Preferred Language
Articles
/
bijps-1604
A Comparative Study for the Accuracy of Three Molecular Docking Programs Using HIV-1 Protease Inhibitors as a Model
...Show More Authors

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.

 

Scopus Crossref
View Publication Preview PDF
Quick Preview PDF
Publication Date
Thu Mar 31 2022
Journal Name
Journal Of The College Of Education For Women
A Pragmatic Study of Identity Representation in American Political Speeches
...Show More Authors

Identity is an influential and flexible concept in social sciences and political studies. The basic sense of identity is looking for uniqueness. In one sense, it is a sign of identification with those we assume they are similar to us or at least in some significant ways they are so. Globalization, migration, modern technologies, media and political conflicts are argued to have a crucial effect on identity representation in terms of the political perspectives specifically in the United States of America. This paper endeavors to investigate how American politicians represent their identities in speeches delivered in different periods of time namely from 2015 to 2018 in terms of the pragmatic paradigm. Three randomly selected speeches by fa

... Show More
View Publication Preview PDF
Crossref (1)
Crossref
Publication Date
Sat Apr 06 2019
Journal Name
International Journal Of English Linguistics
A Morpho- Syntactic study of Contemporary Science Fiction Short Stories
...Show More Authors

The aim of the present study is to research two morphological processes: acronym and compounding (phrasal compounds/ circumlocution) and one syntactic category which are 'existential sentences' in science fiction short stories. The present paper identifies different types and rates of existential sentences. In this respect , 'bare existential and locative’ read the high percentages and may be contrasted with other classifications of English existential sentences which have a verb other than 'be' and a definite expression. 'Phrasal compounds' vary in rates as they constitute notable percentage for those that involve 'lexical means and lexical relations' followed by 'prepositional compounds' , 'conjunctional compounds' , and those invo

... Show More
Publication Date
Wed Dec 14 2022
Journal Name
Journal Of The College Of Languages (jcl)
A Pragma-Stylistic Study of Misdirection in Selected Detective Novels
...Show More Authors

The analysis of detective novels has taken different aspects. The linguistic analysis of them, for example, has tackled the linguistic systems of morphology, phonology, syntax, semantics, and pragmatics. In line with the linguistic analysis, this study explores the various pragmatic and stylistic devices realized through detective novels for the purpose of misdirecting and deceiving the reader. The problem is that when readers try to reach to the truth, they face difficulties. They might not reach to the right solution or infer wrong conclusions because writers use some techniques to hide the truth and mislead them. This study aims at examining these techniques and devices; namely, Grice's Maxims and ambiguity as pragmatic devices on the

... Show More
View Publication Preview PDF
Crossref
Publication Date
Thu Dec 01 2016
Journal Name
Journal Of Cleaner Production
A study of biogas production from date palm fruit wastes
...Show More Authors

View Publication
Scopus (41)
Crossref (38)
Scopus Clarivate Crossref
Publication Date
Tue Sep 09 2014
Journal Name
Iosr Journal Of Mathematics (iosr-jm)
An Efficient Shrinkage Estimator for the Parameters of Simple Linear Regression Model
...Show More Authors

Publication Date
Sun Jul 09 2023
Journal Name
Journal Of Engineering
Studying the Behavior of Asphalt Stabilized Gepseous Soil for Earth Embankment Model
...Show More Authors

The study presents the test results of stabilizing gypseous soil embankment obtained from
Al- Faluja university Campus at Al-Ramady province. The laboratory investigation was divided
into three phases, The physical and chemical properties, the optimum liquid asphalt (emulsion)
requirements (which are manufactured in Iraq) were determined by using one dimensional
unconfined compression strength test.in the first phase , The optimum fluid content was 11%
(6% of emulsion with 5% water content).. At phase two, the effect of Aeration technique was
investigated using both direct shear and permeability test. At phase three for the case of static
load , the pure soil embankment model under dry test condition was investigated

... Show More
View Publication Preview PDF
Crossref (1)
Crossref
Publication Date
Mon Feb 11 2019
Journal Name
Journal Of Pharmaceutical Sciences And Research
Design of experiments model for optimization of spectrophotometric determination of phenylephrine hydrochloride in pure and pharmaceutical formulations using p-bromanil
...Show More Authors

A simple, fast, inexpensive and sensitive method has been proposed to screen and optimize experimental factors that effecting the determination of phenylephrine hydrochloride (PHE.HCl) in pure and pharmaceutical formulations. The method is based on the development of brown-colored charge transfer (CT) complex with p-Bromanil (p-Br) in an alkaline medium (pH=9) with 1.07 min after heating at 80 °C. ‘Design of Experiments’ (DOE) employing ‘Central Composite Face Centered Design’ (CCF) and ‘Response Surface Methodology’ (RSM) were applied as an improvement to traditional ‘One Variable at Time’ (OVAT) approach to evaluate the effects of variations in selected factors (volume of 5×10-3 M p-Br, heating time, and temperature) on

... Show More
View Publication
Scopus
Publication Date
Tue Mar 30 2021
Journal Name
Baghdad Science Journal
Diversity Assessment by Molecular Barcoding and Seed Morphology in Ricinus communis L.: Molecular diversity of Ricinus seeds
...Show More Authors

Fourteen morphologically varied Ricinus communis L. seeds were collected from different localities in Egypt, El-Sudan and Saudi Arabia. Seed morphology and ITS barcoding analysis were performed to assess their diversity and phylogenetic relationship. Sequence’s alignment of nrITS region from different accessions display high levels of genetic similarities. Cluster analysis could not group different accessions according to their geographical distribution. Nevertheless, the genetic barcodes are interestingly matched with the morphological features of the Ricinus seeds. In conclusion, seed morphology proved to be a valuable tool in evaluating biodiversity and phylogenetic relationship in plant species with different loca

... Show More
View Publication Preview PDF
Scopus (2)
Crossref (2)
Scopus Clarivate Crossref
Publication Date
Thu May 06 2010
Journal Name
Dirasat, Pure Sciences
A Study of the Effects of the Solar Cycle 22, on the Critical Frequencies of F1 Layer over Baghdad
...Show More Authors

This paper aims to study the effects of the long term solar activity on the critical frequencies of ionospheric F1 layer over Baghdad city, during the solar cycle 22, within (1988- 1995). It is found that the critical frequency of this layer is closely related to the sunspots number during the years of the solar cycle 22, at a middle latitude region of the world. The study discussed the effect of sunspot numbers and solar events on the electron densities of F1 layer, which is the most important ionospheric parameter.

Publication Date
Fri Mar 01 2024
Journal Name
Baghdad Science Journal
Comparative Study of Genomic DNA Extraction Protocols from Whole Blood for P53 Gene Polymorphism in Persons with and without Prostate Cancer
...Show More Authors

In latest decades, genetic methods have developed into a potent tool in a number of life-attaching applications. In research looking at demographic genetic diversity, QTL detection, marker-assisted selection, and food traceability, DNA-based technologies like PCR are being employed more and more. These approaches call for extraction procedures that provide efficient nucleic acid extraction and the elimination of PCR inhibitors. The first and most important stage in molecular biology is the extraction of DNA from cells. For a molecular scientist, the high quality and integrity of the isolated DNA as well as the extraction method's ease of use and affordability are crucial factors. The present study was designed to establish a simple, fast

... Show More
View Publication Preview PDF
Scopus Crossref