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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 Apr 30 2024
Journal Name
Iraqi Journal Of Science
Assessment of Some Physiological, Immunological and Molecular Biomarkers in Sample of Iraqi Women Undergoing Caesarean Section and Normal Delivery
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     Pregnancy and delivery are physiological conditions that are marked by abrupt alterations to hormones, immunological and molecular characters. The current study aimed to evaluate oxytocin (OT), prolactin (PRL), cortisol and insulin growth factor-2 (IGF-2) levels as physiological biomarkers; programmed cell death protein-1 (PD-1), programmed cell death ligand-1 (PD-L1),interleukin-6 (IL-6) as immunological biomarkers, and single nucleotide polymorphisms (SNPs; rs53576 and rs2254298) of oxytocin receptor gene OXTR as molecular factors in samples of Iraqi women undergoing caesarean section (CS) and normal delivery (ND). Blood samples were collected from 96 pregnant women at term with ages ranging between 16-43 years. Regarding

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Publication Date
Tue Mar 19 2019
Journal Name
Tikrit Journal For Agricultural Sciences
Dependence and Phenotypic and Molecular Labels in Estimations of Genetic of Variance of Some Genotypes of Corn (Zea mays L.)
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Afield experiment was conducted in the college of Agriculture labs Sulaimanya University in 2014 to estimate the genetic variance between 12 genotypes of maize. (SSR) technology was used depending on (PCR) technology. Twenty primers were used for the genetic variance analysis between the studied genotypes and 15 primers showed polymorphic results in repeated experiment caused to experinse 52 alleles which gave 307 bands of range 3.1 by different molecular sizes ranged between 80-1000 pair base the value of PIC reached to phi069 gave high value (0.8785), the range of genetic diversity for studied genotypes reached to (0.625) gave primers pairs phi069 hig value for genetic diversity (0.888). The value of total allele replication ranged at pri

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Publication Date
Sun Apr 03 2016
Journal Name
Journal Of Educational And Psychological Researches
The impact of the model and follows on the collection and Retention of fifth grade students (oiterary) in history
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The first chapter the importance of research and need for education scientists see that the roots of the use of a specimen Wheatley in learning and teaching back to Grayson Wheatley, one of the largest supporters of a modern construction, which lay the groundwork for the specimen stage and the form in which it is. That was attributed to him, often called his name called while some educators based learning strategy on the issue. He sees the learner in this model make him a meaningful understanding of problems during his progress, thereby acting with his colleagues to find solutions to them in small groups. He

        Borders Search: Search by students is determined by th

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Publication Date
Sun Jan 27 2019
Journal Name
Journal Of Accounting And Financial Studies ( Jafs )
The application of the dimensions of TQM and its impact in enhancing the satisfaction of the taxpayers: Applied Study in the General Commission for Taxes
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The concept of TQM is based on one of the concepts that combine administrative and innovative methods. The aim of the research is to demonstrate the dimensions of TQM in enhancing the satisfaction of the taxpayers through a survey of a sample of officials in the General Authority for Taxation and 50 officials. In the collection of data and information, and the results were analyzed using the SPSS program to find the most important compounds and factors in he method of analysis.

The research problem was represented by the non-application of the General Authority for Taxation to the entrances and modern practices in the administrative work. The results of some of the complications that accompany the tax accounting process, which af

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Publication Date
Thu May 21 2026
Journal Name
Al-rafidain University College For Sciences
Use GARCH model to predict the stock market index, Saudi Arabia
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In this paper has been building a statistical model of the Saudi financial market using GARCH models that take into account Volatility in prices during periods of circulation, were also study the effect of the type of random error distribution of the time series on the accuracy of the statistical model, as it were studied two types of statistical distributions are normal distribution and the T distribution. and found by application of a measured data that the best model for the Saudi market is GARCH (1,1) model when the random error distributed t. student's .

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Publication Date
Sun Feb 03 2019
Journal Name
Journal Of The College Of Education For Women
Educational values in the Quran: Surat Luqman and AL- Hujurat model
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The paper has been summarized into the following:
Chapter one: the researcher deals with the problem of the paper, the most important points and the terminology. Chapter two: the researcher deals Surat Luqman from the Aya 12-19 , (the demonstration, the explanations, the values ). In chapter three the researcher deals with Surat AL-Hujurat from Aya 6-12, (the demonstration, the explanations, the values ). Chapter four include (the educational properties for individual and society, the educational applications, and the most important indicators in the texts). Chapter five include the results , the conclusions and the recommendations. One of the basic results that the Quran is a complete educational curriculum, and the texts of Surat Lu

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Publication Date
Sun Dec 20 2020
Journal Name
Journal Of Accounting And Financial Studies ( Jafs )
Suggested Model to audit the oil companies to achieve environmental control
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Oil sector is one of the most important sectors affecting the ecological balance, as activity contributes to the oil companies to influence their working environment, both during the oil exploration and extraction process or during transfer from one place to another process. We will try through this research put an environmental audit program proposal takes into account all the financial aspects, commitment and performance, according to the laws and regulations and agreements as well as relevant international standards, was based on research on the premise that the development of an environmental proposal auditing program that includes environmental controls on oil industry phases which helps reduce or minimize environmental pollutants B

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Publication Date
Wed Aug 30 2023
Journal Name
Baghdad Science Journal
Adherence model to cervical cancer treatment in the Covid-19 era
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Cervical Uterine Cancer is a disease that explains the vulnerability in which women are in terms of reproductive health with an impact on occupational health and public health, even when in Mexico the prevalence rate is lower than the other member countries of the OECD, its impact on Human Development and Local Development shows the importance that the disease have in communities more than in cities where prevention policies through check-ups and medical examinations seem to curb the trend, but show the lack of opportunities and capacities of health centers in rural areas.   To establish the reliability, validity, and correlations between the variables reported in the literature with respect to their weighting in a public hospital. A

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Publication Date
Thu Mar 01 2007
Journal Name
Journal Of Economics And Administrative Sciences
Alternative distribution to estimate the Dose – Response model in bioassay excrement
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 Alternative  distribution  to estimate the Dose – Response  model in bioassay  excrement

This research   concern to study five different distribution (Probit , Logistic, Arc sine , extreme value , One hit  ), to estimate  dose –response model by using m.l.e  and probit method This is done by determining different  weights in each  distribution in addition find all particular statistics for vital model . 

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Publication Date
Thu May 21 2026
Journal Name
Al-fatih Journal
Development of explosive power training with weights in a way the ups and downs and its impact on the improvement of some variables Albyukinmetekih and technical performance of the skill of a leap forward on your hands vaulting modern
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