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bijps-1604
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 09 2018
Journal Name
Baghdad Science Journal
A Comparative Efficiency Study of Two Adsorbent Materials to Remove Eosin Y Dye from Aqueous Solutions
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This study was done to find a cheap, available and ecofriendly materials that can remove eosin y dye from aqueous solutions by adsorption in this study, two adsorbent materials were used, the shells of fresh water clam (Cabicula fluminea) and walnut shells. To make a comparison between the two adsorbents, five experiments were conducted. First, the effects of the contact time, here the nut shell removed the dye quickly, while the C. flumina need more contact time to remove the dye. Second, the effects of adsorbent weight were examined. The nut shell was very promising and for all used adsorbent weight, the R% ranged from 94.87 to 99.29. However C. fluminea was less effective in removing the dye with R% ranged from 47.59 to 55.39. The thi

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Publication Date
Mon Jan 01 2018
Journal Name
Journal Of The College Of Languages (jcl)
Grammatical Behaviour and Uses of Negative and Prohibitive Particles in Semitic Languages: A Comparative Semitic Study
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      Grammatical particles are so important in understanding a text and its meaning in linguistic context. This paper  " Grammatical Behavior and Uses of Negative and Prohibitive Particles in Semitic Languages: A Comparative Semitic Study"

      tackles  a very important topic in Semitic languages. Comparative studies in Semitic languages shed light on  phenomena in different languages that are related or have one common origin. No doubt, such studies have their own effects on language study in general especially when studying a specific phenomenon and explaining it by reliance on the one origin, or by investigating the various phases of its historical development.

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Publication Date
Wed Mar 18 2020
Journal Name
Baghdad Science Journal
A Comparative Study of Heavy Metals and Trace Elements Concentration in Milk Samples Consumed in Iraq
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The measurements of major and trace elements in different brands of milk powder selected from the Iraqis market via the X-ray fluorescence (XRF) Technique have been studied in the present work. The result of the measurements reveals the high concentrations of sodium, phosphorus, sulfur, chlorine, potassium, calcium and magnesium. Furthermore, low concentrations of aluminum, silicon, iron, bromine, molybdenum, iodine, barium, titanium, manganese, cobalt, chrome, nickel, copper, zinc and lead were detected. Neutron activation analysis (NAA) and Kjeldahl technique were also employed to determine the concentrations of nitrogen. It was found that the nitrogen concentration was in the range of (1.96 - 3.23) % which is within the permissible li

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Publication Date
Mon Oct 28 2019
Journal Name
Periodicals Of Engineering And Natural Sciences (pen)
Kinetic profile of silver and zinc oxide nanoparticles by intraperitoneal injection in mice , a comparative study
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Publication Date
Thu Aug 01 2024
Journal Name
Misan Journal For Physical Education Sciences
A comparative study of the reasons for the reluctance of female physical education teachers in “Baqubah” to participate in refereeing sports competitions according to the variable of years of service
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When searching for an answer to the following question: What are the reasons for the reluctance of female physical education teachers in secondary schools to referee sports competitions according to the variable of years of service? It was found that the research aimed to reveal the differences between the opinions of the research sample of physical education teachers in secondary schools (girls) about refereeing sports competitions according to the variable of years of service. To achieve the research goal, it is assumed that there are significant differences between the average opinions of the research sample of female teachers and their reluctance and the reasons for the differences in the practice of refereeing sports competitions accor

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Publication Date
Mon Jan 01 2024
Journal Name
Recent Research On Geotechnical Engineering, Remote Sensing, Geophysics And Earthquake Seismology
Evaluating the Accuracy of iPhone Lidar Sensor for Building Façades Conservation
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Publication Date
Thu Oct 18 2018
Journal Name
Al–bahith Al–a'alami
Public exposure to news satellite channels and its relationship to levels of preference and evaluation of programs: Survey study on a sample of the audience of Baghdad City Cente
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The media, especially the satellite channels in our time, are one of the most important pillars of daily life, public and private, for society and people, and are considered by sociologists and sociologists as one of the most important factors of social upbringing and the most important, as a result of the technological and technological development of the media as well as increasing their numbers and vertical and horizontal expansion locally, As well as entering into the lives of individuals and people and leading them to important sites within their interests and preferences, not to mention the long time spent exposure to those media and benefit from the programs offered or broadcast. , The problem of this research is that there is a l

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Publication Date
Wed Mar 25 2020
Journal Name
International Journal Of Drug Delivery Technology
Study of Molecular Interaction for Antibiotic Drug with Sugar Solutions at Different Temperature
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The interactions of drug amoxicillin with maltose or galactose solutions with a variation of temperature have been discussed by taking in the volumetric and viscometric procedures. Physical properties [densities (ρ) and viscosities (η)] of amoxicillin (AMOX) aqueous solutions and aqueous solutions of two type saccharides (maltose and galactose 0.05m) have been measured at T = (298.15, 303.15 and 308.15) K under atmospheric pressure. The apparent molar volume (ϕv cm3mole-1) has been evaluated from density data and fitted to a Redlich-Mayer equation. The empirical parameters of the Mayer-Redlich equation and apparent molar volume at infinite dilution ذv were explicated in terms of interactions from type solute-solvent and solute

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Publication Date
Sun Jul 01 2012
Journal Name
Journal Of Educational And Psychological Researches
A comparative study between the emotional responses in patients with blood pressure on a scale of music types characteristics compared with responses to some Healthy patients
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The problem of the study and its significance:

           Due to the increasing pressures of life continually, and constant quest behind materialism necessary and frustrations that confront us daily in general, the greater the emergence of a number of cases of disease organic roots psychological causing them because of severity of a lack of response to conventional treatments (drugs), and this is creating in patients a number of emotional disorders resulting from concern the risk of disease

 

     That is interested psychologists and doctors searchin

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Publication Date
Sun Nov 16 2025
Journal Name
Journal Of Baghdad College Of Dentistry
An evaluation of canal transportation and centering ability at different levels of root canals prepared by self-adjusting file using computed tomography (A comparative study)
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Background: The new concepts and technologies continue to change the dynamics of endodontic practices in the world. Rapid and significant changes in techniques, instrument design, and the type of metals used to manufacture endodontic instruments which have been made during the last few years in an attempt to overcome canal preparation errors. The purpose of this study is to measure and compare canal transportation and centering ability of Self Adjusting File with two rotary nickel-titanium (Ni-Ti) systems, ProTaper and BioRaCe at different levels. Material and Methods: Forty five distal roots of mandibular first molars with moderate curvature were selected using Schneider method. Roots were divided randomly into 3 groups of 15 each and were

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