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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
Wed Oct 01 2025
Journal Name
Theory And Practice In Language Studies
A Socio-Pragmatic Study of Profanity and Derogatory Words in Doja Cat’s Songs: A Corpus-Based Study
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Rap songs often feature artists who utilize explicit language to convey feelings such as happiness, sorrow, and anger, reflecting audience expectations and trends within the music industry. This study intends to conduct a socio-pragmatic analysis of explicit, derogatory, and offensive language in the songs of the American artist Doja Cat, employing Hughes’ (1996) Swearing Word Theory, Jay’s (1996) Taboo Words Theory, Luhr’s (2002) classification of social factors for sociolinguistic examination, Salager’s (1997) categories of hedges for pragmatic assessment, and Austin’s (1965, 1989) theory of speech acts. The researchers collected the data using the AntConc corpus analysis tool. The data shows the singer’s frequent use

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Publication Date
Wed Aug 01 2018
Journal Name
Journal Of Economics And Administrative Sciences
Prepare a plan for the Total Productive Maintenance in the light of the concurrent engineering A Field Study in AL-Askandria General Company Machanical Industries and AL-Musaib Electric Power Station
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           Strives Total Productive Maintenance  to increase the overall effectiveness of the equipment through the early involvement in the design and manufacture of equipment productivity. It also operates in an environment of simultaneous engineering work on the synchronization of activities to take advantage of early information by maintenance engineers, design, operation, and that helps to reduce the faults and facilitate future maintenance tasks.

    Has adopted a search in the theoretical concept of the total maintenance productivity and concurrent engineering activities carried out during which the conjunction a

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Publication Date
Sun Jun 20 2021
Journal Name
Baghdad Science Journal
Wireless Propagation Multipaths using Spectral Clustering and Three-Constraint Affinity Matrix Spectral Clustering
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This study focused on spectral clustering (SC) and three-constraint affinity matrix spectral clustering (3CAM-SC) to determine the number of clusters and the membership of the clusters of the COST 2100 channel model (C2CM) multipath dataset simultaneously. Various multipath clustering approaches solve only the number of clusters without taking into consideration the membership of clusters. The problem of giving only the number of clusters is that there is no assurance that the membership of the multipath clusters is accurate even though the number of clusters is correct. SC and 3CAM-SC aimed to solve this problem by determining the membership of the clusters. The cluster and the cluster count were then computed through the cluster-wise J

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Publication Date
Mon Mar 01 2010
Journal Name
Basrah Journal Of Science
Hiding Three Images at one image by Using Wavelet Coefficients at Color Image
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Publication Date
Tue Jun 01 2021
Journal Name
International Journal Of Nonlinear Analysis And Applications
A proposed method for cleaning data from outlier values using the robust rfch method in structural equation modeling
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Publication Date
Sat Nov 27 2021
Journal Name
Route Educational & Social Science Journal
A STYLISTIC ANALYSIS OF ADVERTISING DISCOURSE: A CASE STUDY OF FACEBOOK COMMERCIAL ADVERTISEMENT
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BN Rashid

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Publication Date
Tue Nov 01 2022
Journal Name
Optik
Design new D-π-A materials for sensitizers for dye-sensitized solar cells: Quantum chemical study
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Within this paper, we developed a new series of organic chromophores based on triphenyleamine (TPA) (AL1, AL-2, AL-11 and AL-22) by engineering the structure of the electron donor (D) unit via replacing a phenyle ring or inserting thiophene as a π-linkage. For the sake of scrutinizing the impact of the TPA donating ability and the spacer upon the photovoltaic, absorptional, energetic, and geometrical characteristic of these sensitizers, density functional theory (DFT) and time-dependent DFT (TD-DFT) have been utilized. According to structural characteristics, incorporating the acceptor, π-bridge and TPA does not result in a perfect coplanar conformation in AL-22. We computed EHOMO, ELUMO and bandgap (Eg) energies by performing frequency a

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Publication Date
Tue Jan 21 2025
Journal Name
Periodicals Of Engineering And Natural Sciences (pen)
A comparison between the hierarchical clustering methods for postgraduate students in Iraqi universities for the year 2019-2020 using the cophenetic and delta correlation coefficients
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The educational sector is one of the important sectors in the world, and it is considered one of the means of community development. In addition, it is one of the means of making the country’s renaissance and devel-opment because it represents the factory of thinking minds that make change. There is no doubt that this sector is the same as any other sector. The deficit in the studied scientific planning has been prolonged, which led to its deterioration, and the problems of education remain diverse and inherited from previous time periods, where the hierarchical cluster analysis was used on postgraduate students in universities in Iraq, except for Kurdistan region, and the number of universities that were included in the study was

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Publication Date
Wed Mar 29 2017
Journal Name
Iraqi Journal Of Pharmaceutical Sciences
Preparation and Evaluation of Atenolol Floating Beads as a Controlled Delivery System
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         This study aims to encapsulate atenolol within floating alginate-ethylcellulose beads as an oral controlled-release delivery system using aqueous colloidal polymer dispersion (ACPD) method.To optimize drug entrapment efficiency and dissolution behavior of the prepared beads, different parameters of drug: polymer ratio, polymer mixture ratio, and gelling agent concentration were involved.The prepared beads were investigated with respect to their buoyancy, encapsulation efficiency, and dissolution behavior in the media: 0.1 N HCl (pH 1.2), acetate buffer (pH 4.6) and phosphate buffer (pH 6.8). The release kinetics and mechanism of the drug from the prepared beads was investigated.All prepared atenolol beads remained f

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Publication Date
Tue Mar 11 2014
Journal Name
Baghdad Science Journal
'I-V Characteristic and Crystal Structural Of a-As/c-Si Heterojunctions
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In this research the a-As flims have been prepared by thermal evaporation with thickness 250 nm and rata of deposition (1.04nm/sec) as function to annealing temperature (373 and 373K), from XRD analysis we can see that the degree of crystalline increase with , and I-V characteristic for dark and illumination shows that forward bias current varieties approximately exponentially with voltage bias. Also we found that the quality factor and saturation current dependence on annealing temperatures.