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 Sep 30 2023
Journal Name
Iraqi Journal Of Chemical And Petroleum Engineering
Effect of Heterogeneity on Recovery Factor for Carbonate Reservoirs. A Case Study for Mishrif Formation in West Qurna Oilfield, Southern Iraq
...Show More Authors

Oil recovery could be impacted by the relation between vertical permeability (Kv) and horizontal permeability (Kh) (Kv/Kh). 4816 plugs that have been getting hold of 18 wells of Mishrif formation in the West Qurna oilfield were used. Kv/Kh data provided some scatter, but the mean is ~1. Kv/Kh =1 was used for the Petrel model before upscaling according to the heterogeneity of each layer.

Kv/Kh values for Mishrif Formation in West Qurna Oilfield are 0.8 for relatively homogeneous, 0.4 for heterogeneous rock, and 0.1 for cap rocks (CRII).

   Eclipse TM was used for reservoir simulation. PVT and SCAL data e

... Show More
View Publication Preview PDF
Crossref (16)
Crossref
Publication Date
Sun Jun 16 2019
Journal Name
Al–bahith Al–a'alami
News frames for the phenomenon of terrorism in international satellite channels directed in Arabic An analytical study of the main news bulletins in the Russian channel today 1/2/31/5/2018
...Show More Authors

International satellite channels in Arabic are targeted to the region with their news bulletins and their innovative programs, attracting the interest of the Arab viewers in their news articles and programs with new ideas and methods as well as high technology in the production and synthesis of videos. Therefore, they work on framing the above, And the media policy that governs, so focused the problem of the study to try to answer the question of the President is how to frame the international satellite channels in Arabic to the phenomenon of terrorism? What are the aspects that are working to highlight and aspects that try to hide? The study adopted the survey methodology for the main news bulletins in the Russian channel today for the

... Show More
View Publication Preview PDF
Crossref (1)
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 Jan 31 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
Wed Oct 24 2018
Journal Name
Chemistry Of Materials
Oxidant or Catalyst for Oxidation? A Study of How Structure and Disorder Change the Selectivity for Direct versus Catalytic Oxidation Mediated by Manganese(III,IV) Oxides
...Show More Authors

Structure type and disorder have become important questions in catalyst design, with the most active catalysts often noted to be “disordered” or “amorphous” in nature. To quantify the effects of disorder and structure type systematically, a test set of manganese(III,IV) oxides was developed and their reactivity as oxidants and catalysts tested against three substrates: methylene blue, hydrogen peroxide, and water. We find that disorder destabilizes the materialsthermodynamically, making them stronger chemical oxidantsbut not necessarily better catalysts. For the disproportionation of H2O2 and the oxidative decomposition of methylene blue, MnOx-mediated direct oxidation competes with catalytically mediated oxidation, making the most

... Show More
View Publication
Scopus (24)
Crossref (25)
Scopus Clarivate Crossref
Publication Date
Thu Dec 01 2016
Journal Name
Journal Of Baghdad College Of Dentistry
In Vitro Comparative Assessment of Composite Nanoleakage Using Various Dentine Surface Treatments
...Show More Authors

Background: The treatment of dental tissues proceeding to adhesive procedures is a crucial step in the bonding protocol and decides the clinical success ofrestorations. This study was conducted in vitro, with the aim of evaluating thenanoleakage on the interface between the adhesive system and the dentine treated by five surface modalities using scanning electron microscopy and energydispersiveX-ray spectrometry. Materials and methods: Twenty five extracted premolars teeth were selected in the study. Standardized class V cavities were prepared on the buccal and lingual surfaces then the teeth divided into five main groups of (5 teeth in each group n=10) according to the type of dentine surface treatment that was used: Group (A): dentine was

... Show More
View Publication Preview PDF
Crossref (2)
Crossref
Publication Date
Mon Feb 01 2016
Journal Name
International Journal Of Transportation Engineering And Traffic System, Ijtets
Comparative Modeling of Pavement Surface Texture Variables Using ANN and SPSS Software
...Show More Authors

The health of Roadway pavement surface is considered as one of the major issues for safe driving. Pavement surface condition is usually referred to micro and macro textures which enhances the friction between the pavement surface and vehicular tires, while it provides a proper drainage for heavy rainfall water. Measurement of the surface texture is not yet standardized, and many different techniques are implemented by various road agencies around the world based on the availability of equipment’s, skilled technicians’ and funds. An attempt has been made in this investigation to model the surface macro texture measured from sand patch method (SPM), and the surface micro texture measured from out flow time (OFT) and British pendul

... Show More
Publication Date
Wed Dec 14 2016
Journal Name
Journal Of Baghdad College Of Dentistry
In Vitro Comparative Assessment of Composite Nanoleakage Using Various Dentine Surface Treatments
...Show More Authors

Background: The treatment of dental tissues proceeding to adhesive procedures is a crucial step in the bonding protocol and decides the clinical success ofrestorations. This study was conducted in vitro, with the aim of evaluating thenanoleakage on the interface between the adhesive system and the dentine treated by five surface modalities using scanning electron microscopy and energydispersiveX-ray spectrometry. Materials and methods: Twenty five extracted premolars teeth were selected in the study. Standardized class V cavities were prepared on the buccal and lingual surfaces then the teeth divided into five main groups of (5 teeth in each group n=10) according to the type of dentine surface treatment that was used: Group (A): dentine was

... Show More
View Publication Preview PDF
Crossref (2)
Crossref
Publication Date
Sat Dec 17 2022
Journal Name
Journal Of The College Of Languages (jcl)
The Use of the Definite article in the Ottoman Turkish Language in the Fourteenth and Seventeenth Centuries: Qaboos Namah and Mazaki Collection as a Model: '' Kabusnâme ve Mezâkî Divanı Örneğinde ''14. ve 17. Yüzyılarda Osmanlı Türkçesinde Harf-i Ta'rifin Kullanması Üzerine Bir İnceleme
...Show More Authors

The Turks used the Ottoman Turkish language from the thirteenth century to the twentieth century.  During this period and under the influence of Islamic civilization, a large number of words and structures were used from the Arabic and Persian languages, Therefore, many Arabic grammatical structures were used in the Ottoman Turkish language, such as the definite article simply because it was widely used.

The paper is concerned with the use of the Arabic definite article in the Ottoman Turkish language, and the aim of this contrastive study is to find out the similarities and differences between the two languages ​​in terms of meaning and structure. Since linguistic studies depend on the practical side or applied approach, two

... Show More
View Publication Preview PDF
Crossref