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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 Apr 01 2016
Journal Name
Al–bahith Al–a'alami
Journalism of Paper Newspapers in Light of the Competition of the Electronic Press / (A Field Study of Yemeni Daily Newspapers)
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The researcher seeks to get scientific facts through knowing the relationship between the priorities of Yemeni audience in follow-up paper daily newspapers compared to surfing publics the online journalism sites and the nature of information obtained from online journalism sites and printed paper newspapers and the impact of the daily newspapers in the priority of issues and political events among a sample of a group of Yemeni readers in order to identify the extent to keep up the paper daily newspapers of the development in the field of online journalism and the extent of reading paper newspapers under the intense competition by online journalism sites, and are paper newspapers able to keep pace with the actual developments provided by

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Publication Date
Tue Jul 01 2003
Journal Name
Bulletin Of The Iraq Natural History Museum (p-issn: 1017-8678 , E-issn: 2311-9799)
DESCRIPTION OF THREE NEW SPECIES OF THE GENUS ANTHRENUS GEOFFORY (COLOEOPTERA, DERMESTIDAE) FROM IRAQ
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The present work represents description of three new species of genus Anthrenus
Geoffory from Iraq, these are : A. aradensis sp. nov., A. fabrici sp. nov. and A.
unicolor sp. nov. Locality, host plants and date of collection were given.

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Publication Date
Fri Sep 01 2023
Journal Name
Migration Letters
Organizational Machiavellianism and Its Impact on Employees’ Passion: A Field Study on a Sample of Electronic Payment Companies in Iraq
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Publication Date
Sat Oct 01 2016
Journal Name
Journal Of Economics And Administrative Sciences
ORGANIZATIONAL VALUES AND ITS IMPACT ON STRATEGIC PERFORMANCE A field study a comparison between Two Universities of Baghdad & Al-Nahrain
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ABSTRACT

     The researcher seeks to shed light on the relationship analysis and the impact between organizational values in all its dimensions (Administration Management, Mission, relationship management, environmental management) and strategic performance (financial perspective, customer perspective, the perspective of internal processes, learning and development) in the presidency of Two Universities of Baghdad & Al-Nahrain, it has been formulating three hypotheses for this purpose.

      The main research problem has been the following question: Is there a relationship and the impact of bet

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Publication Date
Thu Aug 28 2025
Journal Name
Sciences Journal Of Physical Education
The impact of a proposal for the curriculum dictated by some of the barriers to the development of motor skills
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The impact of a proposal for the curriculum dictated by some of the barriers to the development of motor skillsA. M. D. Huda Ibrahim RezoukiM. M. Susan Salim DawoodIs the childhood of the most important and most fertile stage of basic education because of their significant impact in building a base on which the stated origin of sound in the early stages older age because the baby at this stage be very vulnerability to environmental factors different surroundings in which to leave their mark on his life in the stages of life other.The Gymnastics of sports long-term training, which begins between the ages very early relative to the rest of other games to reach the stage of the tournament from the age of 13-17 years almost to the women, this a

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Publication Date
Wed Dec 09 2015
Journal Name
Iraqi Journal Of Market Research And Consumer Protection
Effect of Sodium sulfite treatment on the trypsin inhibitors activity, protein isolate and protein solubility of complete and dehulling white bean seeds Phaseolus vulgaris.: Effect of Sodium sulfite treatment on the trypsin inhibitors activity, protein isolate and protein solubility of complete and dehulling white bean seeds Phaseolus vulgaris.
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The study aimed to increase the biological value of white bean. The effect of different concentrations 0.01 ,0.02,0.03,and 0.04 M of sodium sulfite solutions for 1hr at 70 ºC on the trypsin inhibitors activity, protein isolate and protein solubility of complete and dehulling white bean flour were studied.Trypsin inhibitors activity were reduced by 42.97, 58.69, 68.59 and 69.58% in complete white bean flour at 0.01 ,0.02, 0.03, 0.04 M respectively, while the corresponding values were 50.43, 61.00, 75.61 and 85.66% respectively in dehulling white bean flour .Protein isolate value was 13.41% and protein solubility was 2.2% in control sample, Furthermore, the using of chemical treatment showed that protein isolate was reduced gradually and

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Publication Date
Tue Dec 05 2023
Journal Name
Baghdad Science Journal
Enhancing Smart Cities with IoT and Cloud Computing: A Study on Integrating Wireless Ad Hoc Networks for Efficient Communication
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Smart cities have recently undergone a fundamental evolution that has greatly increased their potentials. In reality, recent advances in the Internet of Things (IoT) have created new opportunities by solving a number of critical issues that are allowing innovations for smart cities as well as the creation and computerization of cutting-edge services and applications for the many city partners. In order to further the development of smart cities toward compelling sharing and connection, this study will explore the information innovation in smart cities in light of the Internet of Things (IoT) and cloud computing (CC). IoT data is first collected in the context of smart cities. The data that is gathered is uniform. The Internet of Things,

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Publication Date
Sat Dec 01 2018
Journal Name
Political Sciences Journal
A study in Tunisian - Iraqi Relations and its role in determining strategies for dealing with conflict and peace situations
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If the State attaches great importance to its foreign relations and intends to strengthen them in order to ensure the achievement of the highest national goals and interests. External relations between countries are one of the most prominent features of foreign policy, which depends on a combination of internal and external factors, the modern relations between Tunisia and Tunisia, which goes back to the pre-independence of Tunisia, when Iraq was a supporter of Tunisia's independence from France in the 1940s, Although these relations did not cause any disturbance by the two countries, but they remained weak relations did not develop in all areas except the sports and cultural field, which we will determine the reasons and the pos

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Publication Date
Sun Dec 31 2023
Journal Name
Iraqi Geological Journal
Advanced Geostatistical Techniques for Building 3D Geological Modeling: A Case Study from Cretaceous Reservoir in Bai Hassan Oil Field
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A 3D Geological model was generated using an advanced geostatistical method for the Cretaceous reservoir in the Bai Hassan oil field. In this study, a 3D geological model was built based on data from four wells for the petrophysical property distribution of permeability, porosity, water saturation, and NTG by using Petrel 2021 software. The geological model was divided into a structural model and a property model. The geological structures of the cretaceous reservoir in the Bai Hassan oil field represent elongated anticline folds with two faults, which had been clarified in the 3D Structural model. Thirteen formations represent the Cretaceous reservoir which includes (Shiranish, Mashurah, U.kometan, Kometan Shale, L. Kometan, Gulnen

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Publication Date
Wed Sep 15 2021
Journal Name
Journal Of Baghdad College Of Dentistry
Salivary Cortisol as a Stress Biomarker and Total Viable Count of Salivary Bacterial Microbiome among COVID-19 Patients
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Background: The COVID-19 virus outbreak had a massive effect on many parts of people's lives, as they were advised to quarantine and lockdown to prevent the virus from spreading, which had a big impact on people's mental health, anxiety, and stress. Many internal and external factors lead to stress. This negatively influences the body's homeostasis. As a result, stress may affect the body's capacity to use energy to defend against pathogens. Many recent investigations have found substantial links between human mental stress and the production of hormones, prohormones, and/or immunological chemicals. some of these researches have verified the link between stress and salivary cortisol levels. The aim of this study is to measure salivary corti

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