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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
Baghdad Science Journal
Detecting DNA of multispecies dinoflagellate cysts in the sediment from three estuaries of Makassar strait and fishing port using CO1 primer: Is it CO1 primer suitable for detecting DNA dinoflagellate?
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Most dinoflagellate had a resting cyst in their life cycle.  This cyst was developed in unfavorable environmental condition. The conventional method for identifying dinoflagellate cyst in natural sediment requires morphological observation, isolating, germinating and cultivating the cysts.  PCR is a highly sensitive method for detecting dinoflagellate cyst in the sediment.  The aim of this study is to examine whether CO1 primer could detect DNA of multispecies dinoflagellate cysts in the sediment from our sampling sites. Dinoflagellate cyst DNA was extracted from 16 sediment samples. PCR method using COI primer was running. The sequencing of dinoflagellate cyst DNA was using BLAST. Results showed that there were two clades of dinoflag

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Publication Date
Mon Dec 24 2018
Journal Name
Civil Engineering Journal
Artificial Neural Network Model for the Prediction of Groundwater Quality
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The present article delves into the examination of groundwater quality, based on WQI, for drinking purposes in Baghdad City. Further, for carrying out the investigation, the data was collected from the Ministry of Water Resources of Baghdad, which represents water samples drawn from 114 wells in Al-Karkh and Al-Rusafa sides of Baghdad city. With the aim of further determining WQI, four water parameters such as (i) pH, (ii) Chloride (Cl), (iii) Sulfate (SO4), and (iv) Total dissolved solids (TDS), were taken into consideration. According to the computed WQI, the distribution of the groundwater samples, with respect to their quality classes such as excellent, good, poor, very poor and unfit for human drinking purpose, was found to be

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Publication Date
Sun Jan 08 2023
Journal Name
International Journal Of Research In Social Sciences And Humanities
Evaluating Banking Performance According to the European Model of Institutional Excellence: Case Study at United Bank for Investment and Finance1
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The aim of the research is to identify the impact of the dimensions of the European Excellence Model in evaluating the performance of the bank of the research sample, as well as to interpret which dimensions are more important to the banks of the research sample. Based on the dimensions of this model, the United Bank for Investment and Finance has chosen a research community, and has met with officials of the United Bank for Investment and Finance at various administrative levels to measure the practices of excellence management in the European model, and the analytical approach has been the case study and the construction of the checklist as a tool to collect information. The research has reached the most important results There is a discr

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Publication Date
Wed Jun 30 2021
Journal Name
Iraqi Journal Of Market Research And Consumer Protection
THE ROLE OF SATELLITE CHANNELS IN FORMING TRAFFIC AWARENESS AND PREVENTING ACCIDENTS - A FIELD STUDY: THE ROLE OF SATELLITE CHANNELS IN FORMING TRAFFIC AWARENESS AND PREVENTING ACCIDENTS - A FIELD STUDY
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The importance of the research comes from dealing with the problem of lack of traffic awareness, which causes accidents and the occurrence of human and material losses, and the research aims to study the role of satellite channels in forming traffic awareness among the public, and a sample was chosen from Baghdad consisting of (280) individuals, male and female, and used the questionnaire tool. To obtain the data, which included several questions, the results were analyzed statistically and several results were reached, the most important of which is that there is an interest among the public in following traffic programs at a rate of one to two hours to receive information through traffic programs and to identify and apply gener

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Publication Date
Sat Jul 01 2023
Journal Name
International Journal Of Research In Management
The role of network marketing for the Iraqi cement company in improving entrepreneurial behavior (An exploratory study of the opinions of a sample of company leaders)
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Publication Date
Sat Sep 30 2023
Journal Name
Journal Of Accounting And Financial Studies ( Jafs )
The effect of operational efficiency on some financial indicators according to the CAMEL model of banking financial stability: An applied research on a sample of Iraqi private banks for the period 2010-2020
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Abstract

          The research aims to determine the nature of the Iraqi market in terms of banking financial stability and the extent impact of the operational efficiency on it, Accordingly, chosen 15 relational banks were chosen as an intentional sample that could represent the Iraqi banking system for the period 2010-2020. The operational efficiency variable was measured according to the data envelope model, and banking financial stability used  CAMELS model which includes five indicators (capital adequacy, asset quality, management quality, profitability, and liquidity), so for testing the research hypotheses used the random regression model by adopting the S

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Publication Date
Thu Dec 24 2020
Journal Name
Advances In Civil Engineering
Analytical study on torsional behavior of concrete beams strengthened with fiber reinforced polymer laminates using softened truss model
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This study aimed at evaluating the torsional capacity of reinforced concrete (RC) beams externally wrapped with fiber reinforced polymer (FRP) materials. An analytical model was described and used as a new computational procedure based on the softened truss model (STM) to predict the torsional behavior of RC beams strengthened with FRP. The proposed analytical model was validated with the existing experimental data for rectangular sections strengthened with FRP materials and considering torque-twist relationship and crack pattern at failure. The confined concrete behavior, in the case of FRP wrapping, was considered in the constitutive laws of concrete in the model. Then, an efficient algorithm was developed in MATLAB environment t

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Publication Date
Mon Jan 01 2018
Journal Name
Al–bahith Al–a'alami
Attitudes of University Students about the Statements of Iraqi Political Elites: A Survey Study of a Sample of University Youth in Baghdad
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Various visual media are becoming an increasingly important and active instrument of communication. This fact has led some political parties and leading personalities in Iraq to make use of them as an accepted forum for the discussion of public affairs usually in a manner that conforms to their declared policy. They have to draw as much popular support as they could for the causes which they fight for. As a result, a state of great confusion has been created from the contradictory statements made by the contending parties and gave left grave consequences on all types of the audience receiving them. The problem of the study can be summarized in one major question: What is the opinions of the audience as regards the statements made by the

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Publication Date
Sun Oct 01 2023
Journal Name
Journal Of Medicine And Life
Evaluating the effect of ursodeoxycholic acid (UDCA) in comparison with dexamethasone and diclofenac in a rat model of rheumatoid arthritis
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Publication Date
Wed Dec 29 2021
Journal Name
Journal Of The College Of Education For Women
The Impact of the Seven Principles of Good Practice as a Teaching Technique on EFL Student –Teachers' Performance: سوسن سعود عزيز
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The interest in pre-service teacher training has become influential in teaching English as a foreign language, and the purpose of this training course is to prepare qualified teachers to teach effectively through the application of this technique by undergraduate students. This research aims to find out the effect of using the seven principles of good practice as a teaching technique on the fourth stage student-teachers’ performance at the College of Education for Women/University of Baghdad, during the academic year 2017-2018. The sample includes (60) students selected according to the stratified sampling method. The observational checklist used by the department to assess the student teachers’ performance during the practicum perio

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