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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
Fri Sep 30 2022
Journal Name
College Of Islamic Sciences
Historical development of Islamic jurisprudence - Develop a model
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       Praise be to God, and prayers and peace be upon our master Muhammad, the Messenger of God, and upon his family, companions, and those who are guided by his guidance.

Then:

       Our Islamic jurisprudence and its basic principles are fixed, namely: the Noble Qur’an, then the Prophet’s Sunnah, then consensus, then analogy. However, it is characteristic of what makes it developed to meet the requirements of renewed life, including: sent interests, custom, approval, blocking pretexts, changing times. That is why it went through different stages, growth, brilliance, stagnation and endowment; Therefore, many scholars of Islamic jurisprudence divided its stages into four sections: the stage of inf

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Publication Date
Sun Dec 31 2006
Journal Name
Journal Of Engineering
Theoretical Simulation Of Stress-Strain Relations For Some Iraqiclays Using The Endochronic Model
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Publication Date
Sat Jun 01 2013
Journal Name
Journal Of Economics And Administrative Sciences
Probabilistic Model building using the Transformation Entropy for the Burr type –xii Distribution
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Entropy define as uncertainty measure has been transfared by using the cumulative distribution function and reliability function for the Burr type – xii. In the case of data which suffer from volatility to build a model the probability distribution on every failure of a sample after achieving limitations function, probabilistic distribution. Has been derived formula probability distribution of the new transfer application entropy on the probability distribution of continuous Burr Type-XII and tested a new function and found that it achieved the conditions function probability, been derived mean and function probabilistic aggregate in order to be approved in the generation of data for the purpose of implementation of simulation

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Publication Date
Sun Jan 27 2019
Journal Name
Journal Of The College Of Education For Women
Music and Singing in The Heritage of Baghdadi The 1930s is a Model
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Music and singing are always associated with the movement of society and the emergence of cultural and artistic activities other.
The social and political transformations of the 1930s helped to disseminate the study Music and music in the city of Baghdad and across Iraq This is the beginning of a new era of musical art alongside other arts.
While achieving musical arts A new step was advanced by publishing a technical study among the younger generation they were looking for to contribute to the musical field On the other hand, the city of Baghdad during the period of research many musical and musical performances Egyptian teams have provided many artistic activities and events which have had a significant impact on the development

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Publication Date
Sun Apr 14 2024
Journal Name
Kufa Journal For Agricultural Sciences
Growth and production of three potato cultivars as affected by organic foliar nutrition
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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
Mon Jan 02 2017
Journal Name
Journal Of The College Of Languages (jcl)
Magic comparative study of the Old Testament mediator
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Magic is an attempt to affect people or events either by cheating and charlatanry means or by expecting devil powers in order to bring advantage or to avoid a harm or to bring harm to others or to for see the future and divition .

     Magic is either real by the devil like writing majic works to prevent the marriage of someone and to depart the husband and his wife , causing someone to be distressed the physical and nervous diseases and stopping the stories and the project; majic can be artificial by being intellect and legerdemain and different types of triks and to cancel the magic by using magic or by protecting the self by using Talismans as well as presenting or offering sacrificers to the masters and th

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Publication Date
Tue Sep 02 2025
Journal Name
Chemistry & Biodiversity
Synthesis, In Silico, and Biological Evaluation of Non‐Hydroxamate Benzoic Acid–Based Derivatives as Potential Histone Deacetylase Inhibitors (HDACi)
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ABSTRACT<p>Unregulated epigenetic modifications, including histone acetylation/deacetylation mediated by histone acetyltransferases (HATs) and histone deacetylases (HDACs), contribute to cancer progression. HDACs, often overexpressed in cancer, downregulate tumor suppressor genes, making them crucial targets for treatment. This work aimed to develop non‐hydroxamate benzoic acid–based HDAC inhibitors (HDACi) with comparable effect to the currently four FDA‐approved HDACi, which are known for their poor solubility, poor distribution, and significant side effects. All compounds were structurally verified using FTIR, <sup>1</sup>HNMR, <sup>13</sup>CNMR, and mass spectrometry. In silico ana</p> ... Show More
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Publication Date
Mon Feb 01 2021
Journal Name
Journal Of Physics: Conference Series
The Fear Effect on a Food Chain Prey-Predator Model Incorporating a Prey Refuge and Harvesting
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Abstract<p>In this paper, we investigate the impact of fear on a food chain mathematical model with prey refuge and harvesting. The prey species reproduces by to the law of logistic growth. The model is adapted from version of the Holling type-II prey-first predator and Lotka-Volterra for first predator-second predator model. The conditions, have been examined that assurance the existence of equilibrium points. Uniqueness and boundedness of the solution of the system have been achieve. The local and global dynamical behaviors are discussed and analyzed. In the end, numerical simulations are confirmed the theoretical results that obtained and to display the effectiveness of varying each parameter</p> ... Show More
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