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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 Sep 01 2023
Journal Name
Iraqi Journal Of Physics
Photometry Technique to Map Elements’ Distribution on Comets’ Nuclei Surfaces Using a New Method
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This study is unique in this field. It represents a mix of three branches of technology: photometry, spectroscopy, and image processing. The work treats the image by treating each pixel in the image based on its color, where the color means a specific wavelength on the RGB line; therefore, any image will have many wavelengths from all its pixels. The results of the study are specific and identify the elements on the nucleus’s surface of a comet, not only the details but also their mapping on the nucleus. The work considered 12 elements in two comets (Temple 1 and 67P/Churyumoy-Gerasimenko). The elements have strong emission lines in the visible range, which were recognized by our MATLAB program in the treatment of the image. The percen

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Publication Date
Fri Feb 01 2019
Journal Name
Environmental Technology & Innovation
Cadmium removal using a spiral-wound woven wire meshes packed bed rotating cylinder electrode
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Publication Date
Thu Jun 27 2024
Journal Name
Journal Of Image And Graphics
ALL-FABNET: Acute Lymphocytic Leukemia Segmentation Using a Flipping Attention Block Decoder-Encoder Network
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Melanoma, a highly malignant form of skin cancer, affects individuals of all genders and is associated with high mortality rates, especially in advanced stages. The use of tele-dermatology has emerged as a proficient diagnostic approach for skin lesions and is particularly beneficial in rural areas with limited access to dermatologists. However, accurately, and efficiently segmenting melanoma remains a challenging task due to the significant diversity observed in the morphology, pigmentation, and dimensions of cutaneous nevi. To address this challenge, we propose a novel approach called DenseUNet-169 with a dilated convolution encoder-decoder for automatic segmentation of RGB dermascopic images. By incorporating dilated convolution,

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Publication Date
Tue Aug 01 2023
Journal Name
Baghdad Science Journal
Digital Data Encryption Using a Proposed W-Method Based on AES and DES Algorithms
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This paper proposes a new encryption method. It combines two cipher algorithms, i.e., DES and AES, to generate hybrid keys. This combination strengthens the proposed W-method by generating high randomized keys. Two points can represent the reliability of any encryption technique. Firstly, is the key generation; therefore, our approach merges 64 bits of DES with 64 bits of AES to produce 128 bits as a root key for all remaining keys that are 15. This complexity increases the level of the ciphering process. Moreover, it shifts the operation one bit only to the right. Secondly is the nature of the encryption process. It includes two keys and mixes one round of DES with one round of AES to reduce the performance time. The W-method deals with

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Publication Date
Mon Nov 01 2021
Journal Name
Energies
Solidification Enhancement in a Triple-Tube Latent Heat Energy Storage System Using Twisted Fins
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This work evaluates the influence of combining twisted fins in a triple-tube heat exchanger utilised for latent heat thermal energy storage (LHTES) in three-dimensional numerical simulation and comparing the outcome with the cases of the straight fins and no fins. The phase change material (PCM) is in the annulus between the inner and the outer tube, these tubes include a cold fluid that flows in the counter current path, to solidify the PCM and release the heat storage energy. The performance of the unit was assessed based on the liquid fraction and temperature profiles as well as solidification and the energy storage rate. This study aims to find suitable and efficient fins number and the optimum values of the Re and the inlet tem

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Publication Date
Fri Feb 01 2019
Journal Name
Environmental Technology & Innovation
Cadmium removal using a spiral-wound woven wire meshes packed bed rotating cylinder electrode
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The effect of electrolysis operating parameters on the removal efficiency of cadmium from a simulated wastewater was studied by adopting response surface methodology combined with Box–Behnken Design. As a new electrode design, spiral-wound woven wire mesh rotating cylinder electrode was used for cadmium removal. Current (240–400 mA), rotation speed (200–1000 rpm), initial cadmium concentration (200–600ppm), and cathode mesh number (30–60) were chosen as independent variables while the removal efficiency of cadmium was considered as a response function. The results revealed that the rotation speed has the major effect on the removal efficiency of cadmium. Regression analysis showed good fit of the experimental data to the second-or

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Publication Date
Fri Jan 01 2021
Journal Name
International Journal Of Agricultural And Statistical Sciences
USING A NEW METHOD TO INDUCE TARGETED GENETIC MUTATIONS IN POTATO VIRUS Y (PVY)
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Publication Date
Fri Sep 01 2023
Journal Name
Al-khwarizmi Engineering Journal
A review on Activated Carbon Prepared from Agricultural Waste using Conventional and Microwave Activation
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In the recent years the research on the activated carbon preparation from agro-waste and byproducts have been increased due to their potency for agro-waste elimination. This paper presents a literature review on the synthesis of activated carbon from agro-waste using microwave irradiation method for heating. The applicable approach is highlighted, as well as the effects of activation conditions including carbonization temperature, retention period, and impregnation ratio. The review reveals that the agricultural wastes heated using a chemical process and microwave energy can produce activated carbon with a surface area that is significantly higher than that using the conventional heating method.

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Publication Date
Thu Jul 01 1999
Journal Name
Bulletin Of The Iraq Natural History Museum (p-issn: 1017-8678 , E-issn: 2311-9799)
Biostratigraphy of shirranish formation, well DD.1 (N. Iraq)
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Shiranish formation has been divided into two microfacies units: 1 - Many biowackestone facies and 2 - maly packstone using planktonic foraminifera and other carbonate components in the rock cutting and core slides. Microfacies reflect marin deep shelf margin in the lower part of the formation, the upper part was deeper. The thickness of the formation is determined, depending on addition to the presence of echinoderm framents debris and spines. This is in disagreement with the 195 ft thickness reported by the Oil Exploration Company The age of the formation is estimated depending on the recognized biostratigraphic zone using the index fossils to be Upper - Middle Mastrichtion.

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Publication Date
Thu Jun 01 2023
Journal Name
Baghdad Science Journal
Role of IL-37 and Dectin-1 during Toxoplasmosis
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Toxoplasmosis is a parasitic infection that triggers immune cells to produce cytokines and inflammatory mediators that are responsible for abnormal or aborted immune responses. This study highlights the evaluation of the Dectin-1 receptor and cytokine IL-37 in the serum of 80 patients who had miscarried in the first trimester and were infected with toxoplasmosis, as well as 40 pregnant women in the first trimester who had a successful pregnancy (control groups). The serum was first screened for the T. gondii IgM and IgG antibodies by an enzyme-linked immunosorbent assay (ELISA) and then the serum levels of IL-37 and Dectin-1 were determined. The results showed that the serum level of Dectin-1 was significantly increased in anti-

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