology Reports
Role of endoplasmic reticulum aminopeptidase-1 gene polymorphism (rs13167972) in occurrence susceptibility of ankylosing spondylitis in a sample of Iraqi male patients
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Publication Date
Wed Dec 28 2022
Journal Name
Al–bahith Al–a'alami
Frames of Al-Alam TV channel’s handling of the Iraqi and Lebanese protests Analytical study of the main news bulletin for the period from October 1, 2019, to December 31, 2019
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        In October 2019, Iraq and Lebanon witnessed widespread protests, which aroused the interest of the media, as they began with demands for the provision of services, then escalated with the overthrow of the political system. The researchers chose a satellite channel that represents a direction for a country accused of entering the line of protests. This paper aims to analyze the main bulletin of Al-Alam channel to find out how it deals with the protests in the news. It is classified descriptively, using the survey method and the method of content analysis. The study community was represented by the main news bulletin of Al-Alam channel. The researchers adopted a deliberate sample for the period from 1/10/2019 to

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Publication Date
Sun Jan 08 2023
Journal Name
International Journal Of Research In Social Sciences And Humanities
Evaluating Banking Performance According to the European Model of Institutional Excellence: Case Study at United Bank for Investment and Finance1
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The aim of the research is to identify the impact of the dimensions of the European Excellence Model in evaluating the performance of the bank of the research sample, as well as to interpret which dimensions are more important to the banks of the research sample. Based on the dimensions of this model, the United Bank for Investment and Finance has chosen a research community, and has met with officials of the United Bank for Investment and Finance at various administrative levels to measure the practices of excellence management in the European model, and the analytical approach has been the case study and the construction of the checklist as a tool to collect information. The research has reached the most important results There is a discr

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Publication Date
Mon Jul 10 2023
Journal Name
Journal Of Engineering
Bearing Capacity of a Strip Model Footing on Loose Sand Reinforced With Pomegranate Sticks Mat
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A series of laboratory model tests has been carried out to investigate the using of pomegranate sticks mat as reinforcement to increase the bearing capacity of footing on loose sand. The influence of depth and length of pomegranate sticks layer was examined. In the present research single layer of pomegranate sticks reinforcement was used to strengthen the loose sand stratum beneath the strip footing. The dimensions of the used foundation were 4*20 cm. The reinforcement layer has been embedded at depth 2, 4 and 8 cm under surcharge stresses . Reinforcing layer with length of 8 and 16 cm were used. The final model test results indicated that the inclusion of pomegranate sticks reinforcement is very effective in improvement the loading cap

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Publication Date
Fri Jan 01 2016
Journal Name
Journal Of Cosmetics, Dermatological Sciences And Applications
Tuberculin as Intralesional Therapy for Viral Warts—Single-Blind, Split, Placebo, Controlled Study
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Publication Date
Tue Mar 30 2021
Journal Name
Journal Of Economics And Administrative Sciences
Designing a Quality System using the Goals Programming Method -An Applied Research
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Due to the continuous development in society and the multiplicity of customers' desires and their keeping pace with this development and their search for the quality and durability of the commodity that provides them with the best performance and that meets their needs and desires, all this has led to the consideration of quality as one of the competitive advantages that many industrial companies compete for and which are of interest to customers and are looking for. The research problem showed that the Diyala State Company for Electrical Industries relies on some simple methods and personal experience to monitor the quality of products and does not adopt scientific methods and modern programs. The aim of this research is to desi

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