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 Sep 03 2017
Journal Name
Baghdad Science Journal
Kinetic and Mechanistic Studies for the Gas-phase Reaction of Ozone with 2, 3-Dimethyl-2-Butene and 1, 3-Butadiene
...Show More Authors

The reactions of ozone with 2,3-Dimethyl-2-Butene (CH3)2C=C(CH3)2 and 1,3-Butadiene CH2=CHCH=CH2 have been investigated under atmospheric conditions at 298±3K in air using both relative and absolute rate techniques, and the measured rate coefficients are found to be in good agreement in both techniques used. The obtained results show the addition of ozone to the double bond in these compounds and how it acts as function of the methyl group substituent situated on the double bond. The yields of all the main products have been determined using FTIR and GC-FID and the product studies of these reactions establish a very good idea for the decomposition pathways for the primary formed compounds (ozonides) and give a good information for the effe

... Show More
View Publication Preview PDF
Scopus Crossref
Publication Date
Mon Apr 04 2011
Journal Name
Ibn Al-haitham J.for Pure &appl.sci
Anew Spectrophotometric Method For The Determination of La (III) With 3-Hydroxy -4-(2-hydroxy –Phenyl azo)Naphthalene -1-Sulfonic Acid
...Show More Authors

A simple, rapid and sensitive spectrophotometric method has been proposed for the determination of La (III) using 3-hydroxy -4-(2-hydroxy-phenyl azo) naphthalene -1- sulfonic acid as a chromogenic reagent. This method is based on the formation of a red-pink colored complex, upon the reaction of La(III) with the reagent in an alkaline medium (pH= 9.50), having a maximum absorbance at 459 nm. Beer's law is valid in the concentration range 0.512 µg.ml-1 with a Sandell's sensitivity value of 0.0188 µg.cm-2 and molar absorptivity of 7376.12 L.mol-1.cm-1. The stoichiometric composition of the chelate is 1:3. The effect of the presence of different cations as interferants in the determination of La(III) under the given optimum conditions wer

... Show More
Publication Date
Tue Jan 01 2019
Journal Name
Technologies And Materials For Renewable Energy, Environment And Sustainability: Tmrees19gr
Study of the effect of using nanomaterial in radiological shielding
...Show More Authors

View Publication
Scopus (7)
Crossref (3)
Scopus Clarivate Crossref
Publication Date
Sat Jul 01 2023
Journal Name
Journal Of Accounting And Financial Studies ( Jafs )
A proposed audit program for a comprehensive electronic banking system based on business risks : applied research
...Show More Authors

The research seeks to identify the comprehensive electronic banking system and the role of the auditor in light of the customer's application of electronic systems that depend on the Internet in providing its services, as a proposed audit program has been prepared in accordance with international auditing controls and standards based on the study of the customer's environment and the analysis of external and internal risks in the light of financial and non-financial indicators, the research reached a set of conclusions, most notably, increasing the dependence of banks on the comprehensive banking system for its ability to provide new and diverse banking services, The researcher suggested several recommendations, the most important of whi

... Show More
View Publication Preview PDF
Publication Date
Sun Sep 22 2024
Journal Name
Journal Of Petroleum Research And Studies
Optimizing Gas Lift for Improved Oil Recovery in a Middle East Field: A Genetic Algorithm Approach
...Show More Authors

This paper presents a study of the application of gas lift (GL) to improve oil production in a Middle East field. The field has been experiencing a rapid decline in production due to a drop in reservoir pressure. GL is a widely used artificial lift technique that can be used to increase oil production by reducing the hydrostatic pressure in the wellbore. The study used a full field model to simulate the effects of GL on production. The model was run under different production scenarios, including different water cut and reservoir pressure values. The results showed that GL can significantly increase oil production under all scenarios. The study also found that most wells in the field will soon be closed due to high water cuts. Howev

... Show More
View Publication
Crossref
Publication Date
Sun Aug 31 2025
Journal Name
Journal Of Science In Medicine And Life
Serum Endothelial Specific Molecule 1(EMS 1) and Uric Acid Levels in Severe Preeclampsia
...Show More Authors

Publication Date
Wed Jan 29 2025
Journal Name
Jornal Brasileiro De Patologia E Medicina Laboratorial
First Report of Three Root-Maggot Fly Genera (Diptera: Anthomyiidae) in the Fauna of Iraq
...Show More Authors

Publication Date
Sun Jan 01 2017
Journal Name
International Journal Of Advanced Computer Science And Applications
A Proposed Framework to Investigate the User Acceptance of Personal Health Records in Malaysia using UTAUT2 and PMT
...Show More Authors

View Publication Preview PDF
Crossref (8)
Crossref
Publication Date
Mon Mar 28 2022
Journal Name
Journal Of Physical Education
The Effect of Using a Teaching Aid on Learning Backswing to Handstand on Rings in Youth Artistic Gymnastics
...Show More Authors

               The research aimed at designing a teaching aid for learning backswing into handstand as well as identifying its effect on learning skill performance. The researchers hypothesized statistical differences between pre and post-tests in favor of the research group. They used the experimental method on six (13 – 16) year–old Baghdad club gymnasts. The researchers used the one group design in which all players perform pretests followed by special tests on the teaching aid than are tested posttests. The researchers conclude that the teaching aid positively affected learning the skill as well as the teaching aid was very good and endured the performance of all gymnasts. The researcher recommended making simi

... Show More
Crossref
Publication Date
Fri May 01 2015
Journal Name
Ieee Transactions On Microwave Theory And Techniques
On the Design of Gyroelectric Resonators and Circulators Using a Magnetically Biased 2-D Electron Gas (2-DEG)
...Show More Authors

View Publication
Scopus (3)
Crossref (3)
Scopus Clarivate Crossref