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
Sat Feb 01 2020
Journal Name
Iop Conference Series: Materials Science And Engineering
How geometric reverse engineering techniques can conserve our heritage; a case study in Iraq using 3D laser scanning
...Show More Authors
Abstract<p>Laser scanning has become a popular technique for the acquisition of digital models in the field of cultural heritage conservation and restoration nowadays. Many archaeological sites were lost, damaged, or faded, rather than being passed on to future generations due to many natural or human risks. It is still a challenge to accurately produce the digital and physical model of the missing regions or parts of our cultural heritage objects and restore damaged artefacts. The typical manual restoration can become a tedious and error-prone process; also can cause secondary damage to the relics. Therefore, in this paper, the automatic digital application process of 3D laser modelling of arte</p> ... Show More
View Publication
Scopus (10)
Crossref (5)
Scopus Clarivate Crossref
Publication Date
Tue Jan 01 2013
Journal Name
Al-mustansiriyah Journal Of Science
Encrypting a Text by Using Affine Cipher and Hiding it in the Colored Image by Using the Quantization stage
...Show More Authors

ST Alawi, NA Mustafa, Al-Mustansiriyah Journal of Science, 2013

View Publication
Publication Date
Thu Nov 21 2024
Journal Name
F1000research
Comparison of the severity of urinary tract infections between Metformin and SGL2 Inhibitors among Iraqi Type 2 Diabetics.
...Show More Authors

Background Many antidiabetic medications with distinct modes of action are available, The sodium glucose cotransporter-2 (SGLT-2) inhibitors are among the most recent oral antihyperglycemic medications. The American Diabetes Association recommends metformin, a biguanide medication, as the first option for oral control of type 2 diabetes because it has demonstrated promise in this regard. Aim of the study To evaluate and compare the effects of metformin and SGLT-2 inhibitors on general urine parameters in T2DM patients from Iraq. Method a prospective cohort study where 101 adult patients of both sexes aged under 70 years and newly diagnosed with T2DM, patients were divided into two groups, Metformin group (n=52), where metformin was p

... Show More
View Publication
Crossref
Publication Date
Sat Jan 02 2021
Journal Name
The International Journal Of Nonlinear Analysis And Application
Atan regularized for the high dimensional Poisson regression model
...Show More Authors

Variable selection in Poisson regression with high dimensional data has been widely used in recent years. we proposed in this paper using a penalty function that depends on a function named a penalty. An Atan estimator was compared with Lasso and adaptive lasso. A simulation and application show that an Atan estimator has the advantage in the estimation of coefficient and variables selection.

View Publication Preview PDF
Publication Date
Sun Feb 15 2026
Journal Name
Albahith Alalami
Tendencies of Scientific Research in the Specialized Journalism the Media Researcher Magazine A survey study
...Show More Authors

View Publication
Publication Date
Sat Apr 29 2023
Journal Name
Research Journal Of Pharmacy And Technology
The Wound Healing effect of the Green Synthesized Iron Oxide Nanoparticles: A Study on Mice
...Show More Authors

The extract of fig fruit has shown significant medical usefulness in various fields. The entrance of nanotechnology into the field of medicinal and pharmacology has shown remarkable advantages. Plants contain diverse molecules thatcan reduce metals, and provide a safe, eco-friendly approach for synthesizing nanoparticles. Iron oxide nanoparticles (IONPs) have been reported to possess an antimicrobial effect against some strains of bacteria and moulds. We have aimed to synthesize IONPs from fig fruit extract and investigate the influence of fig extract and IONPs in wound healing of mice. UV-Vis spectroscopy, X-ray diffraction (XRD), and field emission scanning electron microscopy were used to characterize the IONPs that were produced

... Show More
View Publication
Scopus (5)
Crossref (5)
Scopus Crossref
Publication Date
Sun Jun 30 2013
Journal Name
College Of Islamic Sciences
ا Hadiths prohibiting the intimidation of a Muslim in the six books - an analytical study
...Show More Authors

This research deals with the hadiths of intimidation. An analytical study of the serious effects of intimidation in society. Intimidation and intimidation of a Muslim is a serious matter, because of the anxiety, intimidation, and dispossession of others ’rights, but some consider it easy, and others intimidate jokingly or seriously, which may lead to such intimidation to have effects Serious.
For intimidation entails the death of the individual, the disappearance of his mind, or the loss of his money, etc., from here the need was urgent; to show the vision of the prophetic Sunnah in denouncing intimidation, so we had this humble research tagged with (hadiths prohibiting the intimidation of a Muslim in the books The six are an analyt

... Show More
View Publication Preview PDF
Publication Date
Sat Aug 01 2020
Journal Name
Journal Of Water Process Engineering
Humic acid coated sand as a novel sorbent in permeable reactive barrier for environmental remediation of groundwater polluted with copper and cadmium ions
...Show More Authors

Plantation of humic acid nanoparticles on the inert sand through simple impregnation to obtain the permeable reactive barrier (PRB) for treating of groundwater contaminated with copper and cadmium ions. The humic acid was extracted from sewage sludge which is byproduct of the wastewater treatment plant; so, this considers an application of sustainable development. Batch tests signified that the coated sand by humic acid (CSHA) had removal efficiencies exceeded 98 % at contact time, sorbent dosage, and initial pH of 1 h, 0.25 g/50 mL and 7, respectively for 10 mg/L initial concentration and 200 rpm agitation speed. Results proved that physicosorption was the predominant mechanism for metals-CSHA interaction because the sorption data followed

... Show More
View Publication
Crossref (35)
Crossref
Publication Date
Wed Oct 02 2024
Journal Name
Journal Of Craniofacial Surgery
Maxillofacial Trauma in Females: A Retrospective Study
...Show More Authors

Maxillofacial trauma in females is not widely reported. This study aimed to analyze the clinical characteristics and the patterns of maxillofacial injuries in females and to determine the differences in these patterns among different causes. This retrospective study analyzed several variables, including demographic, social, injury-related, and treatment-related variables, and compared these variables in relation to the main etiologies of maxillofacial trauma. The main etiologies of maxillofacial injuries involving females were assault, followed by road traffic accidents, and falls. There were significant differences in relation to the 3 etiologies in age groups (P= 0.002) and marital status (<

... Show More
View Publication
Scopus Clarivate Crossref
Publication Date
Tue Nov 01 2016
Journal Name
Journal Of The College Of Basic Education
A study effect Histological changes in Kidney
...Show More Authors