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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 May 01 2008
Journal Name
2008 International Conference On Computer And Communication Engineering
A binary Particle Swarm Optimization for attacking knapsacks Cipher Algorithm
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Publication Date
Thu Aug 01 2024
Journal Name
Electronics
A Survey: Security Vulnerabilities and Protective Strategies for Graphical Passwords
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As technology advances and develops, the need for strong and simple authentication mechanisms that can help protect data intensifies. The contemporary approach to giving access control is through graphical passwords comprising images, patterns, or graphical items. The objective of this review was to determine the documented security risks that are related to the use of graphical passwords, together with the measures that have been taken to prevent them. The review was intended to present an extensive literature review of the subject matter on graphical password protection and to point toward potential future research directions. Many attacks, such as shoulder surfing attacks, SQL injection attacks, and spyware attacks, can easily ex

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Publication Date
Fri Sep 30 2022
Journal Name
Iraqi Journal Of Chemical And Petroleum Engineering
Polyacrylamide Polymer Gel Systems for Conformance Control Technology: A Review
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Low oil extraction and early high water production are caused in part by reservoir heterogeneity. Huge quantities of water production are prevalent issues that happen in older reservoirs. Polyacrylamide polymer gel systems have been frequently employed as plugging agents in heterogeneous reservoirs to regulate water output and increase sweep efficiency. Polyacrylamide polymer gel systems are classified into three classes depending on their composition and application conditions, which are in-situ monomer gel, in-situ polymer gel, and preformed particle gel (PPG).

   This paper gives a comprehensive review of PPG’s status, preparation, and mechanisms. Many sorts of PPGs are categorized, for example, millimeter-sized preformed p

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Publication Date
Fri Feb 18 2022
Journal Name
Coatings
Non-Polar Gallium Nitride for Photodetection Applications: A Systematic Review
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Ultraviolet photodetectors have been widely utilized in several applications, such as advanced communication, ozone sensing, air purification, flame detection, etc. Gallium nitride and its compound semiconductors have been promising candidates in photodetection applications. Unlike polar gallium nitride-based optoelectronics, non-polar gallium nitride-based optoelectronics have gained huge attention due to the piezoelectric and spontaneous polarization effect–induced quantum confined-stark effect being eliminated. In turn, non-polar gallium nitride-based photodetectors portray higher efficiency and faster response compared to the polar growth direction. To date, however, a systematic literature review of non-polar gallium nitride-

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Publication Date
Thu Jan 01 2015
Journal Name
Journal Of Materials Chemistry A
A novel approach to fabricate zeolite membranes for pervaporation processes
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A method has been demonstrated to synthesise effective zeolite membranes from existing crystals without a hydrothermal synthesis step.

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Publication Date
Sun Feb 28 2021
Journal Name
Journal Of Electrochemical Science And Technology
Simultaneous Removal of Cadmium and Copper from a Binary Solution by Cathodic Deposition Using a Spiral-Wound Woven Wire Meshes Packed Bed Rotating Cylinder Electrode
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Publication Date
Wed Jan 01 2025
Journal Name
Aip Conference Proceedings
Determination of cefotaxime-sodium at nanoscale level by a microflow injection cell via measuring turbidity using five irradiation sources (WSLEDs) with a single solar cell
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This work presents a completely new develop an analyzer, named NAG-5SX1-1D-SSP, that is simple, accurate, reproducible, and affordable for the determination of cefotaxime sodium (CFS) in both pure and pharmaceutical drugs. The analyzer was designed according to flow injection analysis, and conducted to turbidimetric measurements. Ammonium cerium nitrate was utilized as a precipitating agent. After optimizing the conditions, the analysis system exhibited a linear range of 0.008-27 mmol. L-1 (n=29), with a limit of detection of 439.3 ng/sample, a limit of quantification of 0.4805 mg/sample, and a correlation coefficient of 0.9988. The repeatability of the responses was assessed by performing six successive injections of CFS at concentra

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Publication Date
Mon Jan 01 2024
Journal Name
Lecture Notes In Mechanical Engineering
Development and Validation of a Free Piston Engine Linear Generator Simulation Model Including Cycle-To-Cycle Variation and Ignition Timing Sub-Models
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Publication Date
Fri Sep 30 2022
Journal Name
Journal Of Economics And Administrative Sciences
Distinguishing Shapes of Breast Cancer Masses in Ultrasound Images by Using Logistic Regression Model
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The last few years witnessed great and increasing use in the field of medical image analysis. These tools helped the Radiologists and Doctors to consult while making a particular diagnosis. In this study, we used the relationship between statistical measurements, computer vision, and medical images, along with a logistic regression model to extract breast cancer imaging features. These features were used to tell the difference between the shape of a mass (Fibroid vs. Fatty) by looking at the regions of interest (ROI) of the mass. The final fit of the logistic regression model showed that the most important variables that clearly affect breast cancer shape images are Skewness, Kurtosis, Center of mass, and Angle, with an AUCROC of

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Publication Date
Sat May 01 2021
Journal Name
Journal Of Physics: Conference Series
Investigating of Charge Transfer in Cu/F8 Using Donor-Acceptor Model due Quantum Transition
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in this paper, we study and investigate a simple donor-acceptor model for charge transfer formation using a quantum transition theory. The transfer parameters which enhanced the charge transfer and the rate of the charge transfer have been calculated. Then, we study the net charge transfer through interface of Cu/F8 contact devices and evaluate all transfer coefficients. The charge transfer rate of transfer processes is found to be dominated in the low orientation free energy and increased a little in decreased potential at interface comparison to the high potential at interface. The increased transition energy results in increasing the orientation of Cu to F8. The transfer in the system was more active when the system has large driving for

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