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
Wed Feb 01 2023
Journal Name
Journal Of Engineering
Evaluation of Seepage Force and Overall Stability Factor Along Proposed Baghdad Metro Tunnel Across Tigris River
...Show More Authors

Baghdad Metro is a vital project to fulfill the rapidly increased traffic volume requirements. The proposed metro will connect both sides of Baghdad City, passing under the Tigris River. This study is employed finite elements software (PLAXIS 3D) to evaluate the seepage force developed around the sub-river segment during different construction stages and for other water levels of Tigris. The study found that when the water level changes from maximum to minimum, the developed seepage force decreases by (8 to 13%) and (22 to 27%) respectively. The seepage forces were found to be maximum during the excavation stage. The concrete lining process led to a noticeable reduction in seepage forces at all locations. The study also

... Show More
View Publication Preview PDF
Crossref
Publication Date
Sun Jan 01 2023
Journal Name
Chemical Methodologies
Cytotoxicity and Anticancer Effect of Chitosan-Ag NPs-Doxorubicin-Folic Acid Conjugate on Lungs Cell Line
...Show More Authors

This study looked at how the synthetic chitosan-AgNPs-Doxorubicin-folic acid combination affected the A549 cell line in terms of cytotoxicity and anticancer activity. By reducing silver nitrate (AgNO3) and biodegradable chitosan, silver nanoparticles were biosynthesized. The produced conjugate was examined by using FT-IR spectroscopy, atomic force microscopy (AFM), and field emission scanning electron microscopy (FE-SEM). The cytotoxicity assay for the viability of A549 cells revealed that the combination of chitosan, AgNPs, doxorubicin, and folic acid decrease cell viability in a dose-determined by method over 48 hours, which direct to a dependent reduce in the activity of A549 cells. The mechanism analysis of the impacted living cells lea

... Show More
View Publication Preview PDF
Scopus (27)
Scopus
Publication Date
Sun Oct 21 2018
Journal Name
Al-kindy College Medical Journal
Biochemical Risk Determinants of Osteoporosis in Overweight and Obese Postmenopausal Women with Type 2 Diabetes Mellitus
...Show More Authors

Background: Several studies suggested that skeletal system is adversely affected by diabetes and is associated with increased risk of osteoporosis and fragility fractures  

Objectives: The study was a case-control study that designed to assess the level of bone turnover markers (BTMs) among patients with type 2 diabetes mellitus (T2DM) and to investigate the effect of body weight and diabetic control on the level of bone turnover

Type of the study: Cross- sectional study.

Methods: The present study included 100 postmenopausal women with type 2 diabetes mellitus. Sixty-six non-diabetic postmenopausal women were enrolled as a control. Fasting b

... Show More
View Publication Preview PDF
Crossref
Publication Date
Sun Mar 01 2015
Journal Name
Journal Of Engineering
Rehabilitation of Mounemantal, Historical, and Traditional Buildings (Pilot Project strategy in Historical and Traditional Buildings Rehabilitation)
...Show More Authors

The concept of rehabilitation provided an essential richness in the conservation philosophy through sustaining buildings life and adapting them to the contemporary use through a vision which looks at the present and future . In Iraq , the existence of historical buildings and the traditional fabric in the cities required the urban development which enhanced the interests of planning and architectural fields especially the building rehabilitation which requires the architectural intervention , and all that led to elaborate the problem of research which is " The confusion in the concepts of monumental, historical and traditional buildings in Iraq, As well as The insufficient knowledge about rehabilitation and the acts related to it through

... Show More
View Publication Preview PDF
Publication Date
Wed Jul 22 2020
Journal Name
University Of Baghdad
Feasibility of Water Sink-Based Gas Flooding to Enhance Oil Recovery in North Rumaila Oil Field
...Show More Authors

Publication Date
Tue Oct 30 2018
Journal Name
Iraqi Journal Of Physics
Annealing effects on optical and structural properties of chromium oxide thin film deposited by PLD technique
...Show More Authors

Optical properties of chromium oxide (Cr2O3) thin films which were prepared by pulse laser deposition method, onto glass substrates. Different laser energy (500-900) mJ were used to obtain Cr2O3 thin films with thickness ranging from 177.3 to 372.4 nm were measured using Tolansky method. Then films were annealed at temperature equal to 300 °C. Absorption spectra were used to determine the absorption coefficient of the films, and the effects of the annealing temperature on the absorption coefficient were investigated. The absorption edge shifted to red range of wavelength, and the optical constants of Cr2O3 films increases as the annealing temperature increased to 300 °C. X-ray diffraction (XRD) study reveals that Cr2O3 thin films are a

... Show More
View Publication Preview PDF
Crossref
Publication Date
Wed Mar 29 2017
Journal Name
Iraqi Journal Of Pharmaceutical Sciences ( P-issn 1683 - 3597 E-issn 2521 - 3512)
Effects of Losartan versus Enalapril on Serum Uric Acid Levels in Hypertensive Patients with Metabolic Syndrome
...Show More Authors

To investigate the effects of losartan and enalapril on serum uric acid in hypertensive patients with metabolic syndrome, one hundred and twenty six newly diagnosed mild hypertensive patients, having markers of metabolic syndrome included  in the study. The patients were divided into two groups. Group 1 (60 patients) was given losartan (50 mg/ day) and group 2 (66 patients)  enalapril (20 mg/ day) for a duration of 2 months. A control group of seventy apparently healthy individuals were included. Metabolic syndrome was diagnosed according to diagnostic criteria of metabolic syndrome related to the American National Cholesterol Education Program-Adult Treatment Panel III. Serum uric acid levels were measured bef

... Show More
View Publication Preview PDF
Crossref
Publication Date
Sat Jan 25 2020
Journal Name
Indian Journal Of Forensic Medicine & Toxicology
Bioactivity of Gutta flow II versus Modified Gutta Percha based Silicon Endodontic Sealers by Nanobioactive Fillers
...Show More Authors

The success of endodontic therapy is relied on radicular system cleaning, shaping, elimination of micro-organisms, and three dimensional filling of the radicular complex.This study was conducted to develop and assess new root canal sealer incorporating nano-sized bioactive glass into Gutta Flow II. The following concentration was used depend on a pilot study included adding (3%) of 45S5 bioactive glass into the Gutta Flow II. These materials were tested through assessment bioactivity. bioactivity test was undertaken after immersion of the tested samples into PBS for three days, seven days, fourteen days, and twenty eight days using FTIR too. study was found that it’s peaks was appear at level 800-1000 cm-1. The results showed that GFII gr

... Show More
View Publication Preview PDF
Crossref
Publication Date
Sun Feb 10 2019
Journal Name
Iraqi National Journal Of Nursing Specialties
Psychological Burdens of Children with Anorectal Malformation on Mothers at Pediatric Teaching Hospitals in Baghdad City
...Show More Authors

Objective(s): The main aim of the study is to determine the level of burden on mothers toward children with anorectal malformation.
Methodology: A descriptive study was carried out at Welfare Pediatric Teaching Hospital and Central Pediatric Teaching Hospital in Baghdad City. From November 15th, 2017 to April 29th, 2018. Convenient sample comprised of (140) children mothers with anorectal malformation were interviewed for the study. The instrument of study is composed of six domains related mothers' burden toward psychosocial burden as a result of child with anorectal malformation. Validity of the study instrument was determined through a panel of experts and the reliability of the questionnaire is determined in a pilot study among (1

... Show More
View Publication Preview PDF
Publication Date
Sat Feb 15 2025
Journal Name
Iraqi Journal Of Science
Effect of Aluminum Dust Particles on Plasma Parameters at Different Gas Pressure with Different Dust Contents
...Show More Authors

In this work, the effect of aluminum (Al) dust particles on the DC discharge plasma properties in argon was investigated. A magnetron is placed behind the cathode at different pressures and with varying amounts of Al. The plasma temperature (Te) and density (ne) were calculated using the Boltzmann equation and Stark broadening phenomena, which are considered the most important plasma variables through which the other plasma parameters were calculated. The measurements showed that the emission intensity decreases with increasing pressure from 0.06 to 0.4 Torr, and it slightly decreases with the addition of the NPs. The calculations showed that the ne increased and Te decreased with pressure. Both Te and ne were reduced by increasing

... Show More
View Publication Preview PDF
Scopus Crossref