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
Sun Mar 01 2020
Journal Name
Journal Of Engineering
Study the Effect of Particle Sizes and Concentration on the Rheological Properties of Iraqi Bentonite for Using as Drilling Fluids
...Show More Authors

The aim of this study is to identify the effect of particle size and to increase the concentration of Iraqi bentonite on rheological properties in order to evaluate its performance and to know if it can be used as drilling fluid without additives or not. In this study, Iraqi bentonite was carried out by mineral composition (XRD), chemical composition (XRF) and Particle size distribution (PSD), and its rheological properties were measured at different particle size and concentration. The results showed that when the particle size of Iraqi bentonite decreased, and the rheological properties were increased with increased concentration of Iraqi bentonite. Also, Iraqi bentonite was unable to use as drilling fluid without certain additives.

... Show More
View Publication Preview PDF
Crossref (2)
Crossref
Publication Date
Thu Dec 01 2022
Journal Name
Bulletin Of Electrical Engineering And Informatics
A model for incorporating suitable methods of usability evaluation into agile software development
...Show More Authors

The challenge to incorporate usability evaluation values and practices into agile development process is not only persisting but also systemic. Notable contributions of researchers have attempted to isolate and close the gaps between both fields, with the aim of developing usable software. Due to the current absence of a reference model that specifies where and how usability activities need to be considered in the agile development process. This paper proposes a model for identifying appropriate usability evaluation methods alongside the agile development process. By using this model, the development team can apply usability evaluations at the right time at the right place to get the necessary feedback from the end-user. Verificatio

... Show More
View Publication
Scopus (3)
Scopus Crossref
Publication Date
Sun Dec 01 2002
Journal Name
Iraqi Journal Of Physics
A Hyperbolic Potential Field Model for Designing an Einzel Lens of Low Aberrations
...Show More Authors

An analytical model in the form of a hyperbolic function has been suggested for the axial potential distribution of an electrostatic einzel lens. With the aid of this hyperbolic model the relative optical parameters have been computed and investigated in detail as a function of the electrodes voltage ratio for various trajectories of an accelerated charged-particles beam. The electrodes voltage ratio covered a wide range where the lens may be operated at accelerating and decelerating modes. The results have shown that the proposed hyperbolic field has the advantages of producing low aberrations under various magnification conditions and operational modes. The electrodes profile and their three-dimensional diagram have been determined whi

... Show More
View Publication Preview PDF
Publication Date
Sun Jan 01 2023
Journal Name
International Journal Of Economics And Finance Studies
THE ROLE OF TARGET COST MANAGEMENT APPROACH IN REDUCING COSTS FOR THE ACHIEVEMENT OF COMPETITIVE ADVANTAGE AS A MEDIATOR: AN APPLIED STUDY OF THE IRAQI ELECTRICAL INDUSTRY
...Show More Authors

Scopus (18)
Scopus
Publication Date
Tue Jun 01 2021
Journal Name
Political Sciences Journal
The economic dimensions of the railway link between Iraq and Kuwait and the role of national alternatives (Faw port and the dry canal as a model(
...Show More Authors

   Decision-makers in each country work to define a list of internal and external interests, goals and threats to their countries according to the nature of their awareness of these interests, goals and threats. 

  Hence, Iraq is not an exception to this rule, and the process of evaluating its interests and the objectives of its foreign policy is subject to the pattern of awareness of decision-makers and the influencing forces in defining its basic interests, which often witness some kind of difference in defining them, evaluating their importance and determining the size of the threats they face. And among these interests and threats that have witnessed a difference in the assessment of their

... Show More
View Publication Preview PDF
Crossref
Publication Date
Mon Mar 13 2017
Journal Name
Journal Of Baghdad College Of Dentistry
The Effect of Artificial Accelerated Aging on The Color of Ceramic Veneers Cemented With Different Resin Cements (A Comparative In Vitro Study)
...Show More Authors

ABSTRACT Background: Color changes that are detectable to human eye can affect the esthetic appearance of ceramic veneers. The purpose of this study was to evaluate and compare the effect of artificial accelerated aging on the color of ceramic veneers cemented with different resin cements. Materials and Methods: Sixty discs were prepared with 0.5 mm thickness, 30 discs made from IPS e.max press (Ivoclar Vivadent) and 30 discs were made from VITA Enamic (VITA Zahnfabrik). The discs were cemented with three resin cements: Variolink Veneer MV 0 shade (Ivoclar Vivadent), Rely X veneer Translucent shade (3M ESPE) and NX3 Nexus Clear shade (Kerr Corporation) with 0.1 mm thickness. The spectrophotometer Easyshade Advance was used to measure the co

... Show More
View Publication Preview PDF
Crossref (4)
Crossref
Publication Date
Fri Oct 23 2020
Journal Name
Biomed Research International
A Computational Model of the Brain Cortex and Its Synchronization
...Show More Authors

Obtaining the computational models for the functioning of the brain gives us a chance to understand the brain functionality thoroughly. This would help the development of better treatments for neurological illnesses and disorders. We created a cortical model using Python language using the Brian simulator. The Brian simulator is specialized in simulating the neuronal connections and synaptic interconnections. The dynamic connection model has multiple parameters in order to ensure an accurate simulation (Bowman, 2016). We concentrated on the connection weights and studied their effect on the interactivity and connectivity of the cortical neurons in the same cortical layer and across multiple layers. As synchronization helps us to mea

... Show More
View Publication
Crossref (2)
Scopus Clarivate Crossref
Publication Date
Mon Aug 11 2025
Journal Name
Journal Of Physical Education
The Effect of Using Especial Exercises Suggested for Developing of Accuracy Direction by Fencing in Foil for the Players of the National Team of the Young who Handicap
...Show More Authors

View Publication
Publication Date
Fri Jan 01 2021
Journal Name
Journal Of Economics And Administrative Sciences
Formulating a strategy for the Northern Oil Company(Case Study)
...Show More Authors

                  The research aims to present a proposed strategy for the North Oil Company, and the proposed strategy took into account the surrounding environmental conditions and adopted in its formulation on the basis and scientific steps that are comprehensive and realistic, as it covered the main activities of the company (production and exploration activities, refining and refining activities, export and transport of oil, research and development activity, financial activity, information technology, human resources) and the (David) model has been adopted in the environmental analysis of the factors that have been diagnosed according to a

... Show More
View Publication Preview PDF
Crossref
Publication Date
Mon Aug 11 2025
Journal Name
Journal Of Economics And Administrative Sciences
Formulating a strategy for the Northern Oil Company(Case Study)
...Show More Authors

يهدف البحث الى تقديم استراتيجية مقترحة لشركة نفط الشمال ، وأخذت الاستراتيجية المقترحة بنظر الاعتبار الظروف البيئية المحيطة واعتمدت في صياغتها على اسس وخطوات علمية تتسم بالشمولية والواقعية ، اذ انها غطت الانشطة الرئيسية في الشركة (نشاط الانتاج والاستكشاف , نشاط التكرير والتصفية , التصدير ونقل النفط , نشاط البحث والتطوير , النشاط المالي , تقنية المعلومات , الموارد البشرية ) وقد اعتمد نموذج (David) في التحليل البيئي

... Show More
View Publication Preview PDF