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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
Thu Jun 01 2017
Journal Name
Chaos, Solitons & 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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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
Fri Sep 01 2017
Journal Name
International Research Journal Of Engineering And Technology
A POWERFUL AUTOMATED IMAGE INDEXING AND RETRIEVAL TOOL FOR SOCIAL MEDIA Sample
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The Internet image retrieval is an interesting task that needs efforts from image processing and relationship structure analysis. In this paper, has been proposed compressed method when you need to send more than a photo via the internet based on image retrieval. First, face detection is implemented based on local binary patterns. The background is notice based on matching global self-similarities and compared it with the rest of the image backgrounds. The propose algorithm are link the gap between the present image indexing technology, developed in the pixel domain, and the fact that an increasing number of images stored on the computer are previously compressed by JPEG at the source. The similar images are found and send a few images inst

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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
Sun Aug 01 2021
Journal Name
International Journal Of Mechanical Engineering And Robotics Research
Adaptive Approximation-Based Feedback Linearization Control for a Nonlinear Smart Thin Plate
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This paper proposes feedback linearization control (FBLC) based on function approximation technique (FAT) to regulate the vibrational motion of a smart thin plate considering the effect of axial stretching. The FBLC includes designing a nonlinear control law for the stabilization of the target dynamic system while the closedloop dynamics are linear with ensured stability. The objective of the FAT is to estimate the cubic nonlinear restoring force vector using the linear parameterization of weighting and orthogonal basis function matrices. Orthogonal Chebyshev polynomials are used as strong approximators for adaptive schemes. The proposed control architecture is applied to a thin plate with a large deflection that stimulates the axial loadin

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Publication Date
Mon Apr 02 2018
Journal Name
Al-nahrain Journal For Engineering Sciences (njes)
Output Feedback Adaptive Sliding Mode Control Design for a Plate Heat Exchanger
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The heat exchanger is a device used to transfer heat energy between two fluids, hot and cold. In this work, an output feedback adaptive sliding mode controller is designed to control the temperature of the outlet cold water for plate heat exchanger. The measurement of the outlet cold temperature is the only information required. Hence, a sliding mode differentiator was designed to estimate the time derivative of outlet hot water temperature, which it is needed for constructing a sliding variable. The discontinuous gain value of the sliding mode controller is adapted according to a certain adaptation law. Two constraints which imposed on the volumetric flow rate of outlet cold (control input) were considered within the rules of the proposed

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Publication Date
Sun Jul 01 2012
Journal Name
Applied Soft Computing
A new evolutionary based routing protocol for clustered heterogeneous wireless sensor networks
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Publication Date
Sat Jun 29 2013
Journal Name
Wireless Personal Communications
A Low Cost Route Optimization Scheme for Cluster-Based Proxy MIPv6 Protocol
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