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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 May 16 2023
Journal Name
Mathematics
A Mathematical Study for the Transmission of Coronavirus Disease
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Globally, the COVID-19 pandemic’s development has presented significant societal and economic challenges. The carriers of COVID-19 transmission have also been identified as asymptomatic infected people. Yet, most epidemic models do not consider their impact when accounting for the disease’s indirect transmission. This study suggested and investigated a mathematical model replicating the spread of coronavirus disease among asymptomatic infected people. A study was conducted on every aspect of the system’s solution. The equilibrium points and the basic reproduction number were computed. The endemic equilibrium point and the disease-free equilibrium point had both undergone local stability analyses. A geometric technique was used

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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
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
Thu May 18 2023
Journal Name
Journal Of Engineering
Experimental Investigation for TiO2 nanoparticles as a Lubricant-Additive for a Compressor ofWindow Type Air-Conditioner
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The coefficient of performance of a window type Air-Conditioner system can be improved if a reduction in the work of compressor can be achieved by a suitable technique. The present study investigates the effect of dispersing a low concentration of TiO2 nanoparticles in the mineral oil based lubricant, as well as on the overall performance of a window type Air-Conditioner system using R22 as the working fluid. An enhancement in the COP of the refrigeration system has been observed and the existence of an optimum volume fraction noticed, with low concentrations of nanoparticles suspended in the mineral oil. Results showed that the average compressor work reduced by 13.3%, which ultimately resulted in an increase of 11.99% in the COP due to

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Publication Date
Mon May 01 2006
Journal Name
East Mediterr Health J
Prevalence of HCV/HIV co-infection among haemophilia patients in Baghdad
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Abstract To estimate the seroprevalence of HCV infection among HIV-infected haemophiliacs and to demonstrate the most prevalent HCV genotype, 47 HIV-infected haemophilia patients were screened for anti-HCV antibodies. By performing polymerase chain reaction and DNA enzyme immunoassay, HCV-RNA was detected with subsequent genotyping. Seroprevalence of anti-HCV antibodies was 66.0%. Of 31 HCV/HIV co-infected patients, 21 (67.7%) had no history of blood transfusion. We detected 4 HCV genotypes: 1a, 1b, 4 and 4 mixed with 3a, HCV-1b being the most frequent. Contaminated factor VIII (clotting factor) could be responsible for disease acquisition.

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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
Wed Mar 29 2017
Journal Name
Iraqi Journal Of Pharmaceutical Sciences ( P-issn 1683 - 3597 E-issn 2521 - 3512)
A Comparative Biochemical Study of Proteins Profile in Iraqi Children and Adolescent with ?-Thalassemia
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The aim of the present research is to study different protein fractions in sera of children and adolescent with  β –thalassemia major and minor and to compare the results with that of healthy control.One hundred fifty children and adolescents were enrolled in this study,including 50 patients with β- thalassemia major , 50 patients with  β- thalassemia minor as pathological control group and another apparently 50 healthy individuals as a control group. The age of all studied  groups ranged from (4-18)years.Total protein, albumin and immunoglobulins were estimated in sera of all subjects.  A Significant  decrease  was  found  in  the  total  protein and  albumin&nb

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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
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
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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