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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 Oct 15 2023
Journal Name
Bionatura
Examining how PMMA and polyamide denture base materials' physical characteristics are affected by electrolyzed water used as a denture cleaner
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Denture cleansing is an essential step that can stop cross‑contamination and adds to the health of the patient, denture durability, and the general quality of life. A disinfection technique must be practical and devoid of damaging effects on the material's properties used to construct the denture base. The main aim of this study is to evaluate the effect of three concentrations of electrolyzed water denture cleanser on heat cure acrylic and polyamide after immersion in electrolyzed water. The evaluation is based on their efficacy on surface hardness, wettability, and color stability compared with one submerged in distilled water as a control group. The method consists of eighty samples of heat-cured acrylic and polyamide material.

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Publication Date
Sat Dec 01 2018
Journal Name
Journal Of Economics And Administrative Sciences
Comparison between the Methods of Ridge Regression and Liu Type to Estimate the Parameters of the Negative Binomial Regression Model Under Multicollinearity Problem by Using Simulation
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The problem of Multicollinearity is one of the most common problems, which deal to a large extent with the internal correlation between explanatory variables. This problem is especially Appear in economics and applied research, The problem of Multicollinearity has a negative effect on the regression model, such as oversized variance degree and estimation of parameters that are unstable when we use the Least Square Method ( OLS), Therefore, other methods were used to estimate the parameters of the negative binomial model, including the estimated Ridge Regression Method and the Liu type estimator, The negative binomial regression model is a nonline

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Publication Date
Sat Oct 01 2022
Journal Name
The Egyptian Journal Of Hospital Medicine
Laminin Is a Promising Predictive Biomarker for Acute and Chronic Toxoplasmosis
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Publication Date
Tue Oct 16 2018
Journal Name
Springer Science And Business Media Llc
MOGSABAT: a metaheuristic hybrid algorithm for solving multi-objective optimisation problems
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Publication Date
Tue Feb 01 2022
Journal Name
Journal Of Engineering
Self-Repairing Technique Based on Microcapsules for Cementitious Composites- A Review
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Self-repairing technology based on micro-capsules is an efficient solution for repairing cracked cementitious composites. Self-repairing based on microcapsules begins with the occurrence of cracks and develops by releasing self-repairing factors in the cracks located in concrete. Based on previous comprehensive studies, this paper provides an overview of various repairing factors and investigative methodologies. There has recently been a lack of consensus on the most efficient criteria for assessing self-repairing based on microcapsules and the smart solutions for improving capsule survival ratios during mixing. The most commonly utilized self-repairing efficiency assessment indicators are mechanical resistance and durab

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Publication Date
Wed Jul 01 2020
Journal Name
Journal Of Physics: Conference Series
A Multilevel Approach for Stability Conditions in Fractional Time Diffusion Problems
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Abstract<p>The Caputo definition of fractional derivatives introduces solution to the difficulties appears in the numerical treatment of differential equations due its consistency in differentiating constant functions. In the same time the memory and hereditary behaviors of the time fractional order derivatives (TFODE) still common in all definitions of fractional derivatives. The use of properties of companion matrices appears in reformulating multilevel schemes as generalized two level schemes is employed with the Gerschgorin disc theorems to prove stability condition. Caputo fractional derivatives with finite difference representations is considered. Moreover the effect of using the inverse operator which tr</p> ... Show More
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Publication Date
Wed Mar 01 2023
Journal Name
Al-khwarizmi Engineering Journal
Design a radio receiver for solar activity observation in VLF band
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Solar activity monitoring is important in our life because of its direct or indirect influence on our life, not only on ionospheric communications. To study solar activity, researchers need measuring and monitoring instruments, these instruments are mostly expensive and are not available in all universities. In this paper, a very low frequency radio receiver had been designed and implemented with components available in most markets to support the researchers, college students, and radio astronomy amateurs with a minimum input voltage less than 100µV, an output voltage less than 135 m V with no distortion and an overall gain of 34dB. A comparison had been done between two circuit structures using a workbench software program and experim

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Publication Date
Tue Sep 08 2020
Journal Name
Baghdad Science Journal
A Comparison Between Two Shape Parameters Estimators for (Burr-XII) Distribution
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This paper deals with defining Burr-XII, and how to obtain its p.d.f., and CDF, since this distribution is one of failure distribution which is compound distribution from two failure models which are Gamma model and weibull model. Some equipment may have many important parts and the probability distributions representing which may be of different types, so found that Burr by its different compound formulas is the best model to be studied, and estimated its parameter to compute the mean time to failure rate. Here Burr-XII rather than other models is consider  because it is used to model a wide variety of phenomena including crop prices, household income, option market price distributions, risk and travel time. It has two shape-parame

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Publication Date
Mon Jan 01 2024
Journal Name
Lecture Notes In Networks And Systems
Implementing a Smart Low-Cost System for Diagnosing Bacteria in Women
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Publication Date
Sun Dec 31 2023
Journal Name
International Journal Of Intelligent Engineering And Systems
A Ranked-Aware GA with HoG Features for Infant Cry Classification
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