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
Wed Jun 18 2025
Journal Name
Journal Of Baghdad College Of Dentistry
A comparative study to evaluate the shear bond strength of different resin sealers to dentin (An in vitro study)
...Show More Authors

Background: One of the major problems in endodontics is micro-leakage of root canal fillings which might contribute to the failure of endodontic treatment. To avoid this problem, a variety of sealers have been tested. The objective of this, in vitro, study was to evaluate the shear bond strength of four resin based sealers (AH plus, silver free AH26, RealSeal SE and Perma Evolution permanent root canal filling material) to dentin. Materials and Methods: Forty non-carious extracted lower premolars were used. The 2mm of the occlusal surfaces of teeth were sectioned, to expose the dentin surface. The exposed dentin surfaces of teeth were washed with 5ml of 2.5% NaOCl solution followed by 5ml of 17 % EDTA then rinsed by deionized water to remov

... Show More
View Publication Preview PDF
Publication Date
Fri Oct 28 2022
Journal Name
Political Sciences Journal
Applications of contemporary feminist theory and its role in international relations (Singapore as a Model)
...Show More Authors

Since the emergence of the science of international relations as an independent academic scientific field,  various theories and trends have appeared and have tried to understand and explain the international reality and give a clear picture of what is happening within the international system of interactions and influences and the search for tools for stability and peace in international relations. Among these theories is the feminist theory, which is a new intellectual trend on the level of international relations theories,  which tried to give an explanation of what is happening in world politics and in international relations in particular. The main issue that feminist theory is concerned with is the lack of women’s subordination

... Show More
View Publication Preview PDF
Crossref
Publication Date
Sat Feb 01 2025
Journal Name
Advanced Journal Of Chemistry, Section A
Synthesis and Characterization of Heterocyclic Derivatives to Evaluate their Efficiency as Corrosion Inhibitors for Carbon Steel in Saline Medium
...Show More Authors

This work includes preparation of Az, Qz, and Tz derivatives from the reaction of Schiff base (Sb) derivative with anthranilic acid, chloroacetyl chloride, and sodium azide, as well as, the characterization via FT-IR, 1H-NMR, and 13CNMR. The anticorrosion inhibition of these compounds was studied and the measurements of carbon steel (CS) corrosion in sodium chloride solution 3.5% (blank) and inhibitor in solutions were calculated at a temperature range of 293-323 K by the technique of electrochemical polarization. In addition, some thermodynamic and kinetic activation parameters for inhibitor and blank solutions (Ea⋇, ΔH⋇, ΔS⋇, and ΔG⋇) were determined. The results showed high inhibition efficacy for all the prepared compounds,

... Show More
View Publication Preview PDF
Scopus (1)
Scopus
Publication Date
Sat Feb 03 2018
Journal Name
Al- Utroha Journal
Grice’s Maxims in British and American Conversation: A Comparative Study.
...Show More Authors

DBN Rashid, Al- Utroha Journal, 2018

View Publication
Publication Date
Tue Sep 15 2020
Journal Name
Journal Of Baghdad College Of Dentistry
Salivary mucoepidermoid carcinoma, auclair vs brandwein grading system: A histopathological comparative study
...Show More Authors

Background: The grading systems of salivary mucoepidermoid carcinoma depend on different histologic and morphologic features. The aim of this study was to compare between Auclair and Brandwein systems according to their histologic criteria, and the type of cell predominant. Materials and Methods: Twenty-one case included hematoxylin-eosin (H&E) stained tissue slides that were diagnosed as MEC, originally categorized into low and high grade type regardless of the grading system, have meticulously undergone histopathologic review. The sample was graded according to criteria owing to Auclair and Brandwein methods. The predominant type of cells was determined by microscopic examination according to grade of tumor. Results: Regarding the

... Show More
View Publication Preview PDF
Scopus Crossref
Publication Date
Tue Aug 07 2018
Journal Name
Oral And Maxillofacial Surgery
Mandibular war injuries caused by bullets and shell fragments: a comparative study
...Show More Authors

View Publication
Scopus (4)
Crossref (7)
Scopus Clarivate Crossref
Publication Date
Tue Aug 07 2018
Journal Name
Oral And Maxillofacial Surgery
Mandibular war injuries caused by bullets and shell fragments: a comparative study
...Show More Authors

View Publication
Scopus (4)
Crossref (7)
Scopus Crossref
Publication Date
Tue Jun 01 2021
Journal Name
Al-khwarizmi Engineering Journal
Effect of Environmental Factors on the Accuracy of a Quality Inspection System Based on Transfer Learning
...Show More Authors

In this research, a study is introduced on the effect of several environmental factors on the performance of an already constructed quality inspection system, which was designed using a transfer learning approach based on convolutional neural networks. The system comprised two sets of layers, transferred layers set from an already trained model (DenseNet121) and a custom classification layers set. It was designed to discriminate between damaged and undamaged helical gears according to the configuration of the gear regardless to its dimensions, and the model showed good performance discriminating between the two products at ideal conditions of high-resolution images. So, this study aimed at testing the system performance at poo

... Show More
Preview PDF
Scopus (1)
Crossref (1)
Scopus Crossref
Publication Date
Tue Jun 01 2021
Journal Name
Al-khwarizmi Engineering Journal
Effect of Environmental Factors on the Accuracy of a Quality Inspection System Based on Transfer Learning
...Show More Authors

In this research, a study is introduced on the effect of several environmental factors on the performance of an already constructed quality inspection system, which was designed using a transfer learning approach based on convolutional neural networks. The system comprised two sets of layers, transferred layers set from an already trained model (DenseNet121) and a custom classification layers set. It was designed to discriminate between damaged and undamaged helical gears according to the configuration of the gear regardless to its dimensions, and the model showed good performance discriminating between the two products at ideal conditions of high-resolution images.

So, this study aimed at testing the system performance at poor s

... Show More
View Publication Preview PDF
Scopus (1)
Crossref (1)
Scopus Crossref
Publication Date
Sun Oct 01 2017
Journal Name
Journal Of Economics And Administrative Sciences
Mackenzie role model dimensions in the quality of service, "a Prospective study of the views of a sample of Iraqi banks managers
...Show More Authors

The organizational integration forms a necessity according to McKinsey model, especially for service organizations. In the context of various service sector developments, importance adoption of compact mechanisms by these organizations to upgrade their services has increased and senior management must be more aware of environmental, competitive and developmental requirements. It gets more important when it shows in an organization seeking at excellence of making services within its policies and strategies. Subject organizational integration dimensions (strategy, structure, systems, style, staff, shared values, and skills) are effective components in directing behaviors of employees and organization. This motivated both researcher

... Show More
View Publication Preview PDF
Crossref