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
Mon Jun 15 2020
Journal Name
Journal Of Baghdad College Of Dentistry
Evaluation of dental enamel color after fixed orthodontic therapy using two types of protectors to prevent white spot lesions (A prospective clinical study)
...Show More Authors

Background: The aim of this study is to evaluate the color change ∆E of the dental enamel following treatment with 2 kinds of protector (icon infiltrant, clinpro varnish) before fixed orthodontic treatment to avoid the possible white spot lesions. Materials and Methods: Fifty four subjects treated with fixed appliances were divided into 3 groups: the 1st group was control, while the 2nd and 3rd groups were treated with icon infiltrant and clinpro varnish before bonding procedure, respectively. Color parameters (L,a,b) were recorded for the middle and gingival thirds before and after bonding procedure to get the ∆E of each group. Results: One-way ANOVA test showed a non-significant difference in ∆E between the 3 groups a

... Show More
View Publication Preview PDF
Scopus Crossref
Publication Date
Mon Dec 30 2013
Journal Name
Iraqi Journal Of Chemical And Petroleum Engineering
Permeability Prediction of Un-Cored Intervals Using FZI Method and Matrix Density Grouping Method: A Case Study of Abughirab Field/Asmari FM., Iraq
...Show More Authors

Knowledge of permeability is critical for developing an effective reservoir description. Permeability data may be calculated from well tests, cores and logs. Normally, using well log data to derive estimates of permeability is the lowest cost method. This paper will focus on the evaluation of formation permeability in un-cored intervals for Abughirab field/Asmari reservoir in Iraq from core and well log data. Hydraulic flow unit (HFU) concept is strongly related to the flow zone indicator (FZI) which is a function of the reservoir quality index (RQI). Both measures are based on porosity and permeability of cores. It is assumed that samples with similar FZI values belong to the same HFU. A generated method is also used to calculate permea

... Show More
View Publication Preview PDF
Publication Date
Thu Mar 29 2018
Journal Name
Construction Research Congress 2018
Consideration of Worker Safety in the Design Process: A Statistical-Based Approach Using Analysis of Variance (ANOVA)
...Show More Authors

View Publication
Scopus (1)
Crossref (3)
Scopus Crossref
Publication Date
Mon Jun 27 2022
Journal Name
. J Pharm Negative Results
Synthesis, Antioxidant, antibacterial and docking structure of new dihydro-pyrimidine derivatives containing multi phenol
...Show More Authors

Newly series of 6,6’-((2-(Aryl)dihydropyrimidine-1,3(2H,4H)-diyl)bis(methylene))bis(2-methoxy phenol) (3a-i) were synthesized from cyclization of 6,6’-((propane-1,3-diylbis (azanediyl)) bis(methylene)) bis(2-methoxyphenol) with several aryl aldehyde in the presence of acetic acid. The newly compounds characterized from their IR, NMR and EIMs spectra. The antioxidant capacity of these compounds screened by utilizing DPPH and FRAP assays. Compounds 3g and 3i exhibited significant antioxidant capability in both assays. Docking study for these compounds as a potential inhibitors of gyrase enzyme were carried out. Compound 3g exhibited significant inhibition with binding free energies (DG) higher than novobiocin. compounds 2, 3a, 3b, 3

... Show More
Preview PDF
Scopus (3)
Scopus
Publication Date
Tue Jan 08 2019
Journal Name
Iraqi Journal Of Physics
Effect of concentrations ratios of NiO on the efficiency of solar cell for (CdO)1-x(NiO)x thin films
...Show More Authors

CdO:NiO/Si solar cell film was fabricated via deposition of CdO:NiO in different concentrations 1%, 3%, and 5% for NiO thin films in R.T and 723K, on n-type silicon substrate with approximately 200 nm thickness using pulse laser deposition. CdO:NiO/n-Si solar cell photovoltaic properties were examined under 60 mW/cm2 intensity illumination. The highest efficiency of the solar cell is 2.4% when the NiO concentration is 0.05 at 723K.

View Publication Preview PDF
Crossref
Publication Date
Fri Apr 01 2016
Journal Name
Journal Of Economics And Administrative Sciences
Product development For Use Some Of The Lean Production Tools A Practical Research in the General Company for the automotive industry
...Show More Authors

Abstract 

     This research aims to analyze the reality of the production process in an assembly line Cars (RUNNA) in the public company for the automotive industry / Alexandria through the use of some Lean production tools, and data were collected through permanence in the company to identify the problems of the line in order to find appropriate to adopt some Lean production tools solutions, and results showed the presence of Lead time in some stations, which is reflected on the customer's waiting time to get the car, as well as some of the problems existing in the car produced such as high temperature of the car, as the company does not take into account customer preferences,

... Show More
View Publication Preview PDF
Crossref (1)
Crossref
Publication Date
Fri Jul 01 2016
Journal Name
Journal Of Economics And Administrative Sciences
Productive role in the financial performance of the banking: An Empirical Study in a sample of Iraqi banks
...Show More Authors

Abstract :

The research aims to study the basic concepts of banking productivity and discuss different approaches to study what ends to identify the most important possible standards applied to measured within the Iraqi banking environment as well as research into the causes of low and high Iraqi banking productivity and identify possible treatments to curb those reasons as to ensure the rise. And in line with the research problem, which states what is the level of productivity and what are the causes of decline and the rise in private banking research sample individually. And what the Iraqi private banks and what is the relationship between performance and the impact of productivity change in the perform

... Show More
View Publication Preview PDF
Crossref (2)
Crossref
Publication Date
Tue Aug 01 2023
Journal Name
Baghdad Science Journal
A Statistical Study of the Amount of Radiation Generated from Communication Towers in the Nineveh Plain Region, Baghdeda
...Show More Authors

This research presents a statistical study of radiation generated from communication towers in the Nineveh Plain region Baghdeda. The intensity of radiation energy was measured at 10 meters away from the communication tower in different locations, using a (1PC XH-901 Dosimeter/ Personal Dose Alarm / Radiation Detector, dosage rate: 0.01 μSv/h to 150μSv/h) to measure the amount of radiation at various times. Energy densities were measured and compared with standard limits provided by other authorities, such as the International Committee for Radiation Protection. Results were analyzed using SPSS version 26 to implement the data. The results show that the means of the radiation levels measured at all the zones do not statistically differ

... Show More
View Publication Preview PDF
Scopus (1)
Scopus Crossref
Publication Date
Mon Aug 01 2016
Journal Name
Journal Of Economics And Administrative Sciences
The effects of human error in the banking risks - Empirical study in a number of Iraqi private banks
...Show More Authors

Abstract

This research aims to study human error effects in the banking risks in the private banks  through the measurement and testing of human error effect in every kind of banking risks types and stand on the most closely associated with the risks in order to focus on them and make appropriate processors have with respect to and increase the availability of skills and expertise required to carry out banking operations of error-free manner.

Find dealt with human error in terms of meaning and understandable, classifications and types, causes and consequences and its approaches and theories. Also addressed placed banking risks in terms of meaning and concept, species and entr

... Show More
View Publication Preview PDF
Crossref (1)
Crossref
Publication Date
Sun Mar 02 2014
Journal Name
Baghdad Science Journal
We study the effect of Ultra violet rays (A-B) in treatment of Vitiligo (applied Therapy)
...Show More Authors

This research evaluated the effect of (UV)(400-320A)Hz(320-220B)Hz on the patient with vitiligo , using it with our new combing therapy that include the oral (Psorlene ) topical , meladinine solution applied on the Vitiligiousns Lesions , In edition to the instralesnional injection in the Vitiligiousns Lesions by long acting steroid (kenacort-A ) by aprecentage of (5%) , after that we expose the patient to UV . The ruslets of this way of treatment more effective by using of the UV rays in the treatment of vitiligo , while the previous treatment that used the UV ray with or with out the psorlene , the results were not effective on controlling of the Vitiligio diseases comparing by the treatment used in this research as it stop’s the sp

... Show More
View Publication Preview PDF
Crossref