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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
Tue Oct 14 2025
Journal Name
Journal Of Physical Education
A study of some variables biomechanics in clean and jerk for the world champions men and women
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Publication Date
Tue Jan 02 2018
Journal Name
Journal Of Educational And Psychological Researches
The Role of Social service in Addressing Social Problems Aversion for Teenagers (A field Study in Baghdad)
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Adolescence important and sensitive stage in social terms, being a stage where learns teenager bear social responsibilities and composition of their ideas about family life, as well as it is the stage where the teenager looking to himself for an important place in the community to become independent socially people, so it highlights the role of Social Work to do better effort and I believe him in order to prepare for the adolescent stage of adolescence and help him overcome the problems so that makes it adapts to the society in which he lives

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Publication Date
Sun Jan 01 2017
Journal Name
Engineering And Technology Journal
Study of the Diffusion Coefficient and Hardness for a Composite Material when Immersed in Different Solutions Polymer
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Publication Date
Tue Oct 14 2025
Journal Name
Misan Journal For Physical Education Sciences
The impact of three models of training load on the development of the maximum strength for elite boxers
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Publication Date
Thu Dec 15 2022
Journal Name
Aaps Pharmscitech
Formulation and Characterization of Oleogel as a Topical Carrier of Azithromycin
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This study aims to formulate azithromycin oleogel to locally treat skin infections such as acne vulgaris and skin wound infection. Providing a form of azithromycin that can be administered topically is highly desired to prevent unwanted systemic complications including diarrhea, nausea, and abdominal pain. Additionally, it will avoid first pass metabolism, improves patient acceptance, provides an alternative in nauseated patients, decreases the dose by direct contact with the pathological site, and provides a noninvasive and convenient mode of administration. Furthermore, for treating wound infections, the gel will act as a scaffold biomaterial for wound closure besides its antibacterial effect. Herein, we propose the use of grapeseed oil-b

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Publication Date
Wed Mar 30 2022
Journal Name
Journal Of Economics And Administrative Sciences
The Role Of Smart Leadership Dimensions In Crisis Management- A study For Opinions Of Sample Of Administrative Leaderships In A number Of Humanities Colleges At The University Of Mosul
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This research aims at answering many questions raised by the research problem concerning the view of the organizations under consideration for the concept of smart leadership and its most important dimensions, as well as the view of crisis management and its concept and most important methods through research objectives that define and clarify the smart leadership with its dimensions and methods of crisis management.

For the purpose of reaching the results of the research and testing the assumptions about the relationship between smart leadership and methods of crisis management, the researcher adopted a questionnaire, designed especially to be a criterion for the research, as the main tool for data coll

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Publication Date
Tue Dec 31 2019
Journal Name
Biochemical & Cellular Archives
8-HYDROXY-2-DEOXY GUANOSINE IS A NOVEL NEW BIOCHEMICAL MARKER FOR PATIENTS WITH MULTIPLE SCLEROSIS AND CORRELATION WITH PARAOXANASE-1 AND MDA
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Multiple sclerosis (MS) is a chronic, inflammatory demyelinating disease of central nervous system with complex etiopathogenesis that impacts young adults (Lee et al., 2015), and MS impacts younger and middle aged character and leads to a range of disabilities that can alter their daily routines (Yara et al, 2010). Although, the exact cause of MS is still undetermined, the disease is mediated by adaptive immunity through the infiltration of T cells into the central nervous system (Bjelobaba et al, 2017). MS causes the Focal neurological symptomsand biochemical changes in the molecular level and the variation of neural cells such as loss or alteration of sensation, motor function, visible signs such as blurred vision or transient blindness,

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Publication Date
Wed Jan 30 2019
Journal Name
Journal Of The College Of Education For Women
Triumph in the Glorious Qur’an: A Semiotic study
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Triump is a happy end and a positive outcome of any good deed on the part of a human
being, or of any competition or contest in any field. A human being’s life abounds with gain
and loss. If one succeeds one will be happy psychologieally, physieally, etc. if one the other
hard one loses, one wil be in a state. Between loss and gain there are many a step.
However humans work hard to be a great success and a read winner.The life of the world constitutes a huge race-track where people try hard to head towards
the hereafter. Therefore, we find people who succed and gain the Garden, and people whose
habitation is the fire, The Glorious Qur’an has shown us in many a surah the way to success
when Allah mentions ‘great

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Publication Date
Sat Jan 01 2022
Journal Name
Education For Health
Determinants of social accountability for medical schools in Iraq: A qualitative case study
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Publication Date
Sat Jan 01 2011
Journal Name
Journal: Ibn Al-haitham Journal For Pure And Applied Sciences
A Study the effect the direction of the distribution of lighting to improve Images in different lighting by using technique adaptive histogram equalization
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