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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 22 2024
Journal Name
Iraqi Statisticians Journal
Inferential Methods for the Dagum Regression Model
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The Dagum Regression Model, introduced to address limitations in traditional econometric models, provides enhanced flexibility for analyzing data characterized by heavy tails and asymmetry, which is common in income and wealth distributions. This paper develops and applies the Dagum model, demonstrating its advantages over other distributions such as the Log-Normal and Gamma distributions. The model's parameters are estimated using Maximum Likelihood Estimation (MLE) and the Method of Moments (MoM). A simulation study evaluates both methods' performance across various sample sizes, showing that MoM tends to offer more robust and precise estimates, particularly in small samples. These findings provide valuable insights into the ana

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Publication Date
Wed Jan 02 2019
Journal Name
Journal Of The College Of Languages
The Outcomes of War: A Study of the Character After the Crisis of War
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World War II has brought suffering for all people; it has led people to have a nostalgic feeling. The war has many faces all of them are ugly, like death, separation, loneliness, violence, crime, betrayal, and disconnection and many other meanings. Michael Ondaatje in his novel The English Patient (1992) portrays a picture of the effect of World War II on four different characters; Hana a Canadian nurse, The English patient who is Hungarian, Caravaggio a Canadian-Italitan thief, and Kip an Indian sapper. They live together in one house, share their secrets and memories about World War II. Ondaatje brings them together to reveal their secrets and to heal their wounds of the war experience.

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Publication Date
Wed Jan 02 2019
Journal Name
Journal Of The College Of Languages (jcl)
The Outcomes of War: A Study of the Character After the Crisis of War
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World War II has brought suffering for all people; it has led people to have a nostalgic feeling. The war has many faces all of them are ugly, like death, separation, loneliness, violence, crime, betrayal, and disconnection and many other meanings. Michael Ondaatje in his novel The English Patient (1992) portrays a picture of the effect of World War II on four different characters; Hana a Canadian nurse, The English patient who is Hungarian, Caravaggio a Canadian-Italitan thief, and Kip an Indian sapper. They live together in one house, share their secrets and memories about World War II. Ondaatje brings them together to reveal their secrets and to heal their wounds of the war experience.

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Publication Date
Wed Mar 10 2021
Journal Name
Baghdad Science Journal
A Comparison Between the Theoretical Cross Section Based on the Partial Level Density Formulae Calculated by the Exciton Model with the Experimental Data for (_79^197)Au nucleus
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In this paper, the theoretical cross section in pre-equilibrium nuclear reaction has been studied for the reaction  at energy 22.4 MeV. Ericson’s formula of partial level density PLD and their corrections (William’s correction and spin correction) have been substituted  in the theoretical cross section and compared with the experimental data for  nucleus. It has been found that the theoretical cross section with one-component PLD from Ericson’s formula when  doesn’t agree with the experimental value and when . There is little agreement only at the high value of energy range with  the experimental cross section. The theoretical cross section that depends on the one-component William's formula and on-component corrected to spi

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Publication Date
Thu Mar 25 2021
Journal Name
Engineering And Technology Journal
The Effect of the Number of Key-Frames on the Facial Emotion Recognition Accuracy
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Key-frame selection plays an important role in facial expression recognition systems. It helps in selecting the most representative frames that capture the different poses of the face. The effect of the number of selected keyframes has been studied in this paper to find its impact on the final accuracy of the emotion recognition system. Dynamic and static information is employed to select the most effective key-frames of the facial video with a short response time. Firstly, the absolute difference between the successive frames is used to reduce the number of frames and select the candidate ones which then contribute to the clustering process. The static-based information of the reduced sets of frames is then given to the fuzzy C-Means algor

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Publication Date
Sat Apr 30 2022
Journal Name
Sport Tk-revista Euroamericana De Ciencias Del Deporte
The effect of biomechanical feedback on the accuracy of the long serve in badminton
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The primary aim of the study was to find out the values of some biomechanical variables for the long serve skill in badminton and to identify the effect of biomechanical feedback on the performance of long serve. The present study had a single group, pre-post experimental study design. The research community was determined by the intentional method of one group with a pre-and post-test. The players of the Assyrian badminton club constituted the research community. A total of 12 players were present in the research community. The badminton players falling within the age group of 15-17 years for the season 2020-2021 were recruited as the participants for the study. A total of five players were selected as the participant

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Publication Date
Wed Oct 01 2025
Journal Name
Theory And Practice In Language Studies
A Socio-Pragmatic Study of Profanity and Derogatory Words in Doja Cat’s Songs: A Corpus-Based Study
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Rap songs often feature artists who utilize explicit language to convey feelings such as happiness, sorrow, and anger, reflecting audience expectations and trends within the music industry. This study intends to conduct a socio-pragmatic analysis of explicit, derogatory, and offensive language in the songs of the American artist Doja Cat, employing Hughes’ (1996) Swearing Word Theory, Jay’s (1996) Taboo Words Theory, Luhr’s (2002) classification of social factors for sociolinguistic examination, Salager’s (1997) categories of hedges for pragmatic assessment, and Austin’s (1965, 1989) theory of speech acts. The researchers collected the data using the AntConc corpus analysis tool. The data shows the singer’s frequent use

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Publication Date
Thu Dec 01 2016
Journal Name
Journal Of Economics And Administrative Sciences
Usage of non-linear programming in building a mathematical model for production planning according to discount constraints put on bought amount
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Abstract

 This research deals will the declared production planning operation in the general company of planting oils, which have  great role in production operations management who had built mathematical model for correct non-linear programming according to discounting operation during raw materials or half-made materials purchasing operation which concentration of six main products by company but discount included just three products of raw materials, and there were six months taken from the 1st half of 2014 as a planning period has been chosen . Simulated annealing algorithm  application on non-linear model which been more difficulty than possible solution when imposed restric

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Publication Date
Tue Mar 15 2022
Journal Name
Journal Of Baghdad College Of Dentistry
In vitro cytotoxic effect of annona squamosa pulp ex-tract as a mouthwash for children on human normal cell line
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Background: Fruits and their by-products are the primary sources of bioactive chemicals in plants. Because of its phytochemical richness, Annona squamosa fruits have gained the alertness of people willing in health-promoting diets. The purpose of this in vitro study was to evaluate the cytocompatibility effect of ethanolic crude extract of Annona squamosa pulp against a human normal cell line as a mouthwash for children. Material and method: The ethanolic extract of Annona squamosa pulp was extracted using the ultrasonic method and then lyophilized to make it powder. The MTT (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl-2H-tetrazolium bromide) test was performed to investigate the cytotoxic activity of the pulp extract on a human normal cell l

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Publication Date
Tue Mar 15 2022
Journal Name
Journal Of Baghdad College Of Dentistry
Natural preparation of rice husk-derived silica and eggshell-derived calcium carbonate composite as a coating material for dental implant
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Background: The world is in front of two emerging problems being scarceness of virgin re-sources for bioactive materials and the gathering of waste production. Employment of the surplus waste in the mainstream production can resolve these problems. The current study aimed to prepare and characterize a natural composite CaO-SiO2 based bioactive material derived from naturally sustained raw materials. Then deposit this innovative novel bioactive coating composite materials overlying Yttria-stabilized tetragonal zirconia substrate. Mate-rials and method; Hen eggshell-derived calcium carbonate and rice husk-derived silica were extracted from natural resources to prepare the composite coating material. The manufac-tured powder was characterized

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