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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 Mar 04 2022
Journal Name
Environmental Science And Pollution Research
Geographically weighted regression model for physical, social, and economic factors affecting the COVID-19 pandemic spreading
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Abstract<p>This study aims to analyze the spatial distribution of the epidemic spread and the role of the physical, social, and economic characteristics in this spreading. A geographically weighted regression (GWR) model was built within a GIS environment using infection data monitored by the Iraqi Ministry of Health records for 10 months from March to December 2020. The factors adopted in this model are the size of urban interaction areas and human gatherings, movement level and accessibility, and the volume of public services and facilities that attract people. The results show that it would be possible to deal with each administrative unit in proportion to its circumstances in light of the factors that appe</p> ... Show More
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Publication Date
Sun Feb 01 2015
Journal Name
Journal Of Economics And Administrative Sciences
Use of model sales man fuzzy multi-objective linear for speed up and rationing in the transport mechanism used in the General Company for grain Processing
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     Applications of quantitative methods, which had been explicit attention during previous period (the last two centuries) is the method of application sales man or traveling salesman method. According to this interest by the actual need for a lot of the production sectors and companies that distribute their products, whether locally made or the imported for customers or other industry sectors where most of the productive sectors and companies distributed always aspired to (increase profits, imports, the production quantity, quantity of exports. etc. ...) this is the part of the other hand, want to behave during the process of distribution routes that achieve the best or the least or most appropriate.

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Publication Date
Fri Mar 06 2026
Journal Name
Journal Of Baghdad College Of Dentistry
Evaluation of the cleaning efficiency of the isthmus using different rotary instrumentation techniques (In vitro study)
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Background: The aims of the study were to evaluate the unclean/clean root canal surface areas with a histopathological cross section view of the root canal and the isthmus and to evaluate the efficiency of instrumentation to the isthmus using different rotary instrumentation techniques. Materials and Methods:The mesial roots of thirty human mandibular molars were divided into six groups, each group was composed of five roots (10 root canals)which prepared and irrigated as: Group one A: Protaper system to size F2 and hypodermic syringe, Group one B: Protaper system to size F2 and endoactivator system, Group two A:Wave One small then primary file and hypodermic syringe, Group two B:Wave One small then primary file and endoactivator system, Gr

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Publication Date
Sun Sep 03 2017
Journal Name
Baghdad Science Journal
Calculation of Lambda Doubling for 7LiH1 molecule Using the System band emission for electronic transmissions
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The A2?u-X1?g+ emission band system of 7LiH1 molecule has been calculated for Lambda doubling. The relation between wave number ?p , ?Q , ?R conducted the energies of the state of rotation F (J), and (J + 1) with rotational quantum number J, respectively, of 7LiH1 molecule for statehood A2?u using the rotation, fixed vibrational states of both the ground and raised crossovers vibrational against ???= 0 to V ' = 0-4using rotational levels J = 0 to J = 20 have found.

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Publication Date
Sun Sep 02 2012
Journal Name
Baghdad Science Journal
Study of Reactivity Effect on Reactor Power by Using the Neutronic- Thermohydrolic Coupling
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The study deals with reactivity insertion linear and non linear and/or Ramp reactivity expressed as a polynomial in time in the presence of two Feedback mechanisms, using the neutronic-thermohydraulic coupling in order to predict the neutron behavior as a function of time in terms of reactor power. Also, a comparative study has been achieved in the case of the presence of the feedback mechanisms. Insertion of Ramp reactivities in terms of polynomial in time to study the behavior of power and reactivity as a function of time in the presence of two feedback mechanisms (fuel and coolant) has been carried out and the results are displayed as plots, and showed this results corresponding with international results. The present study shows t

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Publication Date
Fri Jan 01 2016
Journal Name
Journal Of American Science
Morphohistological study of the tongue in local mice species by using special stain
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Publication Date
Fri Feb 01 2019
Journal Name
Journal Of Physics: Conference Series
Study the Electronic Properties of Boron Nitride Diamondiod Nanostructure using Ab-initio DFT
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Publication Date
Sat Sep 30 2023
Journal Name
Journal Of Accounting And Financial Studies ( Jafs )
Cyber security technology and the reflection of its application on the quality of financial reports: An exploratory study of a sample of internal and external auditors
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Abstract

                 This research aims to define the roles of auditors by clarifying the concept and risks of cyber security in protecting information and financial data in economic units. Najaf, Babylon and Karbala, then the results were analyzed and the results were presented and analyzed to show that adopting cyber security improves the quality of reports Finance through what it achieves in displaying information with credibility and transparency, in a way that suits the needs of users, and cyber security has a role in managing economic resources more effectively to obtain benefits that would have been lost in the event of an

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Publication Date
Fri Apr 12 2019
Journal Name
Journal Of Economics And Administrative Sciences
Transformational leadership and its role in organizational success An analytical study of the views of a sample of employees at the Faculty of Education, Samarra University
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This research aims to know the role of transformational leadership in the organizational success of the College of Education at Samarra University. The researcher adopted the analytical descriptive method in analyzing the research problem. The research included two main hypotheses that resulted in four hypotheses that were subjected to statistical tests. A sample of (54) The researcher used the survey method as a main tool for collecting data and information as well as visits and structured interviews that took place during the period of application. The research reached a set of conclusions and recommendations among the conclusions that there is an art relationship There is a strong and moral impact between transformational lead

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Publication Date
Sat Oct 01 2016
Journal Name
Journal Of Economics And Administrative Sciences
Strategic planning of human resources and its impact on the stages of a career path :A field research in the Ministry of Health
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Abstract

The objective of this research is to analyze the relationship between the strategic planning for human resources and career path, and I have tested Search the Ministry of  Health and some health centers headquarters in the Karkh district, that is applied in sample Consist of (45) Deputy Director, Head of Depts, Departmental Manager, and health center Manager.

Find interested in studying the two subjects are important and vital, at the level of organizations at the present time, namely the strategic planning of human resources and career path. To achieve the objectives of the research was designed Qusestionnair (31) items to collect  Primary data. and collected t

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