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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
Tue Jan 11 2022
Journal Name
3rd International Scientific Conference Of Alkafeel University (iscku 2021)
Elimination of the broadening in X-ray diffraction lines profile for nanoparticles by using the analysis of diffraction lines method
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In this research, the results of the Integral breadth method were used to analyze the X-ray lines to determine the crystallite size and lattice strain of the zirconium oxide nanoparticles and the value of the crystal size was equal to (8.2nm) and the lattice strain (0.001955), and then the results were compared with three other methods, which are the Scherer and Scherer dynamical diffraction theory and two formulas of the Scherer and Wilson method.the results were as followsScherer crystallite size(7.4nm)and lattice strain(0.011968),Schererdynamic method crystallite size(7.5 nm),Scherrer and Wilson methodcrystallite size( 8.5nm) and lattice strain( 0.001919).And using another formula for Schearer and Wilson methodwe obtain the size of the c

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Publication Date
Sat Oct 01 2011
Journal Name
Journal Of Engineering
MAGNETO HYDRODYNAMIC NATURAL CONVECTION FLOW ON A VERTICAL CYLINDER WITH A PRESENCE OF HEAT GENERATION AND RADIATION
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The present work investigates the effect of magneto – hydrodynamic (MHD) laminar natural convection flow on a vertical cylinder in presence of heat generation and radiation. The governing equations which used are Continuity, Momentum and Energy equations. These equations are transformed to dimensionless equations using Vorticity-Stream Function method and the resulting nonlinear system
of partial differential equations are then solved numerically using finite difference approximation. A thermal boundary condition of a constant wall temperature is considered. A computer program (Fortran 90) was built to calculate the rate of heat transfer in terms of local Nusselt number, total mean Nusselt number, velocity distribution as well as te

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Publication Date
Fri Nov 01 2019
Journal Name
Journal Of Environmental Quality
Effects of Conservation Practices on Soil Quality Compared with a Corn–Soybean Rotation on a Claypan Soil
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Restoration of degraded lands by adoption of recommended conservation management practices can rehabilitate watersheds and lead to improving soil and water quality. The objective was to evaluate the effects of grass buffers (GBs), biomass crops (BCs), grass waterways (GWWs), agroforestry buffers (ABs), landscape positions, and distance from tree base for AB treatment on soil quality compared with row crop (RC) (corn [Zea mays L.]–soybean [Glycine max (L.) Merr.] rotation) on claypan soils. Soil samples were taken from 10‐cm‐depth increments from the soil surface to 30 cm for GB, BC, GWW, and RC with three replicates. Soil samples were collected from

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Publication Date
Thu Apr 25 2019
Journal Name
Iraqi Journal Of Market Research And Consumer Protection
STUDY THE ANTIBACTERIAL ACTIVITY AND INHIBITION EFFECT OF REACTIVE RED (31) DYE FOR THE CORROSION OF CARBON STEEL IN CORROSIVE MEDIA: STUDY THE ANTIBACTERIAL ACTIVITY AND INHIBITION EFFECT OF REACTIVE RED (31) DYE FOR THE CORROSION OF CARBON STEEL IN CORROSIVE MEDIA
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The inhibitive action of Reactive Red (RR31) dye against corrosion of carbon steel in 1M acetic acid solution has been studied using gravimetric method at temperature ranged (288-318)K. The antibacterial activity for the different concentrations of RR31 dye against different bacterial species was studied. The experimental data indicates that this dye acts as a potential inhibitor for carbon-steel in acetic acid medium and the protection efficiency increase with increasing (RR31) dye. The adsorption of (RR31) dye on the carbon steel surface was found to follow Langmuir adsorption isotherm. Thermodynamic data for the adsorption process such as Gibbs free energy change ∆Gads, enthalpy change ∆Hads, and entropy change ∆Sads were estima

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Publication Date
Wed Jun 14 2017
Journal Name
Iraqi Journal Of Market Research And Consumer Protection
ATTITUDE OF OFFICIALS IN THE INDUSTRIAL COMPANY TOWARDS THE PRACTICE OF REVERSE/ AN APPLIED STUDY IN BAGHDAD COMPANY FOR SOFT DRINKS.: ATTITUDE OF OFFICIALS IN THE INDUSTRIAL COMPANY TOWARDS THE PRACTICE OF REVERSE/ AN APPLIED STUDY IN BAGHDAD COMPANY FOR SOFT DRINKS.
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This paper deals with the subject of demarcating as appropriate scientific techniques to rationalize consumption and to control segments of the society for the technical conduct of its handling of the product depending on the mix of elements (product and the volume of demand, Price, promotion and distribution), but inverse manner designed to adjust the working condition of balance between supply and demand and to ensure that rates continue in the marketing process properly, and therefore the research aims to shed light on some of the practices that reflect the Demarketing techniques, As well as the statement of the reality of attitudes towards the practice of those techniques through a sample survey of officials in Baghdad company for so

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Publication Date
Thu Oct 18 2018
Journal Name
Proceedings Of The Future Technologies Conference (ftc) 2018
Using Mouse Dynamics for Continuous User Authentication
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Publication Date
Wed Sep 01 2021
Journal Name
Iop Conference Series: Earth And Environmental Science
Using Ultraviolet Technique for Well Water Disinfection
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Publication Date
Sat Dec 01 2012
Journal Name
Journal Of Engineering
Database for Baghdad Soil Using GIS Techniques
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teen sites Baghdad are made. The sites are divided into two groups, one in Karkh and the other in Rusafa. Assessing the underground conditions can be occurred by drilling vertical holes called exploratory boring into the ground, obtaining soil (disturbed and undisturbed) samples, and testing these samples in a laboratory (civil engineering laboratory /University of Baghdad). From disturbed, the tests involved the grain size analysis and then classified the soil, Atterberg limit, chemical test (organic content, sulphate content, gypsum content and chloride content). From undisturbed samples, the test involved the consolidation test (from this test, the following parameters can be obtained: initial void ratio eo, compression index cc, swel

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Publication Date
Fri Dec 01 2017
Journal Name
Journal Of Economics And Administrative Sciences
The application of quality requirements in the Ministry of Labour and Social Affairs using the international standard (ISO 9001: 2015) Korean case study of the Iraqi Center
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This research aims to study the mechanism of application of international specification requirements (ISO 9001: 2015) at the Iraqi Center- Korean Vocational Training return to vocational training department at the Ministry of Labour and Social Affairs for the purpose of preparing and creating the center to get a certificate of conformity with the requirements of the standard (ISO 9001: 2015) that would elevate the level of performance and services provided in the respondent Center after it is identified and the study of the reality of the quality management system by identifying strengths and weaknesses in the system to diagnose the gap and find ways to address that gap, and adopted the researchers the case study method to conduc

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Publication Date
Mon Feb 06 2023
Journal Name
Journal Of The College Of Basic Education
Synthesis and Characterization of some biologically active transition metal complexes for a ligand derived from dimedone with mixed ligands.
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The aim of the work is synthesis and characterization of bidentate ligand [3-(3-acetylphenylamino)-5,5-dimethylcyclohex-3-enone][HL], from the reaction of dimedone with 3-amino acetophenone to produce the ligand [HL], the reaction was carried out in dry benzene as a solvent under reflux. The prepared ligand [HL] was characterized by FT-IR, UV-Vis spectroscopy, 'H, 8C-NMR spectra, Mass spectra, (C.H.N) and melting point. The mixed ligand complexes were prepared from ligand [HL] was used as a primary ligand while 8-hydroxy quinoline [HQ] was used as a secondary ligand with metal ion M(IT).Where M(IT) = (Mn ,Co ,Ni ,Cu ,Zn ,Cd and Pd) at reflux ,using ethanol as a solvent, KOH as a

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