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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
Sat May 30 2020
Journal Name
Neuroquantology
Comparative Study for Optoelectronic Properties of Zn (Te, Se) Solar Cells
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Publication Date
Thu Feb 01 2024
Journal Name
Baghdad Science Journal
Comparative Study of Gamma- Ray Shielding Parameters for Different Epoxy Composites
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In the current work various types of epoxy composites were added to concrete to enhance its effectiveness as a gamma- ray shield. Four epoxy samples of (E/clay/B4C) S1, (E/Mag/B4C) S2, (EPIL) S3 and (Ep) S4 were used in a comparative study of gamma radiation attenuation properties of these shields that calculating using Mont Carlo code (MCNP-5). Adopting Win X-com software and Artificial Neural Network (ANN), µ/ρ revealed great compliance with MCNP-5. By applying (µ/ρ) output for gamma at different energies, HVL, TVL and MFP have been also estimated. ANN technique was simulated to estimate (µ/ρ) and dose rates. According to the results, µ/ρ of all epoxy samples scored higher than standard concrete. Both S2 and S3 samples having h

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Publication Date
Wed Jan 13 2021
Journal Name
Egyptian Journal Of Chemistry
Development of a nanostructured double-layer coated tablet based on polyethylene glycol/gelatin as a platform for hydrophobic molecules delivery
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The aim of the current study was to develop a nanostructured double-layer for hydrophobic molecules delivery system. The developed double-layer consisted of polyethylene glycol-based polymeric (PEG) followed by gelatin sub coating of the core hydrophobic molecules containing sodium citrate. The polymeric composition ratio of PEG and the amount of the sub coating gelatin were optimized using the two-level fractional method. The nanoparticles were characterized using AFM and FT-IR techniques. The size of these nano capsules was in the range of 39-76 nm depending on drug loading concentration. The drug was effectively loaded into PEG-Gelatin nanoparticles (≈47%). The hydrophobic molecules-release characteristics in terms of controlled-releas

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Publication Date
Sun Dec 01 2019
Journal Name
Journal Of Accounting And Financial Studies ( Jafs )
Application of the excess cash margin model (ECM) to detect the Earning Management in the banking sector: Comparative study between commercial and Islamic banks
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The research draws its importance from identifying the methods of profit management in misleading the financial statements, which in turn is reflected in the decisions of the authorities that relied on these reports, and then the models that help in detecting those methods used by the auditors. Risks. The index (margin of excess cash) was used to detect profit management practices on a group of banks listed in the Iraqi market for securities and the number of (23) banks, including (12) commercial bank and (11) Islamic bank and the results were compared to commercial banks with Islamic banks.((The research started from the hypothesis that the use of the (excess cash margin) model in the banking sector reveals the management

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Publication Date
Sun Jun 30 2019
Journal Name
Journal Of The College Of Education For Women
The Aesthetic of the Textual Interferences in the Poetry of the Ghawani's" A Miracle Nice of your Imagination as a symbol"
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     إنّ التّأمّل في الدّراسات الأدبيّة النّقديّة الحديثة الّتي تنظر إلى النّصّ أنّه لوحة تتشكّل من مجموعة تداخلات نصّيّة سابقة للنصّ المُنتج أو مُعاصرة له، تدفع القارئ إلى الغوص في أعماق النّصوص وتحليلها والكشف عن الآليّات والإجراءات الّتي اعتمدت في إنتاجه، وإظهار الجماليّات الفنّيّة التي شكلت في مُجملها كائنا حيّا يُعبّر عن حالات إنسانيّة مُستمرة الحدوث رغم تقادم الأزمان.

فالبحث هذا يعمد

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Publication Date
Sun Sep 27 2020
Journal Name
Journal Of The College Of Education For Women
Problems Facing Working Women in the Labor Market (The Mall) as a Model:a Field Study in Al-RusafaArea/ Baghdad
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Most studies and research have tried to shed light on unemployment and employment in general, with less focus on the problems facing working women and the resulting social and economic consequences that threaten their human and professional lives. For women, working is one of the basic necessities for the sustainability of human life, and it constitutes an essential axis for both sexes and through it. It also gives a person the status and social status where the individual finds a ready opportunity to practice his intentions and desires, test his abilities and talents, and achieve his ambitions. The availability of full employment in general and the joining of women to the labor market is an important and fundamental factor in the sustai

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Publication Date
Fri Mar 10 2023
Journal Name
Journal Of Namibian Studies : History Politics Culture
The Sufi influence in the Iraqi novel, the Lamia, is a model
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In our research, we seek to shed a light on one of the most important and sensitive issues, namely, the Sufi influence in the Iraqi novel through the lame maqam of the novelist Jumaa Al-Lami, the Sufi discourse contains many semantic paradoxes between the text's apparent pronunciation and its interpretation of the format and the context that produced these patterns, and incited them, which concludes different results from the prevailing provisions and fixed ideas from the narrative text.The Arabic and Iraqi novel in particular became inspired by the power of Sufi discourse by talking about several Sufi figures by referring to it openly, or implicitly inspired by unauthorized concealment, in employing some of the ideas, or summoning

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Publication Date
Sat Jun 01 2013
Journal Name
Journal Of The College Of Languages (jcl)
Dylan Thomas:The Vision of Death as a Prologue to a New Life
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Dylan Thomas (1914-1953) is a modern poet belongs to the apocalyptic movement of the 1940's.This movement is influenced by the doctrines and techniques of surrealism.

              Poetry for him should not be primarily concerned with man in society, but with the celebration of spiritual truth. It should bring to light the hidden causes, hence  his personal interest is to strip darkness and explore the inward motives. To do this he uses a cluster of images: a constant building up and breaking down of images. His poetry depends on the romantic spontaneity, suggestiveness of the Symbolists and the the surrealists' mysterious liberation of the unconsciousness and

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Publication Date
Sat Jun 01 2013
Journal Name
Journal Of The College Of Languages
Dylan Thomas:The vision of Death as a Prologue to a New Life
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Dylan Thomas (1914-1953) is a modern poet belongs to the apocalyptic movement of the 1940's.This movement is influenced by the doctrines and techniques of surrealism. Poetry for him should not be primarily concerned with man in society, but with the celebration of spiritual truth. It should bring to light the hidden causes, hence his personal interest is to strip darkness and explore the inward motives. To do this he uses a cluster of images: a constant building up and breaking down of images. His poetry depends on the romantic spontaneity, suggestiveness of the Symbolists and the the surrealists' mysterious liberation of the unconsciousness and the emotional involvement in the dynamics of life. In "Light Breaks

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Publication Date
Sun Mar 07 2010
Journal Name
Baghdad Science Journal
Study of the properties of Ru-isotopes using the proton-neutron interacting boson model (IBM-2)
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The proton-neutron interacting boson model (IBM-2) has been used to make a schematic study of the Ruthenium ( ) isotopes of mass region around with and . For each isotope of the values of the IBM-2 Hamiltonian parameters, which yield an acceptable results for excitation energies in comparison with those of experimental data, have been determined. Fixed values of the effective charges ( ) and of the proton and neutron g factors ( and ) have been chosen for all isotopes under study. The calculated electric quadrupole moments of state, transitions, the magnetic dipole moments transitions and mixing ratios are in reasonable agreement with the experimental data.

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