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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 Dec 31 2006
Journal Name
Journal Of Engineering
Theoretical Simulation Of Stress-Strain Relations For Some Iraqiclays Using The Endochronic Model
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Publication Date
Sun Jan 27 2019
Journal Name
Journal Of The College Of Education For Women
Music and Singing in The Heritage of Baghdadi The 1930s is a Model
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Music and singing are always associated with the movement of society and the emergence of cultural and artistic activities other.
The social and political transformations of the 1930s helped to disseminate the study Music and music in the city of Baghdad and across Iraq This is the beginning of a new era of musical art alongside other arts.
While achieving musical arts A new step was advanced by publishing a technical study among the younger generation they were looking for to contribute to the musical field On the other hand, the city of Baghdad during the period of research many musical and musical performances Egyptian teams have provided many artistic activities and events which have had a significant impact on the development

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Publication Date
Wed Jul 01 2020
Journal Name
Iop Conference Series: Materials Science And Engineering
Automation in architecture and its effect on the regeneration of traditional buildings: Al-Shawi House as a case study
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Abstract<p>The increased applications of technology in the field of architecture, especially digital technology and aspects of automation, have made a major impact on various aspects of local architecture, especially the traditional ones. As these technologies have succeeded in integrating many technological applications in many traditional and heritage buildings and taking them to more complex uses. And included in it characteristics that were not contained, therefore the research problem was concentrated in the absence of a holistic view of the role of the aspects of automation as a technological and design effect and its mutual effects on traditional buildings (especially the traditional Bagh</p> ... Show More
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Publication Date
Sun Jun 03 2012
Journal Name
Baghdad Science Journal
Batch and Flow-Injection Spectrophotometric Determination of Thymol Using Procaine Hydrochloride as a New Chromogenic Reagent
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New, simple and sensitive batch and Flow-injecton spectrophotometric methods for the determination of Thymol in pure form and in mouth wash preparations have been proposed in this study. These methods were based on a diazotization and coupling reaction between Thymol and diazotized procaine HCl in alkaline medium to form an intense orange-red water-soluble dye that is stable and has a maximum absorption at 474 nm. A graphs of absorbance versus concentration show that Beer’s law is obeyed over the concentration range of 0.4-4.8 and 4-80 µg.ml-1 of Thymol, with detection limits of 0.072 and 1.807 µg.ml-1 of Thymol for batch and FIA methods respectively. The FIA procedure sample throughput was 80 h-1. All different chemical and physical e

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Publication Date
Wed Apr 12 2017
Journal Name
Journal Of Engineering
Cultivation of Chlorella Vulgaris Using Airlift Photobioreactor Sparged with 5%CO2-Air as a Biofixing Process
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The present paper addresses cultivation of Chlorella vulgaris microalgae using airlift photobioreactor that sparged with 5% CO2/air. The experimental data were compared with that obtained from bioreactor aerated with air and unsparged bioreactor. The results showed that the concentration of biomass is 0.36 g l-1 in sparged bioreactor with CO2/air, while, the concentration of biomass reached to 0.069 g l-1 in the unsparged bioreactor. They showed also that aerated bioreactor with CO2/air gives more biomass production even the bioreactor was aerated with air. This study proved that application of sparging system for cultivation of Chlorella vulgaris microalgae using either CO2/air mixture or air has a significant growth rate, since the biorea

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Publication Date
Sun Jan 01 2023
Journal Name
Aip Conference Proceedings
Determination of paracetemol in pharmaceutical preparations samples by spectrophotometer using meta phenylenediamine as a chromogenic agent
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Publication Date
Fri Sep 02 2022
Journal Name
Military Medical Science Letters
SOLID LIPID NANOPARTICLES AS A PROMISING APPROACH FOR DELIVERY OF ANTICANCER AGENTS: REVIEW ARTICLE
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Publication Date
Fri Sep 02 2022
Journal Name
Military Medical Science Letters
SOLID LIPID NANOPARTICLES AS A PROMISING APPROACH FOR DELIVERY OF ANTICANCER AGENTS: REVIEW ARTICLE
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Cancer disease has a complicated pathophysiology and is one of the major causes of death and morbidity. Classical cancer therapies include chemotherapy, radiation therapy, and immunotherapy. A typical treatment is chemotherapy, which delivers cytotoxic medications to patients to suppress the uncontrolled growth of cancerous cells. Conventional oral medication has a number of drawbacks, including a lack of selectivity, cytotoxicity, and multi-drug resistance, all of which offer significant obstacles to effective cancer treatment. Multidrug resistance (MDR) remains a major challenge for effective cancer chemotherapeutic interventions. The advent of nanotechnology approach has developed the field of tumor diagnosis and treatment. Cancer nanote

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Publication Date
Tue Feb 01 2022
Journal Name
Macromolecular Symposia
Synthesis of 5‐Fluorouracil–Naproxen Conjugates as a Mutual Prodrug for Targeting Cancer Tissues
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Abstract<p>A new 5‐fluorouracil–naproxen conjugate is synthesized as a mutual prodrug for targeting cancer tissues. The structure of the target compound and their intermediate are characterized by their melting point, IR, <sup>1</sup>H NMR, <sup>13</sup>C NMR, and elemental microanalysis. The cytotoxic activity is preliminarily evaluated using nonsmall lung cancer CRL‐2049, human breast cancer CAL‐51, and one type of normal cell line; rat embryo fibroblast cell line. The synthesized compound shows a good cytotoxic effect at the cancer cell and no significant effect at rat embryo fibroblast cell line.</p>
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Publication Date
Mon Jan 01 2024
Journal Name
Baghdad Science Journal
A New Approach for Developing Spectrophotometric Determination of Phenylephrine Drug in Pure, Pharmaceutics and Serum Samples Using Sodium Periodate as Oxidizing Agent via a Green Method of CFIA/Merging Zone Technique
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     The research involved a rapid, automated and highly accurate developed CFIA/MZ technique for estimation of phenylephrine hydrochloride (PHE) in pure, dosage forms and biological sample. This method is based on oxidative coupling reaction of 2,4-dinitrophenylhydrazine (DNPH) with PHE in existence of sodium periodate as oxidizing agent in alkaline medium to form a red colored product at ʎmax )520 nm (. A flow rate of 4.3 mL.min-1 using distilled water as a carrier, the method of FIA proved to be as a sensitive and economic analytical tool for estimation of PHE.

Within the concentration range of 5-300 μg.mL-1, a calibration curve was rectilinear, where the detection limit was 3.252 μg.mL

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