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
Sat Jun 30 2012
Journal Name
Al-kindy College Medical Journal
Bowel Cleansing Quality in Morning Versus Evening Preparation Regimens for colonoscopy; a Prospective Study
...Show More Authors

Background :Evening preparation for colonoscopy is often unsatisfactory and inconvenient. This study was performed to compare the efficacy of bowel preparation at two different timings: night before and morning of endoscopy and to compare the cecal intubation rate and disturbance of sleep hours between these two groups.
Methods: In this prospective randomized endoscopist- blinded trial, 150 patients were enrolled between March 2010 and August 2011. Patients aged between 18 to 80 years needing colonoscopy were included. Patients with prior bowel surgery, suspected bowel obstruction or those who didn't completely fulfill the preparation instructions were excluded. Patients received polyethyelen glycol electrolyte preparation in a mornin

... Show More
View Publication Preview PDF
Publication Date
Sat May 01 2021
Journal Name
Journal Of Physics: Conference Series
Loading and Activating a Carbon Surface and Applied for Congo Red Adsorption, Kinetic Study
...Show More Authors
Abstract<p>this paper contains preparation of Active carbon surface (AC) from pro so millet grain husks and Loading and activating by Iron oxide and hydrogen peroxide sequentially to obtain surface (ACIPE). The changes of previous processes on Active carbon surface were diagnosed by Fourier transform infrared spectroscopy (FTIR) and Scanning electron microscopy ( SEM ). These surfaces (AC and ACIPE ) were using as adsorbent for removing of congo red dye from aqueous solutions under certain conditions through batch system. More than one kinetic model was applied to congo red dye adsorption process and it was found that the most kinetic model applied to it is a model ( pseudo second order model). </p> ... Show More
View Publication Preview PDF
Scopus (4)
Scopus Crossref
Publication Date
Sun Mar 07 2010
Journal Name
Baghdad Science Journal
Molecular diagnosis of E.coliO157:H7 Which Isolated from Children with Diarrhea by using Multiplex PCR
...Show More Authors

A total of 96 stool samples were collected from children with bloody diarrhea from two hospitals in Baghdad. All samples were surveyed and examined for the presence of the Escherichia coli O157:H7 and differentiate it from other Non -Sorbitol Fermenting Escherichia coli (NSF E. coli). The Bacterial isolates were identifed by using morphological diagnostic methods, Samples were cultured on liquid enrichment medium, incubated at 37C? for 24 hrs, and then cultured on Cefixime Tellurite -Sorbitol MacConkey Agar (CT- SMAC). 32 non-sorbitol fermenting bacterial isolates were obtained of which 11 were identified as Escherichia coli by using traditional biochemical tests and API20E diagnostic system without differentiation between

... Show More
View Publication Preview PDF
Crossref
Publication Date
Sun Jan 01 2023
Journal Name
Studies In Systems, Decision And Control
Gap Analysis by Readiness Review Including Online Learning During COVID-19 Pandemic Period for Engineering Programs at the College of Engineering—University of Baghdad
...Show More Authors

View Publication
Scopus Crossref
Publication Date
Tue Oct 29 2024
Journal Name
Retos
The effect of special exercises using some auxiliary tools to develop some bio-kinetic abilities and the accuracy of the crushing and snatch forehand strikes among badminton players
...Show More Authors

The best means and ways to develop an athlete's physical and skill capabilities, and among these means is the use of training aids that help develop some bio-kinetic abilities, and prepared exercises have had an important role in improving athletic performance in badminton, where the player must possess physical fitness, explosive power, and strength. Characterized by speed as well as accuracy, awareness, and focus while playing on the court, the badminton player must be physically fit through a continuous movement of small and large muscles to achieve good performance, which requires special physical abilities and skills, and the most important of these bio-kinetic abilities are agility, coordination, and measuring the coordination

... Show More
View Publication Preview PDF
Scopus Crossref
Publication Date
Thu Sep 08 2022
Journal Name
Al-khwarizmi Engineering Journal
Study of Microbial Desalination Cell Performance; Power Generation and Desalination Efficiency using Pure Oxygen in a Cathode Chamber
...Show More Authors

Microbial Desalination Cell (MDC) is capable of desalinating seawater, producing electrical power and treating wastewater. Previously, chemical cathodes were used, which were application restrictions due to operational expenses are quite high, low levels of long-term viability and high toxicity. A pure oxygen cathode was using, external resistance 50 and 150 k Ω were studied with two concentrations of NaCl in the desalination chamber 15-25 g/L which represents the concentration of brackish water and sea water. The highest energy productivity was obtained, which amounted to 44 and 46 mW/m3, and the maximum limit for desalination of saline water was (31% and 26%) for each of 25 g / L and 15 g / L, respectively, when using an ex

... Show More
View Publication Preview PDF
Scopus (8)
Crossref (4)
Scopus Crossref
Publication Date
Mon May 04 2020
Journal Name
Environmental Engineering Research
Experimental and modeling study of water defluoridation using waste granular brick in a continuous up-flow fixed bed
...Show More Authors

Contamination of surface and groundwater with excessive concentrations of fluoride is of significant health hazard. Adsorption of fluoride onto waste materials of no economic value could be a potential approach for the treatment of fluoride-bearing water. This experimental and modeling study was devoted to investigate for the first the fluoride removal using unmodified waste granular brick (WGB) in a fixed bed running in continuous mode. Characterization of WGB was carried out by FT-IR, SEM, and EDX analysis. The batch mode experiments showed that they were affected by several parameters including contact time, initial pH, and sorbent dosage. The best values of these parameters that provided maximum removal percent (82%) with the in

... Show More
Scopus (16)
Crossref (10)
Scopus Clarivate Crossref
Publication Date
Thu Aug 30 2018
Journal Name
Journal Of Engineering
Monitoring Land Cover Change Using Remote Sensing and GIS Techniques: a Case Study of Al-Dalmaj Marsh, Iraq
...Show More Authors

Al-Dalmaj marsh and the near surrounding area is a very promising area for energy resources, tourism, agricultural and industrial activities. Over the past century, the Al-Dalmaje marsh and near surroundings area endrous from a number of changes. The current study highlights the spatial and temporal changes detection in land cover for Al-Dalmaj marsh and near surroundings area using different analyses methods the supervised maximum likelihood classification method, the Normalized  Difference Vegetation Index (NDVI), Geographic Information Systems(GIS),  and Remote Sensing (RS). Techniques spectral indices were used in this study to determine the change of wetlands and drylands area and of other land classes, th

... Show More
View Publication Preview PDF
Crossref (12)
Crossref
Publication Date
Tue Dec 01 2015
Journal Name
Journal Of Al-nahrain University-science
Synthesis of Polyacrylamides from Derivatives 2-Aminobenzothiazole and also Preparation of Dibutylphthalate as a Plasticizer to Estimate Plasticization Behaviour for Prepared Polymers
...Show More Authors

View Publication
Crossref
Publication Date
Sat Aug 01 2020
Journal Name
Jordan Journal Of Physics
Theoretical Simulation of Backscattering Electron Coefficient for SixGe1-x/Si Heterostructure as a Function of Primary Electron Beam Energy and Ge Concentration
...Show More Authors

Abstract: This study aims to investigate the backscattering electron coefficient for SixGe1-x/Si heterostructure sample as a function of primary electron beam energy (0.25-20 keV) and Ge concentration in the alloy. The results obtained have several characteristics that are as follows: the first one is that the intensity of the backscattered signal above the alloy is mainly related to the average atomic number of the SixGe1-x alloy. The second feature is that the backscattering electron coefficient line scan shows a constant value above each layer at low primary electron energies below 5 keV. However, at 5 keV and above, a peak and a dip appeared on the line scan above Si-Ge alloy and Si, respectively, close to the interfacing line

... Show More
View Publication
Scopus (1)
Scopus Clarivate Crossref