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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
Sat Dec 01 2018
Journal Name
Al-khwarizmi Engineering Journal
Biodegradation of Diesel Contaminated Soil Using Single Bacterial Strains and a Mixed Bacterial Consortium
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This study was conducted to assess the hydrocarbon degradation abilities of Sphingomonas paucimobilis, Pentoae species, Staphylococcus aureus, and Enterobacter cloacae, which isolated from diesel contaminated soil samples. Single strains and mixed bacterial consortia have been investigated their ability to degrade 1.0 % (v/v) of diesel oil in Bushnell- Haas medium as sole.carbon.and.energy.source. At temperature 30C, the individual.bacterial.isolates exhibited low growth and low degradation.than did the.mixed. bacterial.culture. After 28 days.of incubation the.combination.of four isolates degraded.an upper limit.of diesel  88.4%. This was. continued.by 85.1% by S. paucimobilis, 84 % by Pentoae sp., 79% by S.aureus, and

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Publication Date
Thu Jun 23 2022
Journal Name
American Scientific Research Journal For Engineering, Technology, And Sciences
A Review of TCP Congestion Control Using Artificial Intelligence in 4G and 5G Networks
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In recent years, the field of research around the congestion problem of 4G and 5G networks has grown, especially those based on artificial intelligence (AI). Although 4G with LTE is seen as a mature technology, there is a continuous improvement in the infrastructure that led to the emergence of 5G networks. As a result of the large services provided in industries, Internet of Things (IoT) applications and smart cities, which have a large amount of exchanged data, a large number of connected devices per area, and high data rates, have brought their own problems and challenges, especially the problem of congestion. In this context, artificial intelligence (AI) models can be considered as one of the main techniques that can be used to solve ne

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Publication Date
Wed Mar 01 2023
Journal Name
Evergreen
Combustion Characteristics of a Free Piston Engine Linear Generator using Various Fuel Injection Durations
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Publication Date
Fri Aug 02 2024
Journal Name
Quantum Studies: Mathematics And Foundations
Implementation of a modified noise-free and noisy multistage quantum cryptography protocol using QISKIT
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Classical cryptography systems exhibit major vulnerabilities because of the rapid development of quan tum computing algorithms and devices. These vulnerabilities were mitigated utilizing quantum key distribution (QKD), which is based on a quantum no-cloning algorithm that assures the safe generation and transmission of the encryption keys. A quantum computing platform, named Qiskit, was utilized by many recent researchers to analyze the security of several QKD protocols, such as BB84 and B92. In this paper, we demonstrate the simulation and implementation of a modified multistage QKD protocol by Qiskit. The simulation and implementation studies were based on the “local_qasm” simulator and the “FakeVigo” backend, respectively. T

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Publication Date
Wed Jan 01 2020
Journal Name
Journal Of Mechanical Engineering Research And Developments
Development of natural convection heat transfer in heat sink using a new fin design
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Publication Date
Tue Sep 01 2009
Journal Name
Journal Of Economics And Administrative Sciences
Comparison of estimation methods for regression model parametersIn the case of the problem of linear multiplicity and abnormal values
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 A simulation study is used to examine the robustness of some estimators on a multiple linear regression model with problems of multicollinearity and non-normal errors, the Ordinary least Squares (LS) ,Ridge Regression, Ridge Least Absolute Value (RLAV), Weighted Ridge (WRID), MM and a robust ridge regression estimator MM estimator, which denoted as RMM this is the modification of the Ridge regression by incorporating robust MM estimator . finialy, we show that RMM is the best among the other estimators

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Publication Date
Tue Feb 01 2022
Journal Name
Advanced Powder Technology
Functionalization of mesoporous MCM-41 for the delivery of curcumin as an anti-inflammatory therapy
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Publication Date
Mon Dec 18 2017
Journal Name
Al-khwarizmi Engineering Journal
Experimental and Theoretical Study for Performance Enhancement of Air Solar Collectors by Using Different Absorbers
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An experimental and theoretical study has been done to investigate the thermal performance of different types of air solar collectors, In this work air solar collector with a dimensions of (120 cm x90 cm x12 cm) , was tested under climate condition of  Baghdad city with a (43° tilt angel)  by using  the absorber plate (1.45 mm thickness, 115 cm height x 84 cm width), which was manufactured from iron painted with a black matt.

The experimental test deals with five types of absorber:-

 Conventional smooth flat plate absorber , Finned absorber , Corrugated absorber plate, Iron wire mesh on absorber And matrix of porous media  on absorber .

The hourly and average efficiency of the collectors

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Publication Date
Wed Apr 12 2017
Journal Name
Ibn Al-haitham Journal For Pure And Applied Science
Synthesis, Characterization and Study Biological Activity of Some New 1, 3, 4-Thiadiazole and Pyrazolone Derivatives Containing Indole Ring
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This work involves synthesis and characterization of some new 1, 3, 4-thiadiazole or pyrazoline derivatives heterocyclic containing indole ring. The new 2-amino-1, 3, 4-thiadiazole derivatives [IV] and [V] a, b were synthesized by cyclization reaction of 2-methyl-1H-indole-carbothiosemicarbazide [III] in H2SO4 acid or by reaction of indole-3-acetic acid or indole-3-butanoic acid with thiosemicarbazide in the presence of phosphorous oxychloride, respectively. Amide derivatives [VI]-[VIII] were synthesized by the reaction equimolar of 2-amino-1, 3, 4-thiadiazoles and (acetyl chloride, benzoyl chloride, anisoyl chloride and heptanoyl chloride) in DMF and pyridine as accepter. The new pyrazolone derivatives [XI] a, b were synthesized from heati

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Publication Date
Fri Dec 23 2022
Journal Name
Iraqi Journal Of Pharmaceutical Sciences ( P-issn 1683 - 3597 E-issn 2521 - 3512)
Aspirin Derivatives Exploration: A Review on Comparison Study with Parent Drug
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In recent decades, drug modification is no longer unusual in the pharmaceutical world as living things are evolving in response to environmental changes. A non-steroidal anti-inflammatory drug (NSAID) such as aspirin is a common over-the-counter drug that can be purchased without medical prescription. Aspirin can inhibit the synthesis of prostaglandin by blocking the cyclooxygenase (COX) which contributes to its properties such as anti-inflammatory, antipyretic, antiplatelet and etc. It is also being considered as a chemopreventive agent due to its antithrombotic actions through the COX’s inhibition. However, the prolonged use of aspirin can cause heartburn, ulceration, and gastro-toxicity in children and adults. This review article hi

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