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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
Mon Aug 01 2022
Journal Name
Journal Of Molecular Liquids
Study to amino acid-based inhibitors as an effective anti-corrosion material
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The inhibitory behavior of L-Cysteine (Cys) and its derivatives towards iron corrosion through density functional theory (DFT) was investigated. The current research study undertakes a rigorous evaluation of global as well as local reactivity descriptors of the Cys in protonated as well as neutral forms and the changes in reactivity after the combination of Cys into di- and tripeptides. The inhibitory effect of di- and tri-peptides increases since, in the molecular structure, the number of reaction centers increase. We computed the adsorption energies (Eads) and low energy complexes with most stability for the adsorption of small peptides and Cys amino acids onto the surfaces of Fe (1 1 1). We found that the adsorption of tri-peptides onto

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Publication Date
Sun Mar 31 2024
Journal Name
Association Of Arab Universities Journal Of Engineering Sciences
Using Solid Waste as A Substitute for Raw Materials in Construction: A Review.
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The main challenge is to protect the environment from future deterioration due to pollution and the lack of natural resources. Therefore, one of the most important things to pay attention to and get rid of its negative impact is solid waste. Solid waste is a double-edged sword according to the way it is dealt with, as neglecting it causes a serious environmental risk from water, air and soil pollution, while dealing with it in the right way makes it an important resource in preserving the environment. Accordingly, the proper management of solid waste and its reuse or recycling is the most important factor. Therefore, attention has been drawn to the use of solid waste in different ways, and the most common way is to use it as an alternative

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Publication Date
Mon Jun 09 2025
Journal Name
Adab Al Rafidayn
Measuring the quality of office services using (LibQUAL + ®): the central library of the University of Baghdad as a model
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Libraries, information centers, and everything related to organizing and preparing information need to be periodically re-evaluated in order to stand on the level of quality, which means improving the general reality of these institutions to ensure sufficient satisfaction from beneficiaries of the services provided. This is what was worked on in this research, as one of the most important quality standards in libraries and information centers, LibQUAL+®, was applied in one of the most important and oldest central university libraries, namely the Central Library of the University of Baghdad at its two locations, Al-Jadriya and Al-Waziriya. The sample of beneficiaries to whom the questionnaire was distributed reached 75 beneficiaries distrib

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Publication Date
Sat May 27 2017
Journal Name
Journal Of Pharmaceutical Sciences And Research
Synthesis, Preliminary Antimicrobial Evaluation and Molecular Docking of new Schiff bases of Ceftizoxime
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Schiff bases of Ceftizoxime sodium were synthesized in an attempt to improve the antimicrobial spectrum of Ceftizoxime. Aminothiazole ring of Ceftizoxime is linked directly through an imino group to different aromatic aldehydes reacted by nucleophilic addition using trimethylamine (TEA), as a catalyst and refluxed in methanol. The antimicrobial activity was evaluated for such Schiff bases using disc diffusion method. Molecular docking was conducted on certain penicillin-binding proteins (PBPs) and carboxypeptidases using 1- click docking software. Schiff bases of Ceftizoxime were prepared with reasonable yields and their chemical structures were confirmed by spectral analysis (FTIR, 1H-NMR) and elemental microanalysis (CHNS). The antibacter

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Publication Date
Mon Sep 25 2017
Journal Name
Ibn Al-haitham Journal For Pure And Applied Sciences
A Comparative Study for the Proton Electronic Stopping Power of Some Polymers by Using Mathematica, SRIM2013, PSTAR, LibdEdx, and Experimental Databases
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The available experimental data of proton electronic stopping power for Polyethylene, Mylar, Kapton and Polystyrene are compared with Mathematica, SRIM2013, PSTAR and libdEdx programs or databases.  The comparison involves sketching out both experimental and databases data for each polymer to discuss the agreement. Further, we use statistical means via standard deviation resulting from the mean normalized difference to describe the precise agreement among the databases and the experimental data. We found that there is not a specific one database can describe the experimental data for certain material at given proton energy.

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Publication Date
Tue Jun 14 2016
Journal Name
Al-academy
Idealism and Realism in The Design: A Comparative Study
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At the beginning of the twentieth century distorting handling totalitarian phenomena of art, which can be called the stage of the test, transition from the theory of ideal theory and other realistic is not cushy, since it requires vision and reading and other concepts, and in light of this dialectic manifested research problem by asking the following Is affected by the design idealism and realism. Through the above mentioned questions, the researcher found rationale for addressing this problem, the study through his research, which is marked (idealism and realism in a comparative study design). And demonstrated the importance of research in the identification of the concept and the effectiveness of the two theories idealism and realism a

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Publication Date
Wed Mar 15 2023
Journal Name
Al-academy
The gratifications of local television sports programs from the audience's point of view Analytical study for the period from 1/7/2022 to 01/10/2022
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The issue of sports media and its role in winning sports and non-sports fans and unifying them towards various issues and events is one of the important topics that have begun to occupy many countries and governments in the world and allocate appropriate spaces for it and provide it with sufficient funds and budgets to advance this reality...

Especially since the concept of the sports official has It changed a lot and turned into an economic concept rather than a sport one through the investment in the field of sports and the entry of capital and contributes to the prosperity of the countries interested in this field.

It is important that includes profit and loss in addition to knowing how to employ and win the masses and e

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Publication Date
Wed Sep 30 2020
Journal Name
College Of Islamic Sciences
The Breadth in the meaning of the "from Surah Maryam as a model.
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Prepositions have a key function, which is to associate parts of a sentence, called letters In addition, it adds the meanings of the verbs to the names, ie reached by them, and called by the coffin characters Qualities..

          I chose to search for the meaning of the preposition "from" in Surat Maryam to know its meanings in terms of originality and expansion, so the title of the research (the meanings of preposition "from" in terms of originality and expansion in Surat Maryam model(

 

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Publication Date
Thu Sep 23 2021
Journal Name
Egyptian Journal Of Chemistry
Some 3,4,5-Trisubstituted-1,2,4-triazole Synthesis, Antimicrobial Activity, and Molecular Docking Studies
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Publication Date
Sun Mar 01 2020
Journal Name
Baghdad Science Journal
A Comparative Study on the Double Prior for Reliability Kumaraswamy Distribution with Numerical Solution
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This work, deals with Kumaraswamy distribution. Kumaraswamy (1976, 1978) showed well known probability distribution functions such as the normal, beta and log-normal but in (1980) Kumaraswamy developed a more general probability density function for double bounded random processes, which is known as Kumaraswamy’s distribution. Classical maximum likelihood and Bayes methods estimator are used to estimate the unknown shape parameter (b). Reliability function are obtained using symmetric loss functions by using three types of informative priors two single priors and one double prior. In addition, a comparison is made for the performance of these estimators with respect to the numerical solution which are found using expansion method. The

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