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 Jun 03 2018
Journal Name
Baghdad Science Journal
Influence of Lead Exposure in the Expression of Calmodulin – Related Genes: A Preliminary Study on Workers Working in Industry of Batteries, In Iraq
...Show More Authors

Most pathological effects of lead on the body are due to ability of lead to bind with important cellular molecules of various tissues and organs leading to formation abnormal molecules and thus to emergence of pathological conditions. To evaluation the risk to the health status of Iraqi workers who work in the batteries industry, expression of three types of calmodulin related genes were examined. Blood samples were collected from worker working in Iraqi industry of batteries (located in Al-Waziriya), then RNAs extraction were done thereby gene expression for Calcium/Calmodulin- dependent protein kinase2 (CaMKK2), C-X-C Chemokine receptor 4 (CXCR4) and mitogen activated protein kinase kinase 6 (MAP2K6) was done for each sample by using RT-q

... Show More
View Publication Preview PDF
Scopus (2)
Crossref (1)
Scopus Clarivate Crossref
Publication Date
Mon Apr 03 2023
Journal Name
Journal Of Educational And Psychological Researches
The Effectiveness of a Training Program for Children with Autism and their Mothers Based on the Picture Exchange Commination System to Confront Some of Basic Disorders for these Children
...Show More Authors

Abstract

The current research aims to examine the effectiveness of a training program for children with autism and their mothers based on the Picture Exchange Communication System to confront some basic disorders in a sample of children with autism. The study sample was (16) children with autism and their mothers in the different centers in Taif city and Tabuk city. The researcher used the quasi-experimental approach, in which two groups were employed: an experimental group and a control group. Children aged ranged from (6-9) years old. In addition, it was used the following tools: a list of estimation of basic disorders for a child with autism between (6-9) years, and a training program for children with autism

... Show More
View Publication Preview PDF
Publication Date
Fri Oct 02 2020
Journal Name
International Development Planning Review
COMPARISON OF THE PERFORMANCE OF THE FOREHANDKICK (STRAIGHT AND ACCOMPANIED BY FORWARD ROTATION) IN TERMS OF ACCURACY AND SPEED AMONG THE PLAYERS OF THE NATIONAL TEAM (ADVANCED CATEGORY) IN TENNIS
...Show More Authors

Publication Date
Wed Oct 02 2024
Journal Name
International Development Planning Review
COMPARISON OF THE PERFORMANCE OF THE FOREHANDKICK (STRAIGHT AND ACCOMPANIED BY FORWARD ROTATION) IN TERMS OF ACCURACY AND SPEED AMONG THE PLAYERS OF THE NATIONAL TEAM (ADVANCED CATEGORY) IN TENNIS
...Show More Authors

Publication Date
Wed Oct 02 2024
Journal Name
International Development Planning Review
COMPARISON OF THE PERFORMANCE OF THE FOREHANDKICK (STRAIGHT AND ACCOMPANIED BY FORWARD ROTATION) IN TERMS OF ACCURACY AND SPEED AMONG THE PLAYERS OF THE NATIONAL TEAM (ADVANCED CATEGORY) IN TENNIS
...Show More Authors

Publication Date
Wed Oct 02 2024
Journal Name
International Development Planning Review
COMPARISON OF THE PERFORMANCE OF THE FOREHANDKICK (STRAIGHT AND ACCOMPANIED BY FORWARD ROTATION) IN TERMS OF ACCURACY AND SPEED AMONG THE PLAYERS OF THE NATIONAL TEAM (ADVANCED CATEGORY) IN TENNIS
...Show More Authors

Publication Date
Sun Aug 30 2020
Journal Name
Journal Of Economics And Administrative Sciences
Improve operational performance by simulating the Holonic manufacturing system A case study at the rubber product plant in Al-Najaf Al-Ashraf
...Show More Authors

The research aims to improve operational performance through the application of the Holonic Manufacturing System (HMS) in the rubber products factory in Najaf. The problem was diagnosed with the weakness of the manufacturing system in the factory to meet customers' demands on time within the available resources of machines and workers, which led to time delays of Processing and delivery, increased costs, and reduced flexibility in the factory, A case study methodology used to identify the reality of the manufacturing system and the actual operational performance in the factory. The simulation was used to represent the proposed (HMS) by using (Excel 2010) based on the actual data and calculate the operational performance measures

... Show More
View Publication Preview PDF
Crossref
Publication Date
Wed Sep 30 2015
Journal Name
College Of Islamic Sciences
Fundamentalist detective On matters of consensus   Of Khala book complete the teacher benefits of Muslim Judge Ayaz (May God have mercy on him): Comparative fundamentalist study
...Show More Authors

Fundamentalist detective
On matters of consensus
  Of Khala book complete the teacher benefits of Muslim
Judge Ayaz
(May God have mercy on him)

View Publication Preview PDF
Publication Date
Tue Sep 01 2020
Journal Name
Baghdad Science Journal
Decolorization of Phenol Red Dye by Immobilized Laccase in Chitosan Beads Using Laccase - Mediator - System Model
...Show More Authors

This work describes the enhancement of phenol red decolorization through immobilizing of laccase in chitosan and enzyme recycling. Commercial laccase from white rot fungus, Trametesversicolor (Tvlac), was immobilizedin to freshly prepared chitosan beads by using glutaraldehyde as a cross linker. Characterization of prepared chitosan was confirmed by FTIR and scanning electron microscope (SEM). Tvlac (46.2 U/mL) immobilized into chitosan beads at 0.8 % glutaraldehyde (v/v) within 24 hrs. Synthetic (HBT) and natural (vanillin) mediators were used to enhance dye decolorizoation. It was found that 89 % of phenol red was decolorized by chitosan beads within 180 min. in the absence of enzyme and mediator, while decolorization percenta

... Show More
View Publication Preview PDF
Scopus (10)
Crossref (5)
Scopus Clarivate Crossref
Publication Date
Mon Nov 01 2021
Journal Name
Energy Reports
Global solar radiation prediction over North Dakota using air temperature: Development of novel hybrid intelligence model
...Show More Authors

View Publication
Scopus (78)
Crossref (79)
Scopus Clarivate Crossref