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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 Sep 29 2024
Journal Name
مجلة نسق
The diplomatic role of IGAD in regional peacemaking: Sudan after 2011 as a case study
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The research discusses the most important goals and means of IGAD in making peace in Sudan and then regional peace.

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Publication Date
Wed Dec 18 2019
Journal Name
Baghdad Science Journal
A Modified Approach by Using Prediction to Build a Best Threshold in ARX Model with Practical Application
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The proposal of nonlinear models is one of the most important methods in time series analysis, which has a wide potential for predicting various phenomena, including physical, engineering and economic, by studying the characteristics of random disturbances in order to arrive at accurate predictions.

In this, the autoregressive model with exogenous variable was built using a threshold as the first method, using two proposed approaches that were used to determine the best cutting point of [the predictability forward (forecasting) and the predictability in the time series (prediction), through the threshold point indicator]. B-J seasonal models are used as a second method based on the principle of the two proposed approaches in dete

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Publication Date
Sun Jun 30 2002
Journal Name
Iraqi Journal Of Chemical And Petroleum Engineering
A Phase Behavior Compositional Model for Jambour Cretaceous Oil Reservoir
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Publication Date
Wed Jun 30 2021
Journal Name
Journal Of Economics And Administrative Sciences
Design a supply chain model for Baghdad Soft Drinks Company
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In this paper, a mathematical model was built for the supply chain to reduce production, inventory, and transportation in Baghdad Company for Soft Drink. The linear programming method was used to solve this mathematical model. We reduced the cost of production by reduced the daily work hours, the company do not need the overtime hours to work at the same levels of production, and the costs of storage in the company's warehouses and agents' stores have been reduced by making use of the stock correctly, which guarantees reducing costs and preserving products from damage. The units transferred from the company were equal to the units demanded by the agents. The company's mathematical model also achieved profits by (84,663,769) by re

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Publication Date
Sun Feb 10 2019
Journal Name
Journal Of The College Of Education For Women
Development and Implementation a Programmable Model for Evaluation Pumping Technique
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This work represents development and implementation a programmable model for evaluating pumping technique and spectroscopic properties of solid state laser, as well as designing and constructing a suitable software program to simulate this techniques . A study of a new approach for Diode Pumped Solid State Laser systems (DPSSL), to build the optimum path technology and to manufacture a new solid state laser gain medium. From this model the threshold input power, output power optimum transmission, slop efficiency and available power were predicted. different systems configuration of diode pumped solid state laser for side pumping, end pump method using different shape type (rod,slab,disk) three main parameters are (energy transfer efficie

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Publication Date
Sun Jan 01 2023
Journal Name
Communications In Mathematical Biology And Neuroscience
A reliable numerical simulation technique for solving COVID-19 model
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Publication Date
Tue Jan 31 2017
Journal Name
Journal Of Engineering
Determine an Equation to Calculate the Annual Maintenance Cost for Public Hospitals (Al Sader City Hospital as a Case Study)
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Maintenance of  hospital buildings and its management are regarded as an important subject which needs attention because hospital buildings are service institutions which are very important to a society, requiring the search for the best procedure to develop maintenance in hospitals. The research is aimed to determine an equation to estimate the annual maintenance cost for public hospital. To achieve this aim, Al-Sader City Hospital maintenance system in Al-Najaf province has been studied with its main elements through survey of data, records and reports relating to maintenance during the years of the study 2008-2014 and to identify the strengths, weaknesses, opportunities and threat points in the current system through Swat analysi

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Publication Date
Tue Mar 30 2021
Journal Name
Journal Of Economics And Administrative Sciences
The effect of creating knowledge according to the model (Nonaka & Takeuchi, 1995) on organizational ambidexterity: A study on a sample of Iraqi private banks
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Purpose - This study relies on the descriptive and analytical approach through collecting and analyzing the necessary data, as this approach focuses on polling the opinions of the research sample and its directions, and aims to develop a model that studies the relationship between knowledge creation and organizational ambidexterity in Iraqi private banks and verifying its validity experimentally.

Design / Methodology / Introduction - A survey was conducted through a questionnaire form to collect data from a sample of (113) managers in private commercial banks. In addition, this study used the AMOS program and the ready-to-use statistical program package (SPSS V.25) to test the proposed hypotheses of the t

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Publication Date
Sun Aug 30 2020
Journal Name
Journal Of Economics And Administrative Sciences
Relational leadership and its effect on organizational energy (A comparative study in the Rafidain and Rashid banks)
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This research aims to test the relationship between "relational leadership as an independent variable and organizational energy as a dependent variable. The current research variables are among the recent and important variables for the development of organizations, and for the purpose of explaining the relationship and influence between the variables, a set of goals has been formulated, including providing the interested and scientific and theoretical information explaining the nature of the variables The research, and the extent to which its causes are reflected in the research sample to increase the interest of the research organization’s organization and make it more appropriate to the required performance in light of a cha

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Publication Date
Thu Jun 15 2017
Journal Name
Journal Of Baghdad College Of Dentistry
Evaluation of the effect of preheating on micro leakage of Class II composites Restoration (A comparative in vitro study)
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Background: The aim of this in vitro study was to evaluate and compare the effect of preheating microleakage among three different filler size composites which include Filtektm Z250 micro hybrid, Z250xt Nano hybrid and nanocomposite Z350xt.  in Class II cavity preparation .

Materials and methods: sixty maxillary first premolars were prepared with class II cavities. Samples were divided into three groups according to material used    group A (FiltekZ250 micro hybrid). Group B(Z250xt Nano hybrid). Group C (nanocomposite Z350xt)and each group divided into two subgroups of ten teeth according to temperature of  composite:

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