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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 Jan 01 2021
Journal Name
Agrosystems, Geosciences & Environment
Cover crop influence on soil water dynamics for a corn–soybean rotation
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Abstract<p>Crop production is reduced by insufficient and/or excess soil water, which can significantly decrease plant growth and development. Therefore, conservation management practices such as cover crops (CCs) are used to optimize soil water dynamics, since CCs can conserve soil water. The objective of this study was to determine the effects of CCs on soil water dynamics on a corn (<italic>Zea mays</italic> L.)–soybean [<italic>Glycine max</italic> (L.) Merr.] rotation at three soil depths over 3 yr. The study was conducted at the Chariton County Cover Crop Soil Health Research and Demonstration Farm (CCSH) in Missouri. Initial CC establishment occurred in 2012. Volumetric soil water </p> ... Show More
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Publication Date
Mon Apr 26 2021
Journal Name
Journal Of Electrical Engineering &amp; Technology
ANFIS Based Reinforcement Learning Strategy for Control A Nonlinear Coupled Tanks System
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Publication Date
Tue May 01 2018
Journal Name
Journal Of Engineering Science And Technology
A proposed dual size design for energy minimization in sub-threshold circuits
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Sub-threshold operation has received a lot of attention in limited performance applications.However, energy optimization of sub-threshold circuits should be performed with the concern of the performance limitation of such circuit. In this paper, a dual size design is proposed for energy minimization of sub-threshold CMOS circuits. The optimal downsizing factor is determined and assigned for some gates on the off-critical paths to minimize the energy at the maximum allowable performance. This assignment is performed using the proposed slack based genetic algorithm which is a heuristic-mixed evolutionary algorithm. Some gates are heuristically assigned to the original and the downsized design based on their slack time determined by static tim

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Publication Date
Wed Feb 20 2019
Journal Name
Iraqi Journal Of Physics
A comparison between PCA and some enhancement filters for denoising astronomical images
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This paper includes a comparison between denoising techniques by using statistical approach, principal component analysis with local pixel grouping (PCA-LPG), this procedure is iterated second time to further improve the denoising performance, and other enhancement filters were used. Like adaptive Wiener low pass-filter to a grayscale image that has been degraded by constant power additive noise, based on statistics estimated from a local neighborhood of each pixel. Performs Median filter of the input noisy image, each output pixel contains the Median value in the M-by-N neighborhood around the corresponding pixel in the input image, Gaussian low pass-filter and Order-statistic filter also be used.

Experimental results shows LPG-

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Publication Date
Fri Mar 15 2019
Journal Name
Journal Of The College Of Education For Women
(A Message in Nile) For Ahmed هbn Imad ibn Yusuf al-Aqfhasi
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Ahmed ibn Imad ibn Yusuf al-Aqfhasi (808 AH / 1405 AD) is a small message that speaks about the Nile River in all its sides, despite its limited papers, but it is one of the manuscripts of the important geographical literature for its geographical, historical, religious and grammatical information. it was not limited to the information of the author alore, but taken from many sources below, which added to the importance of the fact that it has saved us the names of the sources that preceded him in mentioning this river with the names of its authors.The method of the Aqfhasi was characterized by scientific methodology in writing and clarity, with reference to some of the myths that people carried in their minds about the Nile River at tha

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Publication Date
Wed Mar 10 2021
Journal Name
Baghdad Science Journal
peridos for transversal coincidence maps on compact manifolds with a given cohomology
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Publication Date
Tue Jan 01 2013
Journal Name
Iraqi Journal Of Physics
A comparison between PCA and some enhancement filters for denoising astronomical images
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This paper includes a comparison between denoising techniques by using statistical approach, principal component analysis with local pixel grouping (PCA-LPG), this procedure is iterated second time to further improve the denoising performance, and other enhancement filters were used. Like adaptive Wiener low pass-filter to a grayscale image that has been degraded by constant power additive noise, based on statistics estimated from a local neighborhood of each pixel. Performs Median filter of the input noisy image, each output pixel contains the Median value in the M-by-N neighborhood around the corresponding pixel in the input image, Gaussian low pass-filter and Order-statistic filter also be used. Experimental results shows LPG-PCA method

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Publication Date
Thu Jun 01 2017
Journal Name
Chaos, Solitons &amp; Fractals
A semi-analytical iterative method for solving nonlinear thin film flow problems
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Publication Date
Sat Oct 28 2023
Journal Name
Baghdad Science Journal
Small Nuclear RNA 64 (snoRNA64): A novel Tumor Biomarker for Pancreatic Cancer
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The pancreatic ductal adenocarcinoma (PDAC), which represents over 90% of pancreatic cancer cases,
has the highest proliferative and metastatic rate in comparison to other pancreatic cancer compartments. This
study is designed to determine whether small nucleolar RNA, H/ACA box 64 (snoRNA64) is associated with
pancreatic cancer initiation and progression. Gene expression data from the Gene Expression Omnibus (GEO)
repository have shown that snoRNA64 expression is reduced in primary and metastatic pancreatic cancer as
compared to normal tissues based on statistical analysis of the in Silico analysis. Using qPCR techniques,
pancreatic cancer cell lines include PK-1, PK-8, PK-4, and Mia PaCa-2 with differ

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Publication Date
Sun Apr 01 2018
Journal Name
Journal Of Construction Engineering And Management
Developing a Decision-Making Framework to Select Safety Technologies for Highway Construction
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