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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
Sat Nov 22 2025
Journal Name
Jornal Of Al-muthanna For Agricultural Sciences
A Proposed Approach to Agricultural Extension in Iraq for a Better Response to the Needs of farmer’s to Address Their Challenges
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Publication Date
Sat Apr 01 2023
Journal Name
International Journal Of Modern Physics E
Hamiltonian sensitivity in calculating the electromagnetic moments and electroexcitation form factor for the <i>sd</i> nuclei using shell model with Skyrme–Hartree–Fock
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In this work, the nuclear electromagnetic moments for the ground and low-lying excited states for sd shell nuclei have been calculated, resulting in a revised database with 56 magnetic dipole moments and 41 electric quadrupole moments. The shell model calculations are performed for each sd isotope chain, considering the sensitivity of changing the sd two-body effective interactions USDA, USDE, CWH and HBMUSD in the calculation of the one-body transition density matrix elements. The calculations incorporate the single-particle wave functions of the Skyrme interaction to generate a one-body potential in Hartree–Fock theory to calculate the single-particle matrix elements. For most sd shell nuclei, the experimental data are well rep

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Publication Date
Sun Mar 25 2018
Journal Name
Biomedical And Pharmacology Journal
Anti CD20 Monoclonal Antibody (Rituximab) as a Rescue Treatment in Severe and Refractory SLE
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Systemic lupus erythematosus (SLE) is an autoimmune disease with polymorphic expression. B cells have an essential contribution in immune system activation via the production of different cytokines and functioning as potent antigen-presenting cells. Therefore, a drug that particularly targets B cells may represent an ideal therapeutic approach for SLE. Rituximab (RTX), an anti-CD20 monoclonal antibody causing transient B-cell depletion, has been used to manage SLE. This study aims to assess Rituximab effects on lupus nephritis (LN) patients when added to conventional immunosuppressants. Twenty four patients, 15-32 years old, with class III/IV/V LN were involved in this study. All were on steroids before lupus nephritis occurrence. They were

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Publication Date
Wed May 10 2017
Journal Name
Journal Of The College Of Languages (jcl)
Technical methods in foreign language teaching as a new method in foreign language learning
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Unter dem Titel " Technische Methoden im Fremdsprachunterricht als eine neueste Methode im Fremdsprachlernen, die Spiele als Muster"

versteht man, dass die Forschung  sich mit einer neuen Methoden im Fremdsprachunterricht beschäftigt. Von den neuen Methoden im Unterricht sind die Spiele. So man sieht  in den letzten Jahren viele Artikel zum Thema Spiele im Fremdsprschunterricht. Davon gehen wir aus, dass die Spiele im Unterricht eine groβe Rolle spielt, denn diese Methode macht Lust, Spaβ im Lernenprozeβ. Die Spiele im Unterricht bezeichnen als ein Mittel, um Unterricht etwas Schönes , Nützliches und Lebendigs zu sein. Die Spiele sind vielfälltig und unterscheidet sich nach den Themen und Materialien. In dieser F

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Publication Date
Fri Mar 01 2024
Journal Name
Annales Pharmaceutiques Françaises
Adopting video assignments as a tool to improve first-year pharmacy students class engagement
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Publication Date
Sun Mar 25 2018
Journal Name
Biomedical And Pharmacology Journal
Anti CD20 Monoclonal Antibody (Rituximab) as a Rescue Treatment in Severe and Refractory SLE
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Systemic lupus erythematosus (SLE) is an autoimmune disease with polymorphic expression. B cells have an essential contribution in immune system activation via the production of different cytokines and functioning as potent antigen-presenting cells. Therefore, a drug that particularly targets B cells may represent an ideal therapeutic approach for SLE. Rituximab (RTX), an anti-CD20 monoclonal antibody causing transient B-cell depletion, has been used to manage SLE. This study aims to assess Rituximab effects on lupus nephritis (LN) patients when added to conventional immunosuppressants. Twenty four patients, 15-32 years old, with class III/IV/V LN were involved in this study. All were on steroids before lupus nephritis occurrence. They were

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Publication Date
Sun Oct 01 2023
Journal Name
Minerva Dental And Oral Science
Salivary interleukin-1β as a biomarker to differentiate between periodontal health, gingivitis, and periodontitis
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Publication Date
Fri Nov 01 2019
Journal Name
Civil Engineering Journal
Time-Cost-Quality Trade-off Model for Optimal Pile Type Selection Using Discrete Particle Swarm Optimization Algorithm
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The cost of pile foundations is part of the super structure cost, and it became necessary to reduce this cost by studying the pile types then decision-making in the selection of the optimal pile type in terms of cost and time of production and quality .So The main objective of this study is to solve the time–cost–quality trade-off (TCQT) problem by finding an optimal pile type with the target of "minimizing" cost and time while "maximizing" quality. There are many types In the world of piles but  in this paper, the researcher proposed five pile types, one of them is not a traditional, and   developed a model for the problem and then employed particle swarm optimization (PSO) algorithm, as one of evolutionary algorithms with t

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Publication Date
Sun Dec 01 2024
Journal Name
Iraqi Journal Of Physics
Study of the Sensitivity of Carbon Quantum Dots for NO2 Gas Sensor and improve it using Graphene
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Gas sensors are essential for detecting noxious gases that have a detrimental effect on people's health and welfare. Carbon quantum dots (CQDs) are the fundamental component of gas detectors. CQDs and graphene (Gr) were prepared using the electrochemical method. The gas sensitivity of these materials was evaluated at different temperatures (150, 200, 250 °C) to assess their effectiveness. Subsequently, experiments were conducted at different temperatures to ascertain that the combination of CQDs and Gr, with various percentages of Gr and CQDs, exhibited superior gas sensitization properties compared to CQDs alone. This was evaluated based on criteria such as sensitivity, recovery time, and reaction time. Interestingly, the combination was

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Publication Date
Sun Aug 08 2021
Journal Name
Al – Bahith Al – A A‚lami
The Impact of Financial Financing on the Future of the Iraqi Print Press, A Survey Study by the Contactor
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The objectives of this study revolve around identifying the extent of funding impact on the future of the printed Iraqi press, and whether it threatens their chances of survival, stating the extent of technological development on the income of the printed newspaper, and identifying the causes of the financial crisis on the newspaper. This research is classified as descriptive research, and the researcher used the survey method, and adopted the questionnaire of the views of the contactors, in five Iraqi newspapers (morning - extent - time - the way of the people - the call). The research community included (68) respondents, whereby the comprehensive inventory method was used to define the research community, and the researcher used t

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