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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 Sep 01 2016
Journal Name
Journal Of Engineering
Sliding Mode Vibration Suppression Control Design for a Smart Beam
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Active vibration control is the main problem in different structure. Smart material like piezoelectric make a structure smart, adaptive and self-controlling so, they are effective in active vibration control. In this paper piezoelectric elements are used as sensors and actuators in flexible structures for sensing and actuating purposes, and to control the vibration of a cantilever beam by using sliding mode control. The sliding mode controller (SMC) is designed to attenuate the vibration induced by initial tip displacement which is equal to 15 mm.  It is designed based on the balance realization reduction method where three states are selected for the reduced model from the 24th states that describe the c

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Publication Date
Thu Mar 01 2012
Journal Name
Journal Of Economics And Administrative Sciences
Nadaraya-Watson Estimator a Smoothing Technique for Estimating Regression Function
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    The using of the parametric models and the subsequent estimation methods require the presence of many of the primary conditions to be met by those models to represent the population under study adequately, these prompting researchers to search for more flexible models of parametric models and these models were nonparametric models.

    In this manuscript were compared to the so-called Nadaraya-Watson estimator in two cases (use of fixed bandwidth and variable) through simulation with different models and samples sizes.  Through simulation experiments and the results showed that for the first and second models preferred NW with fixed bandwidth fo

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Publication Date
Sat Jun 01 2013
Journal Name
International Journal Of Astronomy And Astrophysics
Distances Scale Determination for a Planetary Nebula in Galagtic Bulge
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ABSTRACT Planetary Nebulae (PN) distances represent the fundamental parameter for the determination the physical properties of the central star of PN. In this paper the distances scale to Planetary Nebulae in the Galactic bulge were calculated re- lated to previous distances scales. The proposed distance scale was done by recalibrated the previous distance scale technique CKS/D82. This scale limited for nearby PN (D ≤ 3.5 kpc), so the surface fluxes less than other distance scales. With these criteria the results showed that the proposed distance scale is more accurate than other scales related to the observations for adopted sample of PN distances, also the limit of ionized radius (Rio) for all both optically thick and optically thin in

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Publication Date
Wed Oct 01 2008
Journal Name
2008 First International Conference On Distributed Framework And Applications
A strategy for Grid based t-way test data generation
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Publication Date
Thu Dec 01 2022
Journal Name
International Journal Of Electrical And Computer Engineering (ijece)
A survey on bio-signal analysis for human-robot interaction
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<span lang="EN-US">The use of bio-signals analysis in human-robot interaction is rapidly increasing. There is an urgent demand for it in various applications, including health care, rehabilitation, research, technology, and manufacturing. Despite several state-of-the-art bio-signals analyses in human-robot interaction (HRI) research, it is unclear which one is the best. In this paper, the following topics will be discussed: robotic systems should be given priority in the rehabilitation and aid of amputees and disabled people; second, domains of feature extraction approaches now in use, which are divided into three main sections (time, frequency, and time-frequency). The various domains will be discussed, then a discussion of e

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Publication Date
Thu Feb 01 2024
Journal Name
Baghdad Science Journal
A Novel Gravity ‎Optimization Algorithm for Extractive Arabic Text Summarization
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An automatic text summarization system mimics how humans summarize by picking the most ‎significant sentences in a source text. However, the complexities of the Arabic language have become ‎challenging to obtain information quickly and effectively. The main disadvantage of the ‎traditional approaches is that they are strictly constrained (especially for the Arabic language) by the ‎accuracy of sentence feature ‎functions, weighting schemes, ‎and similarity calculations. On the other hand, the meta-heuristic search approaches have a feature tha

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Publication Date
Sat May 01 2021
Journal Name
Journal Of Physics: Conference Series
A Parallel Adaptive Genetic Algorithm for Job Shop Scheduling Problem
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Publication Date
Sat Sep 01 2012
Journal Name
2012 International Conference On Statistics In Science, Business And Engineering (icssbe)
A proposal method for selecting smoothing parameter with missing values
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In this paper we proposed a new method for selecting a smoothing parameter in kernel estimator to estimate a nonparametric regression function in the presence of missing values. The proposed method is based on work on the golden ratio and Surah AL-E-Imran in the Qur'an. Simulation experiments were conducted to study a small sample behavior. The results proved the superiority the proposed on the competition method for selecting smoothing parameter.

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Publication Date
Sat Mar 26 2022
Journal Name
Al-rafidain Journal Of Medical Sciences ( Issn: 2789-3219 )
Major Drivers for COVID-19 Vaccine Acceptance: A Scoping Review
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Objective: To review and identify the major drivers for COVID-19 vaccine acceptance. Methods: A scoping review of studies of COVID-19 vaccine perceptions and barriers to using the COVID-19 vaccines. Two search engines, including PubMed and Google Scholar, were purposefully searched. Results: Eight studies from different countries were reviewed to categorize factors influencing people's acceptance of COVID-19 according to the Health Belief Model (HBM). Perceived susceptibility, and severity of the disease (COVID-19), in addition to perceived benefits of COVID-19 vaccination and "cues to action", can enhance vaccination acceptance. In contrast, perceived barriers to the COVID-19 vaccine can increase people's hesitancy to be vaccinated

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Publication Date
Sat Nov 01 2014
Journal Name
American Journal Of Dermatology And Venereology
Direct Electrical Current is A New Therapeutic Option for Vitiligo
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* Khalifa E. Sharquie1, Hayder Al-Hamamy2, Adil A. Noaimi1, Mohammed A. Al-Marsomy3, Husam Ali Salman4, American Journal of Dermatology and Venereology, 2014 - Cited by 2

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