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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 Jan 01 2021
Journal Name
E3s Web Of Conferences 318, 03002 (2021)
A Comparative Study on Behavior of RC Columns Strengthened by CFRP and Steel Jacket
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This paper studies the behavior of axially loaded RC columns which are confined with carbon fiber reinforced polymers’ sheet (CFRP) and steel jackets (SJ). The study is based on twelve axially loaded RC columns tested up to failure. It is divided into three schemes based on its strengthening type; each scheme has four columns. The main parameters in this study were the compressive strength of the concrete and steel reinforcement ratio. Furthermore, the results of the experimental test showed a substantial enhancement in the column's load-carrying capacity. When compared to the original columns, the CFRP sheet had a significant effect on improving the ductility of the column by increasing the axial deformation by about 59.2 to 95.7

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Publication Date
Thu Jul 08 2021
Journal Name
Turkish Online Journal Of Qualitative Inquiry (tojqi)
Civil Protection of Rights contiguous to Author’s Royalty in Iraqi Law A comparative study
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Publication Date
Thu Jan 01 2015
Journal Name
Conference Proceedings Of The Society For Experimental Mechanics Series
A comparative study of mode decomposition to relate next-ERA, PCA, and ICA modes
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This paper discusses a comparative study to relate parametric and non-parametric mode decomposition algorithms for response-only data. Three popular mode decomposition algorithms are included in this study: the Eigensystem Realization Algorithm with the Natural Excitation Technique (NExT-ERA) for the parametric algorithm, as well as the Principal Component Analysis (PCA) and the Independent Component Analysis (ICA) for the non-parametric algorithms. A comprehensive parametric study is provided for (i) different response types, (ii) excitation types, (iii) system damping, and (iv) sensor spatial resolution to compare the mode shapes and modal coordinates of using a 10-DOF building model. The mode decomposition results are also compared using

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Publication Date
Sun Oct 01 2017
Journal Name
International Journal Of Oral And Maxillofacial Surgery
Characteristics of mandibular injuries caused by bullets and improvised explosive devices: a comparative study
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The purpose of this study was to investigate the difference in mandibular trauma caused by two mechanisms for the delivery of missile injuries: firearms and improvised explosive devices (IEDs). The data investigated included sex, age, mechanism of injury, and other clinical and radiographic manifestations. Seventy consecutive patients, predominantly male, with a mean age of 28.6 ± 14 years (range 2–60 years) were enrolled: 38 patients (54.3%) sustained mandibular fractures caused by bullet injuries and 32 patients (45.7%) had mandibular fractures caused by IED explosion injuries. The study revealed that the differences in most of the investigated variables were not statistically significant; the only significant differences were the inci

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Publication Date
Sat Aug 01 2015
Journal Name
2015 37th Annual International Conference Of The Ieee Engineering In Medicine And Biology Society (embc)
Tsallis entropy as a biomarker for detection of Alzheimer's disease
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Publication Date
Fri Feb 28 2025
Journal Name
Energies
Synergizing Machine Learning and Physical Models for Enhanced Gas Production Forecasting: A Comparative Study of Short- and Long-Term Feasibility
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Advanced strategies for production forecasting, operational optimization, and decision-making enhancement have been employed through reservoir management and machine learning (ML) techniques. A hybrid model is established to predict future gas output in a gas reservoir through historical production data, including reservoir pressure, cumulative gas production, and cumulative water production for 67 months. The procedure starts with data preprocessing and applies seasonal exponential smoothing (SES) to capture seasonality and trends in production data, while an Artificial Neural Network (ANN) captures complicated spatiotemporal connections. The history replication in the models is quantified for accuracy through metric keys such as m

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Publication Date
Wed Feb 12 2020
Journal Name
Journal Of Xi'an University Of Architecture & Technology
A COMPARATIVE STUDY OF DIRECTIVES IN SAMUEL BECKETT’S ‘END GAME’ AND ‘WAITING FOR GODOT’
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DBN Rashid, JOURNAL OF XI'AN UNIVERSITY OF ARCHITECTURE & TECHNOLOGY, 2020

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Publication Date
Wed Mar 18 2020
Journal Name
Baghdad Science Journal
The A Comparative Study of the Adsorption of Crystal Violet Dye from Aqueous Solution on Rice Husk and Charcoal
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            In this work, the adsorption of crystal violet dye from aqueous solution on charcoal and rice husk has been investigated, where the impact of variable factors (contact time; the dosage of adsorbent, pH, temperature, and ionic strength) have been studied. It has been found that charcoal and rice husk have an appropriate adsorption limit with regards to the expulsion of crystal violet dye from fluid arrangements. The harmony adsorption is for all intents and purposes accomplished in 45 min for charcoal and 60 min for rice husk. The amount of crystal violet dye adsorbed (0.4 g of charcoal and 0.5 g of rice husk) increased with an increasing pH and the value of 11 is the best

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Publication Date
Mon Jan 01 2007
Journal Name
Journal Of The Faculty Of Medicine Baghdad
Herbal activation of mammary gland; a comparative
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Seventy five adult virgin female Norway rats (60 experimental and 15 controls) were used toevaluate the effect of seeds of three herbs (Fennel, Cumin and Garden cress) on their mammaryglands. Experimental animals were fed with these herbs (each type of herb seeds was given to twentyexperimental rats) for fourteen days. Rats were sacrificed and mammary gland sections wereobtained, stained then morphometrically assessed. Serum prolactin level was performed too.Results revealed that Garden cress seeds are the strongest lactogenic agent among the three. BothFennel and Cumin seeds were shown to be very weak galactagogues.

Publication Date
Fri Nov 03 2023
Journal Name
Al-rafidain Journal Of Medical Sciences ( Issn 2789-3219 )
The Effectiveness of Autogenous Dentin Graft as a Biomaterial in Optimizing the Esthetic Outcomes of Immediate Dental Implants: A Prospective Clinical Study
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Background: Immediate implant placement in the maxillary anterior region was challenging, especially with the jumping gap and limited primary implant stability. Objective: To assess the autogenous dentin graft biomaterial's ability to improve the esthetic outcomes of an immediately inserted implant. Methods: Twenty patients with non-restorable retained roots in the maxillary non-molar region surrounded by natural sound teeth were included in this study after a complete clinical and radiological examination, including patient health and clinical fitness for the immediate dental implant procedure. A single dental implant was inserted for each patient, and the resulting jump distance was filled with the mineralized dentin graft and co

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