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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 Oct 01 2023
Journal Name
Applied Sciences
Multiobjective Optimization of Stereolithography for Dental Bridge Based on a Simple Shape Model Using Taguchi and Response Surface Methods
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Stereolithography (SLA) has become an essential photocuring 3D printing process for producing parts of complex shapes from photosensitive resin exposed to UV light. The selection of the best printing parameters for good accuracy and surface quality can be further complicated by the geometric complexity of the models. This work introduces multiobjective optimization of SLA printing of 3D dental bridges based on simple CAD objects. The effect of the best combination of a low-cost resin 3D printer’s machine parameter settings, namely normal exposure time, bottom exposure time and bottom layers for less dimensional deviation and surface roughness, was studied. A multiobjective optimization method was utilized, combining the Taguchi me

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Publication Date
Tue Jan 14 2020
Journal Name
College Of Islamic Sciences
The Origin of Creation in Khattab (The Beginning of Creation) by Imam Ali (as) and Genesis (Comparative Study)
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The research aims to answer the questions that revolve in the mind of mankind about how to create creation, how it existed prior to creation, who created existence, and the characteristics of that presence. The researcher also wanted to show that the culture of Imam Ali (peace be upon him) In the book of Adam, peace be upon him, God has punished Adam (peace be upon him) for not having sinned. Because his wife is the one who fed him the fruit of the tree, and this is contrary to what was stated in the sermon of Imam (peace be upon him) who Z Adam (peace be upon him) is the one who trusted Satan and Gwighth.We note that the approach of the rhetoric has pointed to the creation of angels and did not refer to the creation of Eve and the class

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Publication Date
Tue Mar 31 2020
Journal Name
College Of Islamic Sciences
The Origin of Creation in Khattab (The Beginning of Creation) by Imam Ali (as) and Genesis (Comparative Study)
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The research aims to answer the questions that revolve in the mind of mankind about how to create creation, how it existed prior to creation, who created existence, and the characteristics of that presence. The researcher also wanted to show that the culture of Imam Ali (peace be upon him) In the book of Adam, peace be upon him, God has punished Adam (peace be upon him) for not having sinned. Because his wife is the one who fed him the fruit of the tree, and this is contrary to what was stated in the sermon of Imam (peace be upon him) who Z Adam (peace be upon him) is the one who trusted Satan and Gwighth.

We note that the approach of the rhetoric has pointed to the creation of angels and did not refer to

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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 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
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
Sat Feb 01 2020
Journal Name
Journal Of Economics And Administrative Sciences
Effect of applying the CAMEL model to profitability of banks )An applied study on a number of Iraqi banks for the period 2010-2016(
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The evaluation of banks plays an important role in maintaining the interests of customers with the bank as well as providing continuous supervision and control by the Central Bank. The Central Bank of Iraq conducted an assessment of the Iraqi banks through the implementation of the CAMEL model during a certain period. This evaluation did not continue. The research provides continuity to the Central Bank's assessment and as a step to continue the evaluation process for all banks through the use of the CAMEL model. ROA and ROE by using the regression model for four Iraqi banks registered in the Iraqi market for securities during the period 2010-2016. The results showed that the capital and profitability indicators have a significan

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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
Mon May 01 2006
Journal Name
East Mediterr Health J
Prevalence of HCV/HIV co-infection among haemophilia patients in Baghdad
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Abstract To estimate the seroprevalence of HCV infection among HIV-infected haemophiliacs and to demonstrate the most prevalent HCV genotype, 47 HIV-infected haemophilia patients were screened for anti-HCV antibodies. By performing polymerase chain reaction and DNA enzyme immunoassay, HCV-RNA was detected with subsequent genotyping. Seroprevalence of anti-HCV antibodies was 66.0%. Of 31 HCV/HIV co-infected patients, 21 (67.7%) had no history of blood transfusion. We detected 4 HCV genotypes: 1a, 1b, 4 and 4 mixed with 3a, HCV-1b being the most frequent. Contaminated factor VIII (clotting factor) could be responsible for disease acquisition.

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