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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
Baghdad Science Journal
Study of the Anticancer and Antimicrobial Biological Activity of a New Series of Thiohydantoin Derivatives
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        Recently, some prostate cancer patients have acquired resistance to the second -generation drugs (anzalutamide and apalutamide) prescribed for the treatment of this disease due to the emergence of the F876L mutation, which represents a challenge to modern medicine. In this study, a new series of 2-thiohydantoin derivatives were prepared through the reaction of different derivatives of maleimide (1c-4c) with isothiocyanate derivatives. The prepared compounds were diagnosed using FT-IR,1H-NMR ,13C-NMR, Mass spectra. The prepared series compounds has been studied against prostate cancer cells. The MTT assay was used to determine the activity of the prepared compounds against prostate cancer cells. The da

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Publication Date
Sun Feb 17 2019
Journal Name
Iraqi Journal Of Physics
Nucleon momentum distributions and elastic electron scattering form factors for 58Ni, 60Ni, 62Ni, and 64Ni isotopes using the framework of coherent fluctuation model
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The nucleon momentum distributions (NMD) and elastic electron scattering form factors of the ground state for some 1f-2p-shell nuclei, such as 58Ni, 60Ni, 62Ni, and 64Ni
isotopes have been calculated in the framework of the coherent fluctuation model (CFM) and expressed in terms of the weight function lf(x)l. The weight function (fluctuation function) has been related to the nucleon density distribution (NDD) of the nuclei and determined from the theory and experiment. The NDD is derived from a simple method based on the use of the single particle wave functions of the harmonic oscillator potential and the occupation numbers of the states. The feature of the l

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Publication Date
Tue Jan 01 2019
Journal Name
Journal Of Global Pharma Technology
A Modified Version of Generalized Standard Addition Method as Quantitative Determination of Lysineacetyl salicylate-Glycine Complex
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Publication Date
Wed May 29 2019
Journal Name
Iraqi Journal Of Physics
Improvement the efficiency of SnO2/n-Si detector by engraving method using a CNC machine
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Tin oxide was deposited by using vacuum thermal method on silicon wafer engraved by Computer Numerical Controlled (CNC) Machine. The inscription was engraved by diamond-made brine. Deep 0.05 mm in the form of concentric squares. Electrical results in the dark were shown high value of forward current and the high value of the detection factor from 6.42 before engraving to 10.41 after engraving. (I-V) characters in illumination with powers (50, 100, 150, 200, 250) mW/cm2 show Improved properties of the detector, Especially at power (150, 200, 250) mW/cm2. Response improved in rise time from 2.4 μs to 0.72 μs and time of inactivity improved 515.2 μs to 44.2 μs. Sensitivity angle increased at zone from 40o to 65o.

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Publication Date
Mon Dec 16 2024
Journal Name
Light & Engineering
The Design and Experimental Realization of a Laser-Based Heating System Using Recycled Laser Module
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Laser is a powerful device that has a wide range of applications in fields ranging from materials science and manufacturing to medicine and fibre optic communications. One remarkable

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Publication Date
Sun Jul 09 2023
Journal Name
Journal Of Engineering
Fabricating a new Rheometer for Concrete
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A new concrete rheometer is introduced including its innovation, actual design, working rules,
calibration, and reliability. A modified design of Tattersall two-point device is created. Some of
components are purchased from local and foreign markets, while other components and the
manufacturing process are locally fabricated. The matching viscosity method of determining the mixer
viscometer constants is demonstrated and followed to relate torque and rotational speed to yield stress
and viscosity (Bingham parameters). The calibration procedures and its calculation are explained.
Water is used as a Newtonian fluid, while; cement paste (cement + water) with w/c ratio equal to
(0.442) is used as a non-Newtonian fluid. Th

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Publication Date
Sat Apr 21 2012
Journal Name
Arabian Journal For Science And Engineering
A Procedure for Analysing Reinforced Embankments
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Publication Date
Mon Mar 01 2010
Journal Name
Journal Of Economics And Administrative Sciences
Pais estimator for the reliability function of the Pareto model of Type I failure
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In this paper an estimator of reliability function for the pareto dist. Of the first kind has been derived and then a simulation approach by Monte-Calro method was made to compare the Bayers estimator of reliability function and the maximum likelihood estimator for this function. It has been found that the Bayes. estimator was better than maximum likelihood estimator for all sample sizes using Integral mean square error(IMSE).

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Publication Date
Sun Dec 04 2016
Journal Name
Baghdad Science Journal
A study of anti fungal activity of a combination of essential oils from medical herbs against water molds
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The aim of this study is to evaluate the anti fungal activity of a combination of essential oils against water molds. HPLC analysis was done to evaluate the quantity and quality of the active compounds in this combination which extracted from three herbs( Peppermint Menthapiperita ,Thyme Thymusvulgaris, Common sage Salvia officinalis L.) and the active compounds are Camphor,Menthol,,Thujone and Thymol with different concentrations. In this study (MIC) , (MFC) were measured and (LD50) determined after 48,96 h from fingerlings treatment of common carp in aquariums .The results of (MIC) were 0.025µl/ml for Aphanomyces sp. and 0.015µl/ml for both Achlya sp. and Fusariumsolani which showed significant differences(p<0.05) from Malachite gre

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Publication Date
Sun Mar 27 2022
Journal Name
Sport Tk-revista Euroamericana De Ciencias Del Deporte
Effect of resistance training on the biomechanics and accuracy of serve receiving skills in volleyball
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This study aimed to identify the effect of resistance training on the biomechanics and accuracy of serve receiving skills in volleyball. The research community was composed of 26 young volleyball players of Baghdad volleyball clubs. A total of 4 players were selected for the preliminary experiment, while 14 participants were recruited as the main sample for the study. In the present study, a set of resistance exercises were designed by the researchers for the volleyball players of the sample. Exercises were performed by the sample participants during the course of study. The biomechanical variables considered in the present study were: Preparation moment (shoulder joint angle, hip angle, knee joint angle), moment of pr

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