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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 Dec 22 2024
Journal Name
Journal Of Petroleum Research And Studies
Optimizing Well Placement with Genetic Algorithms: A Case Study
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Maximizing the net present value (NPV) of oil field development is heavily dependent on optimizing well placement. The traditional approach entails the use of expert intuition to design well configurations and locations, followed by economic analysis and reservoir simulation to determine the most effective plan. However, this approach often proves inadequate due to the complexity and nonlinearity of reservoirs. In recent years, computational techniques have been developed to optimize well placement by defining decision variables (such as well coordinates), objective functions (such as NPV or cumulative oil production), and constraints. This paper presents a study on the use of genetic algorithms for well placement optimization, a ty

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Publication Date
Mon Jan 01 2024
Journal Name
Aip Conference Proceedings
Negative skin friction evaluation and mitigation: A review study
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Publication Date
Sun Sep 06 2009
Journal Name
Baghdad Science Journal
Synthesis of several Urea plast Resins using Different Aldehydes Preparation of some Alkyde Resins and Empolyment of the prepared Resins as Additives for AZO Dyes
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Urea formaldehyde resin was prepared by using basic media by yield 95%. The Remaining of ureaplasts resin were prepared in acetic acid media by high yield. Alkyde resins were prepared by condensation polymerization by react Succinic, Maleic, Phthalic anhydrides with Ethylene glycol or Glycerol. Select samples of the prepared alkyde resins were mixed with Azo dyes in special ratio. The mixtures were used as coatings for wood, and compaised with pure dyes. The Coating that some alkyde resins showed better adhesion from using dyes alone. Preparation of wood coating by mixing ureaplast resins and alkyde resins with Azo dyes in special ratios. The coating showed better adhesion, brighter colors and better resistance to heat from Preceding coat

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Publication Date
Tue Dec 31 2019
Journal Name
МИР НАУКИ, КУЛЬТУРЫ, ОБРАЗОВАНИЯ
GLUTTONICO-DISCURSIVE APHORISMS, MAXIMS, SENTATIONS, PAREMIAS (PROVERBS AND SAYINGS) AS A NATIONAL SOCIO-CULTURAL CODE OF ARABOPHONES
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The article deals with glutton-discursive aphorisms, maxims, sentations, paremias (proverbs and sayings) of different peoples, which reflect their character traits and aspects of life in the family, collective, society, everyday realities, which indicates the close connection of paremias with the language en vironment. Attention is focused on the parodies used in 73% of cases and nominating personality characteristics using the socio-cultural code of arabophones. It is proved that this vocabulary as the national socio-cultural code of arabophones are used to increase the capacity of the statement, and express the emotional and aesthetic positions of a person

Publication Date
Thu Dec 01 2022
Journal Name
Journal Of Medicine And Life
Renal stone density on native CT-scan as a predictor of treatment outcomes in shock wave lithotripsy
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Extracorporeal shock wave lithotripsy (ESWL) is considered a standard treatment for nephrolith or kidney stones measuring less than 20 mm. Anatomical, machine-related, and stone factors play pivotal roles in treatment outcomes, the latter being the leading role. This paper examined the relationship between stone density on native CT scans and ESWL treatment to remove renal stones concerning several treatments. One hundred and twenty patients (64 males and 56 females) were enrolled and completed the study from April 2019 to September 2020. Inclusion criteria were a single renal pelvis stone of 5–20 mm to be treated for the first time in adult patients with no urinary or musculoskeletal anatomical abnormalities. We assessed patients

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Publication Date
Wed Aug 12 2015
Journal Name
J. Genet. Environ. Resour. Conserv
Effect of arbuscular mycorrhizal fungi as a biocontrol agent and organic matter against fusarium wilt in tomato
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The objective of this investigation was to study the effects of a mixture of three arbuscular mycorrhizae (Glomus etunicatum, G. leptotichum and Rhizophagus intraradices) on the development of fusarium wilt disease in tomato plants in the presence and absence of organic matter (peatmoss). Results indicated an increase in mycorrhizal root dry weight especially in the presence of the organic matter, on the other hand this parameter was significantly decreased when Fusarium oxysporum f. sp. Lycopersiciwas added simultaneously with the mycorrhiza, Moreover, mycorrhiza and organic matter significantly reduced the damping off seedling disease, disease severity and rate of infection of tomato leaves and roots caused by the pathogenic fungus, These

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Publication Date
Wed May 10 2023
Journal Name
Journal Of Planner And Development
Analysis and evaluation of related factors affecting community Participation as a policy to upgrade residential slums area
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have suffered from deteriorating residential neighborhoods, poor economic, social and urban living conditions of the population and deteriorating the infrastructural and superior services. These problems were the secretions of these cities' rapid urbanization. Based on the principles of sustainable urban planning and in order to achieve adequate opportunities for the lives of the population and provide them with sustainable livelihoods, policies have emerged to upgrade along the lines of community participation and programmes to reform and develop those neighbourhoods, raise their efficiency and make them livable. Thus, the problem of research was identified "The absence of a comprehensive cognitive perception of the most prominent facto

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Publication Date
Wed Jan 01 2020
Journal Name
Desalination And Water Treatment
Stabilization of phenol trapped by agricultural waste: a study of the influence of ambient temperature on the adsorbed phenol
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Stabilization of phenol trapped by agricultural waste: a study of the influence of ambient temperature on the adsorbed phenol

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Publication Date
Mon Jan 01 2018
Journal Name
Al-kindy College Medical Journal
Metabolic Syndrome; Comparing the Results of Three Definition Criteria in an Iraqi Sample
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Background: Different diagnostic definition and criteria have been recommended by different expert groups for the diagnosis of metabolic syndrome, however, it’s prevalence in the same population could differ depending on the definition used yielding different results. In Iraq, there is a lack of research comparing these different diagnostic definitions. Objective: To find out the most suitable metabolic syndrome definition to be used for Iraqi people.  Methods: 320 participants were recruited for this study, 53.4% men and 46.6% women, aged between 25-85 years, visiting Baghdad Teaching Hospital, the prevalence of metabolic syndrome according to different definitions were compared and the agreement was assessed by the Kappa st

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Publication Date
Fri Sep 04 2015
Journal Name
International Journal Of Academic Research In Progressive Education And Development
The Influence of Three Teaching Methods on Undergraduate Physics Students' Group Work Skill
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The purpose of this study is to compare the influence of three teaching methods, as represented by problem-based learning (PBL), the PBL with lecture method, and the conventional teaching on undergraduate physics students' group work skills among bachelor’s degree physics students. In this study, the pre- and post-test were done and the instruments were administered to the students for data collection. The actual sample size comprises of 122 students, who were selected randomly from the physics department, college of education in iraq. Overall, the statistical results rejected null hypothesis of this study. Thus, using the PBL without or with lecture method enhances the skills of the group work among the bachelor’s degree physics studen

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