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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 Jun 26 2023
Journal Name
International Conference On Scientific Research & Innovation (icsri 2022)
Age and gender profile of coronavirus disease 2019 (COVID 19) in Quarantine Center in Baghdad, Iraq
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Publication Date
Mon Dec 30 2002
Journal Name
Iraqi Journal Of Chemical And Petroleum Engineering
Thermal Conductivity Characteristics of Polymer composites Based on Polyethylene Wastes Filled with Post-Industry Wood Wastes
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Publication Date
Wed Jun 01 2022
Journal Name
Iraqi Journal Of Physics
Synthesis and Characterization of Ternary BexZn1-xO Nano Thin Films prepared by Pulsed Laser Deposition Technique
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         Beryllium Zinc Oxide (BexZn1-xO) ternary nano thin films were deposited using the pulsed laser deposition (PLD) technique under a vacuum condition of 10-3 torr at room temperature on glass substrates with different films thicknesses, (300, 600 and 900 nm). UV-Vis spectra study found the optical band gap for Be0.2Zn0.8O to be  (3.42, 3.51 and 3.65 eV) for the (300, 600 and 900nm) film thicknesses, respectively which is larger than the value of zinc oxide ZnO (3.36eV) and smaller than that of beryllium oxide BeO (10.6eV). While the X-ray diffraction (XRD) pattern analysis of ZnO, BeO and Be 0.2 Zn 0.8 O powder and nano-thin films indicated a hexa

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Publication Date
Mon Mar 15 2021
Journal Name
Al-academy
Semiotics of Visual Composition in Iraqi Contemporary Theatrical Show: اسيل ليث احمد-عبد الرحمن داخل احمد
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The theatrical field has witnessed a huge development that included the semantic and formal sides, considering that the theatrical experience has gone through a long period of description and the dominance of literature and linguistics, thus the theatrical experience has been open to many workings and uses of high quality in forming and composing the visual system. The semiotics had a role in presenting transformed sign forms and features generated in the theatrical space. Thus (costumes, décor, makeup, lighting, and actor) are considered elements with sign forms and attributes that together constitute integrated semiotic unit that include all the layouts in the scenographic space. The two researchers determined on semiotics due to its

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Publication Date
Wed Sep 30 2020
Journal Name
Journal Of Accounting And Financial Studies ( Jafs )
Internet banking services and their impact on customer's: Applied Research on Sample of Iraqi Commercial Banks
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This research examines the issue of Internet banking services and their impact on customer's perceived value to know the potential of Iraqi commercial Banks to provide Internet banking services as well as determine the customer's level of perception of the value of such services. The research aims to demonstrate the effect that Internet banking services have on the customer's perceived value and to find how online banking services can be used to add value that the customer perceive. The main findings were that research sample banks don't have a sophisticated network of electronic Windows through which banking services are provided to allow customers to manage their accounts, and perform various operational operations through the

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Publication Date
Fri Jan 01 2021
Journal Name
Annals Of Parasitology
Association between genetic polymorphism of IL-27 (rs153109) and toxoplasmosis in Iraqi women with recurrent abortion
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Publication Date
Thu Jul 01 2021
Journal Name
Journal Of Mechanical Engineering Research And Developments
Numerical Investigation of Natural Convection Heat Transfer in Partially Filled Porous Enclosure Subjected to Constant Heat
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Steady natural convection in a square enclosure with wall length (L= 20 cm) partially filled by saturated porous medium with same fluid (lower layer) and air (upper layer) is investigated. The conceptual study of the achievements of the heat transfer is performed under effects of bottom heating by constant heat flux (q=150,300,450,600W/m2 ) for three heaters size (0.2,0.14,0.07)m with symmetrically cooling with constant temperature on two vertical walls and adiabatic top wall. The relevant filled studied parameters are four different porous medium heights (Hp=0.25L,0.5L, 0.75L, L), Darcey number (Da1) 3.025×10-8 and (Da2) 8.852×10-4 ) and Rayleigh number range (60.354 - 241.41), (1.304×106 – 5.2166×106 ) for Da1 and Da2 cases respecti

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Publication Date
Fri Feb 19 2021
Journal Name
Journal Of Pure And Applied Microbiology
Biological Control of Phytopathogenic Fungi by Kluyveromyces marxianus and Torulaspora delbrueckii Isolated from Iraqi Date Vinegar
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Yeasts are distributed in all environments and have been reported as potential biocontrol agents against various phytopathogenic fungi. To investigate their enzymatic and biological activities, 32 yeasts were isolated from 15 date vinegar samples. Evaluation of the antagonistic activities of isolated yeasts against the plant pathogens Fusarium oxysporium, Sclerotinia sclerotiorum, and Macrophomina phaseolina indicated that there are two yeasts had the highest inhibitory effect against plant pathogens, these yeasts identified as Kluyveromyces marxianus and Torulaspora delbrueckii using traditional and molecular methods. These yeast isolates were tested for fungal cell wall degrading enzymes (in vitro), and results indicated that the

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Publication Date
Sun Jun 21 2020
Journal Name
Iraqi Journal Of Pharmaceutical Sciences ( P-issn 1683 - 3597 E-issn 2521 - 3512)
Preparation, in vitro and ex-vivo Evaluation of Mirtazapine Nanosuspension and Nanoparticles Incorporated in Orodispersible Tablets
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          The objective of the present investigation was to enhance the solubility of practically insoluble mirtazapine by preparing nanosuspension, prepared by using solvent anti solvent technology. Mirtazapine is practically insoluble in water which act as antidepressant .It was prepared as nano particles in order to improve its solubility and dissolution rate. Twenty formulas were prepared and different stabilizing agents were used with different concentrations such as poly vinyl pyrrolidone (PVPK-90), poly vinyl alcohol (PVA), poloxamer 188 and poloxamer 407. The ratios of drug to stabilizers used to prepare the nanoparticles were 1: 1 and 1:2. The prepared nanoparticles were evaluated for

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Publication Date
Sat Nov 04 2023
Journal Name
Iraqi Journal Of Pharmaceutical Sciences( P-issn 1683 - 3597 E-issn 2521 - 3512)
Synthesis and Preliminary Anti-Inflammatory and Anti-Microbial Evaluation of New 4,5-Dihydro-1H-Pyrazole Derivatives
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Abstract      Organic compounds with pyrazole cores have a variety of uses, notably in the pharmaceutical and agrochemical sectors. The interest in creating pyrazole compounds, examining their many features, and looking for potential uses is growing. Our work has concert with synthesis of  chalcones and pyrazolines, then finally pyrazoline-aniline derivatives and evaluation their anti-inflammatory, antibacterial and antifungal activities

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