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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 Jul 24 2020
Journal Name
Al-kindy College Medical Journal
A review study of targeting of AAK1 and JAK1/2 using baricitinib in COVID-19 infected human cells
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     The outbreak of a current public health coronavirus 2019 disease is a causative agent of a serious acute respiratory syndrome and even death. COVID-19 has exposed to multi-suggested pharmaceutical agents to control this global disease. Baricitinib, a well-known antirheumatic agent, was one of them. This article reviews the likely pros and cons of baricitinib in attenuation of COVID-19 based on the mechanism of drug action as well as its pharmacokinetics. The inhibitory effect of baricitinib on receptor mediated endocytosis promoter, AKK1, and on JAK-STAT signaling pathway is benefacial in inhibition of both viral assembling and inflammation. Also, its pharmacokinetic has encouraged the physicians toward the drug

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Publication Date
Fri Oct 07 2022
Journal Name
Texas Journal Of Engineering And Technology
Estimation of Pore Pressure and In-Situ Stresses for Halfaya Oil Field: A Case Study
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Publication Date
Mon Jun 19 2023
Journal Name
Journal Of Engineering
Study of Some Mechanical Properties for a Polymer Material Reinforcement with Chip or Powder Copper
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In this paper, chip and powder copper are used as reinforcing phase in polyester matrix to form composites. Mechanical properties such as flexural strength and impact test of polymer reinforcement copper (powder and chip) were done, the maximum flexural strength for the polymer reinforcement with copper (powder and chip) are (85.13 Mpa) and (50.08 Mpa) respectively was obtained, while the maximum observation energy of the impact test for the polymer reinforcement with copper (powder and chip) are (0.85 J) and (0.4 J) respectively  

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Publication Date
Thu May 23 2019
Journal Name
The International Journal Of Artificial Organs
Real-time classification of shoulder girdle motions for multifunctional prosthetic hand control: A preliminary study
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In every country in the world, there are a number of amputees who have been exposed to some accidents that led to the loss of their upper limbs. The aim of this study is to suggest a system for real-time classification of five classes of shoulder girdle motions for high-level upper limb amputees using a pattern recognition system. In the suggested system, the wavelet transform was utilized for feature extraction, and the extreme learning machine was used as a classifier. The system was tested on four intact-limbed subjects and one amputee, with eight channels involving five electromyography channels and three-axis accelerometer sensor. The study shows that the suggested pattern recognition system has the ability to classify the sho

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Publication Date
Wed Jun 29 2022
Journal Name
Iraqi Journal Of Chemical And Petroleum Engineering
A Comparison Study for The Performance of Polyethersulfone Ultrafiltration Mixed Matrix Membranes in The Removal of Heavy Metal Ions from Aqueous Solutions
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Polyethersulfone (PES) ultrafiltration membrane blending NaX zeolite crystals as a hydrophilic additive was examined for zinc (II) and lead ions Pb (II) removal from aqueous solutions. The effect of NaX zeolite content on the permeation flux and removal efficiency was studied. The results showed that adding zeolite to the polymer matrix enhanced the permeation flux. The permeation flux of all the zeolite/PES matrix membranes was higher than the pristine membrane. No significant improvement was observed in the removal of Zn (II) ions using all prepared membranes as the removal percentage did not raise above 29.2%. However, the removal percentage of Pb (II) ions was enhanced to 97% using a membrane containing 0.9%wt. zeolite. Also, it was

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Publication Date
Sat May 29 2021
Journal Name
Journal Of Legal And Political Thought
The Possibility of Compensation for the Loss of View Caused by Public Projects – A Legal Study in Light of the Approach of U.S. Courts
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Despite the great economic and commercial importance given to real estate by virtue of its view of the landscape or public roads, US courts have differed in their position on compensation for damages resulting from blocking that view or vision by public projects. Some courts compensated for such damages, other courts approved such compensation. Hence, this research came to shed light on the extent of the possibility of compensation for blocking the view or vision as a result of public projects, and the research has supported us with many judicial decisions.

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Publication Date
Mon Jan 01 2018
Journal Name
Research Journal Of Pharmacy And Technology
Molecular Genetic variability in the D-loop region for females with Breast Cancer and the effect of the Chemotherapy
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Publication Date
Wed Apr 01 2015
Journal Name
Journal Of Economics And Administrative Sciences
Dimensions of performance to provide nursing services: a comparative analytical research in Baghdad of Rusafa Health Organization
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     This research aims to study the performance of operations to provide nursing services, which included dimensions (quality, timeliness, leadership skills, behavioral manifestations, relationships with others, problem-solving and decision-making, job performance) and its effects in nursing performance. The research to prove the value of the performance of service delivery processes dimensions by nursing staffs working in Iraqi hospitals, nursing and measuring performance. To find out the nature of nursing services, and a comparison between hospitals to measure the extent of the application dimensional among themselves, and that by relying on the dimensions of a global study, which was measu

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Publication Date
Mon Jan 01 2024
Journal Name
Journal Of The College Of Languages (jcl)
A comparative study of Educational Commonalities in Ibn al-Wardi's Lamiyah and Qaboos- Nameh: مشتركات تعليمى در لاميه ی ابن الوردى و قابوسنامه؛ بررسى مقايسه اى
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A literary-educational work is a work that explains wisdom to the reader and presents moral, educational and instructional issues in a literary form. Qaboos-nameh or Nasihat al-Muluk is an educational and educational book that has a special place in the field of ethics and guidance, where the author guides his children. Also, Ibn al-Wardi's Lamiyah or Nasihat al-Akhwan is a poem containing moral advice and advice in 77 verses that Ibn al-Wardi wrote to his son.

     It seems that the main goal of Ibn al-Wardi and Onsur AL-maali in Lamia and Qaboos-nameh was to express educational and moral issues and spread and convey them to future generations. Ibn al-Wardi, like Onsur AL-maali, listed moral points such as knowledge, humility

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Publication Date
Mon Dec 25 2017
Journal Name
Biomedical And Pharmacology Journal
Evaluation of Crestal Bone Loss and Alkaline Phosphatase Level in Saliva According To Different Flap Designs in Single-Tooth Dental Implant Surgery (A Clinical Comparative Study)
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