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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 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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Publication Date
Thu Dec 15 2022
Journal Name
Al-academy
The controversy of aesthetic interpretation between the sculptures and their titles Contemporary Iraqi Sculpture "Experiments in Contemporary Iraqi Sculpture Exhibition as a Model"
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The research tagged with the controversy of aesthetic interpretation between the sculptures and their titles in contemporary Iraqi sculpture, “Exhibition of Experiments in Contemporary Iraqi Sculpture as a Model”, and it is one of the new research that contributes to strengthening the critical path in the Iraqi fine movement, as the first chapter dealt with the research problem stemming from the question: What is the impact of the aesthetic hermeneutic controversy between the title and the title in contemporary Iraqi sculpture?, and do the titles of the sculptural works help to understand or enhance their contents?, The research objective included: To identify the controversy of the aesthetic interpretation of sculptures and their ti

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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
Sat Jun 01 2024
Journal Name
Materials And Structures
Exploring the efficacy of sawdust ash as a mineral filler substitute for the production of asphalt mixtures
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Many waste materials can be repurposed effectively within asphalt concrete to enhance the performance and sustainability of pavement. One of these waste materials is sawdust ash (SDA). This study explores the beneficial use of SDA as a substitute for limestone dust (LD) mineral filler in asphalt concrete. The replacement rate was 0%, 15%, 30%, 45%, and 60% by weight of total mineral filler. Scanning electron microscopy (SEM) was employed to assess the surface morphology of Sawdust (SD), SDA, and LD. In addition, a series of tests, including Marshall stability and flow, indirect tensile strength,moisture susceptibility, and repeated uniaxial loading tests, were conducted to examine the performance characteristics of asphalt mixtures of diffe

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Publication Date
Sun Jan 01 2023
Journal Name
Communications In Mathematical Biology And Neuroscience
Stability and Hopf bifurcation of an epidemiological model with effect of delay the awareness programs and vaccination: analysis and simulation
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Publication Date
Mon Jan 01 2018
Journal Name
World Journal Of Dentistry
Obturation of Lateral Canals by a New Reciprocating Spreader and a Conventional Finger Spreader by Lateral Condensation Technique: in vitro Comparative Study
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Publication Date
Sat Oct 19 2024
Journal Name
Mustansiriyah Journal Of Sports Science
Traditional Championships sports (Zurkhaneh and Sumo): a comparative historical study of historical origins and traditional rituals
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Many societies have some sports that play a pivotal role in enhancing human physical strength and martial arts and preserving religious values and beliefs. The most prominent of these traditional heroic sports are Zurkhaneh and Sumo, two sports that have their historical origins in the Iranian and Japanese cultural heritage. The research aims at shed light on the historical origins, symbolic rituals, and traditional elements of the sports of Zurkhaneh and Sumo, and to highlight the distinctive characteristics of the sports of Zurkhaneh and Sumo through objective analysis and comparison. The methodology used in this research is the historical approach, using the method of comparative analysis. This method includes analyzing information deriv

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Publication Date
Thu Mar 25 2021
Journal Name
International Journal Of Drug Delivery Technology
A comparative study of retinol-binding protein-4 and progranulin in iraqi women with thyroid disorder
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Thyroid hormones (TH) regulate the metabolic processes required for normal development and growth; also, to organizemetabolism in adults, any defect in thyroid function leads to abnormality in thyroid hormones level. The current study hasbeen designed to find the relationship between retinol-binding protein-4 and progranulin in the serum of Iraqi women withhypothyroidism and hyperthyroidism, also, to study whether these patients are exposed to a risk of developing diabetes mellitus,and PGRN may be a biomarker in detection early stage of diabetes mellitus.Materials and Methods: in this study, serum samples were obtained from 50 Iraqis women patients, [25 patients withhypothyroidism (G2) and 25 patients with hyperthyroidism (G3)] in addition

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Publication Date
Tue Oct 09 2018
Journal Name
Bulletin Of The Iraq Natural History Museum (p-issn: 1017-8678 , E-issn: 2311-9799)
A COMPARATIVE HISTOLOGICAL STUDY OF THYROID TISSUE IN CARP FISH CYPRINUS CARPSIO AND MICE SWISS ALBICANS
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    This histological study was carried out to compare between the thyroid gland of mice (as a model of the mammals) and the thyroid tissue of fish.  Unlike mice, the thyroid gland of fish can't be recognized by naked eye.  The present study revealed that the thyroid of mice varied from that of fish by the location and the histological structure. The study classified the physiological state of the thyroid of mice into three states and that of the fish into only two states. Accordingly, the study concluded that the metabolism of thyroid fish was of moderate type.

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Publication Date
Mon Jun 30 2025
Journal Name
Infotech Spectrum: Iraqi Journal Of Data Science
Evaluating AI Language Models in News Retrieval: A Comparative Study Of ChatGPT-Plus and DeepSeek (R1)
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The increasing complexity of how humans interact with and process information has demonstrated significant advancements in Natural Language Processing (NLP), transitioning from task-specific architectures to generalized frameworks applicable across multiple tasks. Despite their success, challenges persist in specialized domains such as translation, where instruction tuning may prioritize fluency over accuracy. Against this backdrop, the present study conducts a comparative evaluation of ChatGPT-Plus and DeepSeek (R1) on a high-fidelity bilingual retrieval-and-translation task. A single standardize prompt directs each model to access the Arabic-language news section of the College of Medicine, University of Baghdad, retrieve the three most r

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