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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
Wed Jan 01 2020
Journal Name
Annals Of Tropical Medicine And Public Health
Dithiocarbamates derivatives as anticancer agents: A Review
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Publication Date
Wed Jan 02 2013
Journal Name
Journal Of The Faculty Of Medicine Baghdad
Rotavirus infection as a cause watery diarrhea
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SummaryBackground: Rotavirus infection is the most commoncause of watery viral diarrhea in children younger than 5 years of age; it is a major cause of childhood morbidity and mortality.Objective:The aim of the study is todetermine the clinical picture, age distribution of patients with rotavirus infection and their maternal educational background.Patients &methods: A total of 202 patients suffering from diarrhea were included in this study, over 6 months period( from 1stof March 2011to 30th of August 2011),in Children Welfare Teaching hospital. History and physical examinationwere carried out, anthropometrics measures were done and plotted on Centers for Disease Control& World Health Organization charts to determine the nut

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Publication Date
Tue Jun 01 2021
Journal Name
The Journal Of Continuing Education In Nursing
Debate as a Teaching Strategy in Nursing
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Debate is a teaching strategy in nursing education that enhances students' critical thinking. Although debate can be an effective teaching strategy, it is not without limitations. This article discusses the advantages and disadvantages of debate as a teaching strategy in nursing. Also, evaluating debates and choosing topics are highlighted. [ J Contin Educ Nurs . 2021;52(6):263–265.]

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Publication Date
Fri Oct 02 2020
Journal Name
Biochemical & Cellular Archives
Retinoids and rexinoids as vitamin A analogs.
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Vitamin A, namely retinol is still the most proper agent for modulating so many biochemical reactions and biological functions in different tissues and organs. In addition to the provitamins A and α, βand γ-carotenoids that are present in various foods from either animal or plant origin, retinoids and rexinoids form the natural and synthetic analogs that are chemically related or unrelated and can be added as food supplements for deficiency disorders of vitamin A or used to alleviate or treat certain health problems such as skin carcinoma, acne, skin aging and dermatitis.

Publication Date
Mon Mar 07 2022
Journal Name
Journal Of Educational And Psychological Researches
Math Word Problems in Mathematics Books for the First Three Grads of the Basic Stage in Palestine (An analytical and Evaluative Study)
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This study aimed at revealing the degree of availability of standards of word problems in mathematics books for the first three grades of the basic stage in Palestine. For this purpose, the researcher prepared an analysis tool and a list of criteria consisting of two areas: linguistic formulation and mathematical content. Every area had seven items. The results of the study showed that the third-grade mathematics book has the highest degree of availability of the standards with 85.75%, and then came the second-grade mathematics book with 83.12%. Finally, the first-grade mathematics book came with 80.13%. In the light of the previous results, the researcher recommended to develop the language of word problems, to take into account their i

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Publication Date
Mon Aug 18 2025
Journal Name
Journal Of Physical Education
A Comparative Study of Mental Alertness Between Inactive and Active Individuals In Baghdad University Students Aged 18 – 22 Years Old
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Publication Date
Thu Dec 15 2022
Journal Name
Al-adab Journal
Metaphors and comparisons as a means of rethinking the phenomena of the surrounding world
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The article characterizes metaphors and comparisons as a means of rethinking the phenomena of the surrounding world; two directions are named within which metaphors and comparisons are studied: 1) the linguo-classification direction combines several classifications of metaphors and comparisons, which are basically focused on comparing two denotations through the meanings of word forms that are part of the trope; 2) the theoretical and conceptual direction is associated with the concept of conceptual displacement and is the basis of the theoretical and methodological study of metaphor and comparison, i.e. the modern theory of metaphor is being formed; The main attention is focused on the comparative concept of Aristotle, which postul

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Publication Date
Wed Aug 01 2018
Journal Name
Journal Of Economics And Administrative Sciences
The Impact of Using the international standard for Training (ISO-10015) to Improve the Quality of the Control Activity – A Survey Study at the Federal Board of Supreme Audit.
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The great  importance of training made it as an investment for the organization, and assert the Quality of performance which support it by prepare the employee to the Current and future Jobs . The Research problem a rounded about How to measure the impact of training based on (ISO 10015) and its effect on the Quality of performance , How to evaluation the results of training to attained the training goals . The Research aims to find out the effects of application of international standard guidelines (ISO 10015) to attained the quality of audit work achieved in the Federal Board of Supreme Audit. The Research sought to achieve a number of objectives cognitive and applied on the basis of four key assumptions, and other su

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Publication Date
Wed Jan 01 2025
Journal Name
Aip Conference Proceedings
Comparative analysis of parameter estimation methods for Meixner process using wavelet packet transform
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The current research creates an overall relative analysis concerning the estimation of Meixner process parameters via the wavelet packet transform. Of noteworthy presentation relevance, it compares the moment method and the wavelet packet estimator for the four parameters of the Meixner process. In this paper, the research focuses on finding the best threshold value using the square root log and modified square root log methods with the wavelet packets in the presence of noise to enhance the efficiency and effectiveness of the denoising process for the financial asset market signal. In this regard, a simulation study compares the performance of moment estimation and wavelet packets for different sample sizes. The results show that wavelet p

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Publication Date
Mon May 01 2017
Journal Name
The Journal Of Immunology
Resveratrol improves a murine model of asthma through alterations in the gut microbiome
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Abstract<p>Asthma is a condition characterized by bronchial spasms, inflammation, and mucous hypersecretion which leads to difficulties in respiration. Asthmatic patients are usually presented with recurrent attacks of coughing, wheezing, and shortness of breath which could be life-threatening. More than three million cases of asthma in the United States are diagnosed annually. Resveratrol, a polyphenolic stilbene, is known to be useful in controlling asthmatic attacks via different molecular mechanisms within the lung epithelium and infiltrating immune cells. However, few studies mentioned the effect of resveratrol on the microbiome in ovalbumin-induced asthma mouse model. In this study, we ind</p> ... Show More
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