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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
Fri Dec 23 2022
Journal Name
Iraqi Journal Of Pharmaceutical Sciences ( P-issn 1683 - 3597 E-issn 2521 - 3512)
Sensitive Cloud Point Extraction Method for the Determination of Isoxsuprine Hydrochloride in Pharmaceutical forms using Spectrophotometry
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      A simple and highly sensitive cloud point extraction process was suggested for preconcentration of micrograms amount of isoxsuprine hydrochloride (ISX) in pure and pharmaceutical samples. After diazotization coupling of ISX with diazotized sulfadimidine in alkaline medium, the azo-dye product quantitatively extracted into the Triton X-114 rich phase, dissolved in ethanol and determined spectrophotometrically at 490 nm. The suggested reaction was studied with and without extraction and simple comparison between the batch and CPE methods was achieved. Analytical variables including concentrations of reagent, Triton X-114 and base, incubated temperature, and time were carefully studied. Under the selected optimum conditions,

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Publication Date
Fri Dec 01 2023
Journal Name
Iop Conference Series: Earth And Environmental Science
Study of Mouth Depth for Some Local Cyprinidae
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Abstract<p>The aim of this study was to identify the depth of the mouth and its shape in some local fish belonging to the Cyprinidae family, and the extent to which the depth of the mouth is related to the way of feeding and the nature of food as well as the feeding habits of those species collected specifically from the Tigris River, the results showed a relationship of depth oral cavity with head length was highly significant at (P < 0.01) for all studied species. Also, there was a highly significant relationship between the height of the pharyngeal tooth-bearing bone and the depth of the oral cavity for fish of this local family.</p>
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Publication Date
Sun Sep 01 2013
Journal Name
Baghdad Science Journal
Theoretical Study of Thermal Cracking For Acenaphthylene Molecule
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Density Functional Theory (DFT) calculations were carried out to study the thermal cracking for acenaphthylene molecule to estimate the bond energies for breaking C8b-C5a , C5a-C5 , C5-C4 , and C5-H5 bonds as well as the activation energies. It was found that for C8b-C5a , C5-C4 , and C5-H5 reactions it is often possible to identify one pathway for bond breakage through the singlet or triplet states. The atomic charges , dipole moment and nuclear – nuclear repulsion energy supported the breakage bond .Also, it was found that the activation energy value for C5-H5 bond breakage is lower than that required for C8b-C5a , C5a-C5 , C5-C4 bonds which refer to C5-H5 bond in acenaphthylene molecule are weaker than C8b-C5a , C5a-C5 , C5-C

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Publication Date
Sun Jun 12 2011
Journal Name
Baghdad Science Journal
Study of optical properties for Ge - GaAs Heterojunction
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Publication Date
Thu Jun 01 2023
Journal Name
Iraqi Journal Of Physics
Studying the Effect of Initial Conditions and System Parameters on the Behavior of a Chaotic Duffing System
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This work presents a five-period chaotic system called the Duffing system, in which the effect of changing the initial conditions and system parameters d, g and w, on the behavior of the chaotic system, is studied. This work provides a complete analysis of system properties such as time series, attractors, and Fast Fourier Transformation Spectrum (FFT). The system shows periodic behavior when the initial conditions xi and yi equal 0.8 and 0, respectively, then the system becomes quasi-chaotic when the initial conditions xi and yi equal 0 and 0, and when the system parameters d, g and w equal 0.02, 8 and 0.09. Finally, the system exhibits hyperchaotic behavior at the first two conditions, 0 and 0, and the bandwidth of the chaotic

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Publication Date
Tue Aug 01 2023
Journal Name
Baghdad Science Journal
The Ecological Risk Assessment of Mercury Contamination in a Mangrove Ecosystem of the Segara Anakan Cilacap, Indonesia
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Ecological risk assessment of mercury contaminant has a means to analyze the ecological risk aspect of ecosystem using the potential impact of mercury pollution in soil, water and organism. The ecological risk assessment in a coastal area can be shown by mangrove zonation, clustering and interpolation of mercury accumulation. This research aims to analyze ecological risk assessment of potential mercury (including bioaccumulation and translocation) using indicators of species distribution, clustering, zonation and interpolation of mercury accumulation. The results showed that the Segara Anakan had a high risk of mercury pollution, using indicators like as the potential of mercury contaminant in water body was 0137±0.0137 ppm, substrate a

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Publication Date
Sun Jul 25 2021
Journal Name
Natural Resources Research
Effect of Water Flooding on Oil Reservoir Permeability: Saturation Index Prediction Model for Giant Oil Reservoirs, Southern Iraq
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Publication Date
Thu Jun 30 2022
Journal Name
Journal Of Economics And Administrative Sciences
Estimation of Time of Survival Rate by Using Clayton Function for the Exponential Distribution with Practical Application
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Each phenomenon contains several variables. Studying these variables, we find mathematical formula to get the joint distribution and the copula that are a useful and good tool to find the amount of correlation, where the survival function was used to measure the relationship of age with the level of cretonne in the remaining blood of the person. The Spss program was also used to extract the influencing variables from a group of variables using factor analysis and then using the Clayton copula function that is used to find the shared binary distributions using multivariate distributions, where the bivariate distribution was calculated, and then the survival function value was calculated for a sample size (50) drawn from Yarmouk Ho

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Publication Date
Wed Apr 01 2020
Journal Name
Indian Journal Of Forensic And Toxicology
Antifungal activity of silver nanoparticles using penicillium chrysogenum extract against the formation of biofilm for candida glabrata
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Publication Date
Sat Jan 01 2022
Journal Name
Revista Iberoamericana De PsicologĂ­a Del Ejercicio Y El Deporte
THE EFFECT OF USING GAMES IN DEVELOPING SOME CONCEPTS OF TRAFFIC SAFETY FOR FIFTH GRADE PRIMARY STUDENTS
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Abstract The purpose of this paper is to preparing small games for fifth graders. And to identify the impact of these small games in developing some concepts of traffic safety for fifth graders. The two researchers used the experimental method to solve the research problem, and the research community was identified with students. The fifth grade of primary school in the province of Baghdad and a sample was chosen from the private Baghdad Primary School, which numbered (60) male and female students. They were distributed equally into two groups by simple random method (experimental and control groups). As for the most important conclusions reached by the two researchers, it is the presence of an effect of small games in developing some conce

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