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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
Sun Feb 17 2019
Journal Name
Iraqi Journal Of Physics
A Study of the electronic structure of CdS Nanocrystals using density functional theory
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Density Functional Theory at the generalized-gradient approximation level coupled with large unit cell method is used to simulate the electronic structure of (II-VI) zinc-blende cadmium sulfide nanocrystals that have dimensions 2-2.5 nm. The calculated properties include lattice constant, conduction and valence bands width, energy of the highest occupied orbital, energy of the lowest unoccupied orbital, energy gap, density of states etc. Results show that lattice constant and energy gap converge to definite values. However, highest occupied orbital, lowest unoccupied orbital fluctuates indefinitely depending on the shape of the nanocrystal.

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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
Thu Jun 30 2022
Journal Name
Journal Of Economics And Administrative Sciences
Methods of Forecasting Credit Losses in A Sample of Iraqi Banks - A Comparative Analysis
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  The general trend in Iraqi banks is focused towards the application of international financial reporting standards, especially the international financial reporting standard IFRS 9 “Financial Instruments”, in addition to the directives issued on the Central Bank of Iraq’s instructions for the year 2018 regarding the development of expected credit losses models, and not to adhere to a specific method for calculating these losses and authorizing the banks’ departments to adopt the method of calculating losses that suits the nature of the bank’s activity and to be consistent in its use from time to time. The research problem revolves around the different methodologies for calculatin

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Publication Date
Mon Jun 01 2020
Journal Name
Iraqi Journal Of Physics
Theoretical Model for Spectroscopic Study of Cu+2, Co+2, and Fe+3 Dissolved in Ethanol with A Different Concentrations
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The absorption spectrum for three types of metal ions in different concentrations has been studying experimentally and theoretically. The examination model is by Gaius model in order to find the best fitting curve and the equation controlled with this behavior. The three metal ions are (Copper chloride Cu+2, Iron chloride Fe+3, and Cobalt chloride Co+2) with different concentrations (10-4, 10-5, 10-6, 10-7) gm/m3. The spectroscopic study included UV-visible and fluorescence spectrum for all different concentrations sample. The results refer to several peaks that appear from the absorption spectrum in the high concentration of all metal ions solution.

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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 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
Sat Jan 20 2024
Journal Name
Ibn Al-haitham Journal For Pure And Applied Sciences
Development of the Properties of Zinc Polycarboxylate Cement Used as a Basis for Dental Fillings Using Zink Oxide Nanoparticles Prepared by Green Chemistry Method
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Most dental supplies don't seem to be much of a barrier against germ infiltration. Therefore, the filling must be done with perfect caution and high antimicrobial effectiveness. When dental erosion occurs due to germs that lead to caries, a dental filling is used, creating a small microscopic space between the dental filling and the root end infiltration. This allowed the tooth to be penetrated for the second time, which was the research problem. Adding two compounds to antibacterial fillers (zinc polycarboxylate cement) made them work better: Firstly, was zinc oxide  (ZnO) that was made chemically, and secondly, was green ZnO nanoparticles that were made from orange peels and mixed with ZPCC in different amounts. The study was conducte

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Publication Date
Wed Jan 24 2024
Journal Name
Pharmacia
Novel anticoagulants in the management of atrial fibrillation: A comprehensive comparative analysis
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Background: Atrial fibrillation (AF) stands as the most prevalent cardiac arrhythmia, with associated risks of stroke and systemic thromboembolism. While vitamin K antagonists, specifically warfarin, have historically been the mainstay for stroke prevention in AF, they come with inherent limitations.

Aim: This review seeks to offer a comprehensive analysis of the efficacy, safety, and clinical advantages of novel oral anticoagulants (NOACs) compared to traditional warfarin in AF management.

Method: A meticulous examination of pivotal clinical trials, meta-analyses, and recent research publications was conducted.

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Publication Date
Sun Sep 04 2011
Journal Name
Baghdad Science Journal
A Mathematical Approach for Computing the Linear Equivalence of a Periodic Key-Stream Sequence Using Fourier Transform
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A mathematical method with a new algorithm with the aid of Matlab language is proposed to compute the linear equivalence (or the recursion length) of the pseudo-random key-stream periodic sequences using Fourier transform. The proposed method enables the computation of the linear equivalence to determine the degree of the complexity of any binary or real periodic sequences produced from linear or nonlinear key-stream generators. The procedure can be used with comparatively greater computational ease and efficiency. The results of this algorithm are compared with Berlekamp-Massey (BM) method and good results are obtained where the results of the Fourier transform are more accurate than those of (BM) method for computing the linear equivalenc

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Publication Date
Fri Dec 31 2010
Journal Name
Journal Of Legal Sciences
The moment of concluding the contract according to the United Nations Convention on Contracts for the International Sale of Goods (1980) (A comparative study with some Arab and foreign legislations)
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There are two ways that the contract might be formed with (contracting between persons who are attended and contracting between absence persons).the need for determining the precise moment of the contract , is so clear because there is a specify period separate between the declaration of acceptance and the knowledge with it .and it is clear from the four theories known for jurisprudence (theory of the declaration of the acceptance, theory of exporting the acceptance , theory of the arrival of the acceptance , theory of the knowledge with the acceptance ) . It is difficult to promote one theory on another one if we look at each one and the justification of its supporters and what the opponents of each theory expose. Legal background and diff

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