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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 Mar 30 2021
Journal Name
Baghdad Science Journal
Diversity Assessment by Molecular Barcoding and Seed Morphology in Ricinus communis L.: Molecular diversity of Ricinus seeds
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Fourteen morphologically varied Ricinus communis L. seeds were collected from different localities in Egypt, El-Sudan and Saudi Arabia. Seed morphology and ITS barcoding analysis were performed to assess their diversity and phylogenetic relationship. Sequence’s alignment of nrITS region from different accessions display high levels of genetic similarities. Cluster analysis could not group different accessions according to their geographical distribution. Nevertheless, the genetic barcodes are interestingly matched with the morphological features of the Ricinus seeds. In conclusion, seed morphology proved to be a valuable tool in evaluating biodiversity and phylogenetic relationship in plant species with different loca

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Publication Date
Fri Dec 01 2017
Journal Name
Journal Of Accounting And Financial Studies ( Jafs )
Suggested Model for auditing the performance of municipal institutions to verify the services provided
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The services provided by the municipal institutions of the basic things needed by the man in his daily life and the evolution of cities basically depends on these services and therefore has paid most of the world's attention to this vital facility and give him the biggest concern for the welfare of the citizens, as is the research problem that there is no program scrutiny to evaluate the performance of municipal institutions contribute to measuring the efficiency and effectiveness of the services provided and was based on research on the premise that the preparation of the existence of audit program to evaluate the performance of municipal institutions contribute to measuring the efficiency and effectiveness of services provided has reac

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Publication Date
Tue Jan 01 2019
Journal Name
Australian Journal Of Mathematical Analysis And Applications
Formulation of approximate mathematical model for incoming water to some dams on Tigris and Euphrates Rivers using spline function
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n this paper, we formulate three mathematical models using spline functions, such as linear, quadratic and cubic functions to approximate the mathematical model for incoming water to some dams. We will implement this model on dams of both rivers; dams on the Tigris are Mosul and Amara while dams on the Euphrates are Hadetha and Al-Hindya.

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Publication Date
Tue Jan 29 2019
Journal Name
Journal Of The College Of Education For Women
Begging Phenomenon Between the Destitution Plight and the Material Greedy - A Field Study in the City of Baghdad
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Begging is an ancient social phenomenon since the Man's creation. It was simple at its beginning to get a living and the family needed, but presently, this simple social phenomenon converted to a big phenomenon which controlled by competent groups away from the values and principles. Their doings are far from humanity representing by the cutting of a hand or a foot and facial distortion or removed eye as a way of attracting people's emotions to get material and incorporeal helps; these doings became a trade which is exchanged by slave traders. Furthermore, different illegal and greedy methods were followed as a way of blackmailing others; contrariwise other cases of begging are doing by a people who real poor and needy. In this case, the

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Publication Date
Thu Mar 01 2018
Journal Name
Ieee Systems Journal
A Comprehensive Survey of the Current Trends and Extensions for the Proxy Mobile IPv6 Protocol
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Publication Date
Sat Jul 27 2019
Journal Name
Sensors
Neurophysiological Characterization of a Non-Human Primate Model of Traumatic Spinal Cord Injury Utilizing Fine-Wire EMG Electrodes
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This study aims to characterize traumatic spinal cord injury (TSCI) neurophysiologically using an intramuscular fine-wire electromyography (EMG) electrode pair. EMG data were collected from an agonist-antagonist pair of tail muscles of Macaca fasicularis, pre- and post-lesion, and for a treatment and control group. The EMG signals were decomposed into multi-resolution subsets using wavelet transforms (WT), then the relative power (RP) was calculated for each individual reconstructed EMG sub-band. Linear mixed models were developed to test three hypotheses: (i) asymmetrical volitional activity of left and right side tail muscles (ii) the effect of the experimental TSCI on the frequency content of the EMG signal, (iii) and the effect

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Publication Date
Sat Feb 09 2019
Journal Name
Journal Of The College Of Education For Women
The women at Al-Sakhaawi Book "A;-Dhau Al-Lami", Study in the social life
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In our previous research , we study the method of women by ( al – sakhaawi " died 902
ah/1496a.c"book witch called ( al- dhau, al-lami) .
So in this paper , we will discuss the social life of women in the mamluk period through the
same book ,especially when the sakhaawi devoted a full part for women in the same book
called it (mhagam ,al –nessa)wich it translations a large number of women like wives
,daughters ,sisters ,and maids of mamluk sultans ,so that make my able to know a lot about
the social life of woman which we study it like a social aspects of women, here wealth,
business, professions ,and in the last we study the habits of them marriage .

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Publication Date
Tue Aug 01 2023
Journal Name
Baghdad Science Journal
Spectrophotometric Determination of Micro Amount of Chromium (III) Using Sodium 4-((4,5-diphenyl-imidazol-2-yl)diazenyl)-3-hydroxynaphthalene-1-sulfonate in the Presence of Surfactant, Study of Thermodynamic Functions and Their Analytical Applications
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          Using sodium4-((4,5-diphenyl-imidazol-2-yl)diazenyl)-3-hydroxynaphthalene-1-sulfonate (SDPIHN) as a chromogenic reagent in presence of non-ionic surfactant (Triton x-100) to estimate the chromium(III)  ion if the wavelength of this reagent 463 nm to form a dark greenish-brown complex in wavelength 586 nm at pH=10,the complex was stable for longer than 24 hours. Beer's low, molar absorptivity 0.244×104L.mol-1.cm-1, and Sandal's sensitivity 0.021 µg/cm2 are all observed in the concentration range 1-11 µg/mL. The limits of detection (LOD) and limit of quantification (LOQ), respectively, were 0.117 µg/mL and 0.385µg/mL. (mole ratio technique, job's method) were employed to

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Publication Date
Sun May 28 2017
Journal Name
Ibn Al-haitham Journal For Pure And Applied Science
On-Line Navigational Problem of a Mobile Robot Using Genetic Algorithm
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Publication Date
Thu Jul 01 2021
Journal Name
Periodicals Of Engineering And Natural Sciences (pen)
A proposed encryption technique of different texts using circular link lists
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