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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 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
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
Tue Jul 22 2025
Journal Name
Al-rafidain Journal Of Medical Sciences ( Issn 2789-3219 )
Effectiveness of Intralesional Vitamin D and Bleomycin Injections in Treating Recalcitrant Plantar Wart: A Comparative Study
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Background: Intralesional injections of vitamin D and bleomycin have gained growing clinical interest in the treatment of recalcitrant plantar warts, with pain as a major limitation associated with their use. Objective: To assess the clinical outcomes of vitamin D and bleomycin in managing treatment-resistant plantar warts. Methods: An interventional comparative study conducted on patients diagnosed with recalcitrant plantar warts over 9 months and not treated for two months. Patients were divided randomly into two groups: group A (24 patients received intralesional vitamin D) and group B (24 patients received intralesional bleomycin). The clearance rate and pain score were estimated by visual analogue scale (VAS). Results: 48 patie

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Publication Date
Sat Jan 05 2019
Journal Name
Iraqi Journal Of Physics
Study of nuclear structure for carbon isotopes using local scale transformation technique in shell model
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This work is devoted to study the properties of the ground states such as the root-mean square ( ) proton, charge, neutron and matter radii, nuclear density distributions and elastic electron scattering charge form factors for Carbon Isotopes (9C, 12C, 13C, 15C, 16C, 17C, 19C and 22C). The calculations are based on two approaches; the first is by applying the transformed harmonic-oscillator (THO) wavefunctions in local scale transformation (LST) to all nuclear subshells for only 9C, 12C, 13C and 22C. In the second approach, the 9C, 15C, 16C, 17C and 19C isotopes are studied by dividing the whole nuclear system into two parts; the first is the compact core part and the second is the halo part. The core and halo parts are studied using the

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Publication Date
Sun Apr 01 2018
Journal Name
Al–bahith Al–a'alami
Effectiveness of sports television programs in the development of sports culture among youth: field study
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The aim of the research is to determine the extent to which young people watch television sports programs and the impact of viewing on the level of sports culture among young people and the impact of demographic variables on youth over the viewing of sports programs, The study was conducted on a sample of (200) male and female students from the faculties of the University of Baghdad, where a questionnaire form composed of several axes and questions was prepared to measure the effectiveness of sports programs in youth culture, The statistical program used spss to empty data and extract results by frequency, percentages, correlations, The research reached several results, the most important of which is that there is a strong influence of s

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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
Sat Jan 01 2022
Journal Name
Pharmacia
Synthesis, docking study, and structureactivity relationship of novel niflumic acid derivatives acting as anticancer agents by inhibiting VEGFR or EGFR tyrosine kinase activities
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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 Mar 15 2021
Journal Name
Al-academy
Semiotics of Musical Sign in Iraqi Pantomime Show (Ahriman) as a Model: علي عدي صاحب-شيماء حسين طاهر
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The musical sign was associated with the first appearances of acting that are based on human gestures and expressive and silent movements, and they contributed in accentuating and clarifying these gestures and explain their meanings and indications, and they remained with them until these gestures turned into artistic theatrical shows so that the musical sign would have many functions and constitute the main pillars for this kind of show.
The musical sign is a language not much different than the human language in the semiotic analysis. There has been an increased interest in it and its use in the mime shows by the graduates who realized its necessity and significance in the pantomime show intellectually, artistically and aesthetical

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