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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
Sun Feb 10 2019
Journal Name
Iraqi Journal Of Physics
A nonlinear edge –preserving smoothing filter for edge detection on color and gray satellite images
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A nonlinear filter for smoothing color and gray images
corrupted by Gaussian noise is presented in this paper. The proposed
filter designed to reduce the noise in the R,G, and B bands of the
color images and preserving the edges. This filter applied in order to
prepare images for further processing such as edge detection and
image segmentation.
The results of computer simulations show that the proposed
filter gave satisfactory results when compared with the results of
conventional filters such as Gaussian low pass filter and median filter
by using Cross Correlation Coefficient (ccc) criteria.

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Publication Date
Fri Feb 08 2019
Journal Name
Iraqi Journal Of Laser
Fusion Splicing for a Large Mode Area Photonic Crystal Fiber with Conventional Single Mode Fiber
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In this paper the experimentally obtained conditions for the fusion splicing with photonic crystal fibers (PCF) having large mode areas were reported. The physical mechanism of the splice loss and the microhole collapse property of photonic crystal fiber (PCF) were studied. By controlling the arc-power and the arc-time of a conventional electric arc fusion splicer (FSM-60S), the minimum loss of splicing for fusion two conventional single mode fibers (SMF-28) was (0.00dB), which has similar mode field diameter. For splicing PCF (LMA-10) with a conventional single mode fiber (SMF-28), the loss was increased due to the mode field mismatch.

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Publication Date
Mon May 11 2020
Journal Name
Baghdad Science Journal
DEO: A Dynamic Event Order Strategy for t-way Sequence Covering Array Test Data Generation
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Sequence covering array (SCA) generation is an active research area in recent years. Unlike the sequence-less covering arrays (CA), the order of sequence varies in the test case generation process. This paper reviews the state-of-the-art of the SCA strategies, earlier works reported that finding a minimal size of a test suite is considered as an NP-Hard problem. In addition, most of the existing strategies for SCA generation have a high order of complexity due to the generation of all combinatorial interactions by adopting one-test-at-a-time fashion. Reducing the complexity by adopting one-parameter- at-a-time for SCA generation is a challenging process. In addition, this reduction facilitates the supporting for a higher strength of cove

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Publication Date
Sun Jun 05 2022
Journal Name
Network
A Computationally Efficient Gradient Algorithm for Downlink Training Sequence Optimization in FDD Massive MIMO Systems
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Future wireless networks will require advance physical-layer techniques to meet the requirements of Internet of Everything (IoE) applications and massive communication systems. To this end, a massive MIMO (m-MIMO) system is to date considered one of the key technologies for future wireless networks. This is due to the capability of m-MIMO to bring a significant improvement in the spectral efficiency and energy efficiency. However, designing an efficient downlink (DL) training sequence for fast channel state information (CSI) estimation, i.e., with limited coherence time, in a frequency division duplex (FDD) m-MIMO system when users exhibit different correlation patterns, i.e., span distinct channel covariance matrices, is to date ve

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Publication Date
Fri Mar 20 2020
Journal Name
Remote Sensing
Lossy and Lossless Video Frame Compression: A Novel Approach for High-Temporal Video Data Analytics
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The smart city concept has attracted high research attention in recent years within diverse application domains, such as crime suspect identification, border security, transportation, aerospace, and so on. Specific focus has been on increased automation using data driven approaches, while leveraging remote sensing and real-time streaming of heterogenous data from various resources, including unmanned aerial vehicles, surveillance cameras, and low-earth-orbit satellites. One of the core challenges in exploitation of such high temporal data streams, specifically videos, is the trade-off between the quality of video streaming and limited transmission bandwidth. An optimal compromise is needed between video quality and subsequently, rec

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Publication Date
Wed Dec 30 2009
Journal Name
Iraqi Journal Of Chemical And Petroleum Engineering
Mass Transfer Correlations for a Rotating Cylinder Electrode under lsothermal and Controlled Heat Transfer Condition
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Mass transfer correlations for iron rotating cylinder electrode in chloride/sulphate solution, under isothermal and
controlled heat transfer conditions, were derived. Limiting current density values for the oxygen reduction reaction from
potentiostatic experiments at different bulk temperatures and various turbulent flow rates, under isothermal and heat
transfer conditions, were used for such derivation. The corelations were analogous to that obtained by Eisenberg et all
and other workers.

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Publication Date
Mon Sep 01 2025
Journal Name
Microbial Biosystems
Harnessing cyanobacteria for a greener tomorrow: CO₂ mitigation and bioconversion to sustainable chemicals and fuels
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Publication Date
Sat Dec 01 2018
Journal Name
Applied Soft Computing
A new evolutionary algorithm with locally assisted heuristic for complex detection in protein interaction networks
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Publication Date
Mon Mar 08 2021
Journal Name
Baghdad Science Journal
A stuy Some physical properties for play (vunyl alcohol) in aquecous solution at four temperatures
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The densities and visconsities of solutions of poly(vinyl alcohol)(PVA) molccuar weight (14)kg.mol-1in water up to 0.035%mol.kg-1

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Publication Date
Tue Oct 13 2020
Journal Name
2020 Ieee International Conference On Mechatronics And Automation (icma)
A Robust Multi-Channel EEG Signals Preprocessing Method for Enhanced Upper Extremity Motor Imagery Decoding
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