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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
Tue Aug 02 2022
Journal Name
Journal Of Legal Sciences
Expropriation of foreign investments - a comparative study
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The right to property is one of the most prominent and most important of the fundamental rights that the individual enjoys, whether national or foreign, both of them have their own private property that may not be affected except for the requirements of the country's economic development or what is known as the public benefit, and the Iraqi legislator did not specify what is meant by the removal of foreign investment. Of the bilateral international agreements (BITS), as it determined its terms and methods, the properties of foreign investors may be expropriated in a direct and indirect way.

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Publication Date
Wed Dec 30 2020
Journal Name
Journal Of Planner And Development
Urban improvement, a mechanism of tourism development: Tébessa (Algeria) as a model
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The tourism industry has become, currently, an art, an industry and a science. It is also one of the components that make up touristic regions. Tourist attractions are no longer the exclusive visits of museums and archeological sites, but also involve other service facilities. It is, therefore, imperative that the authorities should become aware of the degradation of tourist resorts and prevent them from getting worse. Moreover, the authorities should take a set of decisions concerning the protection of the urban aspect with its historical, social, and environmental dimensions, as well as, adapting it to the modern requirements that can bring comfort to the citizens and tourists at physical and psychological levels.

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Publication Date
Sat Dec 01 2018
Journal Name
Al-khwarizmi Engineering Journal
A study of Land Zoning in the base of Traffic Noise Pollution Levels using ArcGIS: Kirkuk City as a Case Study
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This study is an approach to assign the land area of  Kirkuk city [ a city located in the northern of Iraq, 236 kilometers north of  Baghdad  and 83 kilometers  south of  Erbil [ Climatic atlas of  Iraq, 1941-1970  ]  into different  multi zones by using Satellite image and Arc Map10.3,  zones of different traffic noise pollutions. Land zonings process like what achieved in this paper will help and of it’s of a high interest point for the future of Kirkuk city especially urban

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Publication Date
Tue Jan 09 2024
Journal Name
Wasit Journal Of Sports Sciences
A Comparative Analytical Study of Some Biomechanical Variables and Their Relationship to The Accuracy of The Performance of The Shooting Skill of Jumping High in The Weak and Strong Foot the Players for Youth Handball
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The research aims to identify the most important variables affecting shooting from jumping high and compare them for the two foot the weak and strong, where the researchers adopted the descriptive method, and the sample was chosen by the intentional method, which consists of (4) players from the Iraqi Sports Army Club, where these variables were studied and their impact on The accuracy of aiming at the two men, and the researchers concluded that most of the players have more accuracy in aiming at the strong leg than at the weak leg, which leads to the loss of many real opportunities during the match because of the players changing the situation or wasting the available opportunity when the position of correction is an opportunity for the w

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Publication Date
Wed Mar 16 2022
Journal Name
Journal Of Educational And Psychological Researches
Biology Textbook for Scientific Sixth Class in Iraq (A Comparative Study)
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The textbook is the primary means of creativity and thinking, which has a major role in the development of the readership and mental abilities of the student. It is the basic tool in education in Iraq for the teacher and the student, which cannot be dispensed in any educational program. The current study aimed at the book of the biology of the sixth grade of science in Iraq (comparative study). It was compared to the book of biology for the twelve grade in the Kingdom of Jordan to identify the ratio of similarity and differences between them, in addition, to identify the weaknesses in the Iraq curriculum and developing appropriate solutions and suggestions to address them. The sample was represented with books of biology (six-science cla

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Publication Date
Thu Nov 01 2018
Journal Name
Italian Journal Of Vascular And Endovascular Surgery
Retroperitoneal versus transperitoneal approach for aortoiliac occlusive disease: a comparative study
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Publication Date
Sun Sep 01 2024
Journal Name
Green Analytical Chemistry
Green methods for determination of paracetamol in drug samples: A comparative study
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Publication Date
Sat Jul 01 2023
Journal Name
Journal Of Analytical Chemistry
A Spectrophotometric Method for Tetracycline Determination in its Bulk Powder and Pharmaceutical Formulations Using Flow Injection and Batch Procedures: a Comparative Study
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A reliable and environmental analytical method was developed for the direct determination of tetracycline using flow injection analysis (FIA) and batch procedures with spectrophotometric detection. The developed method is based on the reaction between a chromogenic reagent (vanadium (III) solution) and tetracycline at room temperature and in a neutral medium, resulting in the formation of an intense brown product that shows maximum absorption at 395 nm. The analytical conditions were improved by the application of experimental design. The proposed method was successfully used to analyze samples of commercial medications and verified throughout the concentration ranges of 25–250 and 3–25 µg/mL for both FIA and batch procedures, respecti

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Publication Date
Wed Mar 10 2021
Journal Name
Baghdad Science Journal
Various Extracts of Some Medicinal Plants as Inhibitors for Beta-lactamase Activity
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The inhibitory effect of acetone, ethanol, and aqueous extracts of ten medicinal plants on β-lactamase from Staphylococcus sciuri and Klebsiella pneumoniae was investigated in vitro by starch-iodine agar plate method. The results revealed the success of starch-iodine method for the detection of the inhibition of β-lactamase activity by the various extracts of each individual plant. The acetone extracts of Catharanthus roseus, Eucalyptus camaldulensis, and Schinus terebinthifolius induced an inhibitory effect on β-lactamase from Staphylococcus sciuri. On the other hand, acetone extracts from only Eucalyptus camaldulensis, and Schinus

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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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