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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
Sat Jan 01 2011
Journal Name
International Journal Of Data Analysis Techniques And Strategies
A class of efficient and modified testimators for the mean of normal distribution using complete data
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Publication Date
Fri Mar 01 2024
Journal Name
Baghdad Science Journal
Deep Learning Techniques in the Cancer-Related Medical Domain: A Transfer Deep Learning Ensemble Model for Lung Cancer Prediction
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Problem: Cancer is regarded as one of the world's deadliest diseases. Machine learning and its new branch (deep learning) algorithms can facilitate the way of dealing with cancer, especially in the field of cancer prevention and detection. Traditional ways of analyzing cancer data have their limits, and cancer data is growing quickly. This makes it possible for deep learning to move forward with its powerful abilities to analyze and process cancer data. Aims: In the current study, a deep-learning medical support system for the prediction of lung cancer is presented. Methods: The study uses three different deep learning models (EfficientNetB3, ResNet50 and ResNet101) with the transfer learning concept. The three models are trained using a

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Publication Date
Wed Oct 31 2018
Journal Name
Heat Transfer-asian Research
Comparative study on heat transfer enhancement of nanofluids flow in ribs tube using CFD simulation
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Publication Date
Sat Apr 01 2023
Journal Name
Journal Of Engineering
Comparative Study of Water Desalination using Reverse Osmosis (RO) and Electro-dialysis Systems (ED): Review
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The increasing drinking water demand in many countries leads to an increase in the use of desalination plants, which are considered a great solution for water treatment processes. Reverse osmosis (RO) and electro-dialysis (ED) systems are the most popular membrane processes used to desalinate water at high salinity. Both systems work by separating the ionic contaminates and disposing of them as a brine solution, but ED uses electrical current as a driving force while RO uses osmotic pressure. A direct comparison of reverse osmosis and electro-dialysis systems is needed to highlight process development similarities and variances. This work aims to provide an overview of previous studies on reverse osmosis and electro-dial

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Publication Date
Sun Oct 15 2023
Journal Name
Bionatura
Nesfatin-1 is a biomarker that plays a role in the inflammatory process of coronary artery diseases in Iraqi patients with non-alcoholic fatty liver disease.
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Amis: NAFLD is considered to be the most common cause of liver conditions worldwide. Also, it is a primary reason that leads to coronary artery diseases, limiting blood flow to the heart. Therefore, This study aimed to evaluate the serum level of Nesfatin-1 and its ability to indicate the prognosis of CAD in patients with NAFLD. Material & Methods: one-hundred eighty Individuals were enrolled in the study, including In both genders, blood was collected from each Individual and sent to the laboratory for biochemical tests. Findings: Data from the current study showed a significant increase in Nesfatin-1 in the CAD group and a significant decrease in Nesfatin-1 in the NAFLD group compared to the control group. In addition, there w

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Publication Date
Sun Mar 06 2022
Journal Name
Al–bahith Al–a'alami
DEPENDENCE OF MEDIA OFFICES ON THE CABINET'S WEBSITE AS A SOURCE OF INFORMATION
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     The research aimed to identify the extent to which the media offices in the ministries depend on the website of the Iraqi Council of Ministers as a source of information. Such goal includes a set of sub-goals: Knowing the reasons for media offices' reliance on the information provided by the Cabinet's website; and revealing the benefit derived from relying on the Cabinet's website.

The researcher used the survey method to screen and comprehend the extent to which the media offices in the ministries depend on the website of the Iraqi Council of Ministers as a source of information.

The mechanism of comprehensive account of the limits of research wa

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Publication Date
Tue Jan 12 2021
Journal Name
Pollution Research
DETERMINATION OF ANILINE IN WASTEWATER BY CLOUDPOINT EXTRACTION FOLLOWED BY HPLC USING 8-HYDROXYQUINOLINE AS A DERIVATIZATION AGENT
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A procedure, depending on the derivatization and determination of aniline was depicted andvalidated in this study. 8-hydroxyquinoline (8-HQ) was used as the derivatizing agent for thedetermination of aniline. An optimization study was performed for the derivatization reaction, i.e.,the diazonium coupling reaction, the optimum parameters were as follows: 22 mM of hydrochloricacid, 54mM of sodium hydroxide, and 1.8mM of sodium nitrate. The optimization study of themethod of cloud point extraction (CPE) revealed that the extraction solvent was 0.5 ml of Triton X-100, the optimum temperature was 90 °C, and the incubation time was 25 min. The linearity,correlation coefficients, molar absorptivities, and limits of detection were improved using t

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Publication Date
Wed Nov 01 2023
Journal Name
Iraqi Journal Of Pharmaceutical Sciences ( P-issn 1683 - 3597 E-issn 2521 - 3512)
Preparation and characterization of Posaconazole as a Nano-micelles using d-α-Tocopheryl polyethylene glycol 1000 succinate (TPGS)
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It is important to note that Posaconazole (POCZ) is a newly developed extended-spectrum triazole that belongs to BCS class II and has a solubility of less than 1µg/ml. In patients with a weakened immune system, POCZ has been shown to be effective as an antifungal treatment for invasive infections caused by candida and aspergillus species. The nano-micelles technique can be used to increase POCZ solubility. In order to increase their apparent solubility in water, nano-micelles are made by combining macromolecules that self-assemble into ordered structures capable of entrapping hydrophobic drug molecules in the interior domain. Dispersed colloidal systems, of which nano-micelles are a subset, are a large and diverse group. Composed of a p

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Publication Date
Mon Jul 01 2019
Journal Name
Journal Of Engineering
Speed Controller of Three Phase Induction Motor Using Sliding Mode Controller
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In this paper, an adaptive integral Sliding Mode Control (SMC) is employed to control the speed of Three-Phase Induction Motor. The strategy used is the field oriented control as ac drive system. The SMC is used to estimate the frequency that required to generates three phase voltage of Space Vector Pulse Width Modulation (SVPWM) invertor . When the SMC is used with current controller, the quadratic component of stator current is estimated by the controller. Instead of using current controller, this paper proposed estimating the frequency of stator voltage since that the slip speed is function of the quadratic current . The simulation results of using the SMC showed that a good dynamic response can be obtained under load

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Publication Date
Wed Feb 01 2023
Journal Name
Journal Of Engineering
Checking the Accuracy of Selected Formulae for both Clear Water and Live Bed Bridge Scour
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Due to severe scouring, many bridges failed worldwide. Therefore, the safety of the existing bridge (after contrition) mainly depends on the continuous monitoring of local scour at the substructure. However, the bridge's safety before construction mainly depends on the consideration of local scour estimation at the bridge substructure. Estimating the local scour at the bridge piers is usually done using the available formulae. Almost all the formulae used in estimating local scour at the bridge piers were derived from laboratory data. It is essential to test the performance of proposed local scour formulae using field data. In this study, the performance of selected bridge scours estimation formulae was validated and sta

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