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
Tue Sep 11 2018
Journal Name
Iraqi Journal Of Physics
An experimental cross-section measurement of 10B(n,α)7Li reaction on counting alpha particles track density
...Show More Authors

The present work determines the particle size based only on the number of tracks detected in a cluster created by a hot particle on the CR-39 solid state nuclear track detector and depending on the exposure time. The mathematical model of the cross section developed here gives the relationship between alpha particle emitting from the (n, α) reaction and the number of tracks created and distribution of tracks created on the surface of the track detector. In an experiment performed during this work, disc of boron compound (boric acid or sodium tetraborate) of different weights were prepared and exposed to thermal neutron from the source. Chemical etching is processes of path formation in the detector, during which a suitable etching solut

... Show More
View Publication
Crossref
Publication Date
Mon Aug 11 2025
Journal Name
Journal Of Baghdad College Of Dentistry
Correlation between Streptococci Mutans and salivary IgA in relation to some oral parameters in saliva of children
...Show More Authors

Background: Saliva plays an important role in oral health. Several salivary proteins are involved in the antimicrobial defence mechanism and are able to eliminate or inhibit bacterial growth in the oral cavity. Secretory IgA (SIgA) is one of the principal antibodies present in saliva, could help oral immunity by preventing microbial adherence, neutralizing enzymes and toxins. The aim of this study was to investigate the relationship between salivary Streptococcus Mutans (SM) count and S IgA in stimulated whole saliva in children with primary dentition compared to those with permanent teeth in relation to some oral hygiene parameters. Material and methods: Stimulated whole saliva was collected from 50 children (25 with primary dentation and

... Show More
View Publication Preview PDF
Publication Date
Sun Dec 30 2012
Journal Name
Al-kindy College Medical Journal
Effect of Metformin Therapy on Reducing Leptin Resistance and Enhancing Ovulation in Women with Polycystic Ovary Syndrome
...Show More Authors

Background: The relation between insulin resistance ,leptin levels and other hormones in women with polycystic ovary syndrome(PCOS) is still controversial.Metformin therapy is proved effective in reducing insulin resistance and also in some studies it was seen to be effective in reducing leptin levels.
Al- Kindy Col Med J 2012 ; Vol .8 No. (2) p: 65
Objective: to study the effect of metformin on reducing leptin levels and enhancing ovulation in PCOS women.
Methods:metformin 500mg 3 times daily for 3 months was was given to 36 women
with proved PCOS, in addition to that, other parameters were included.
Results:28 women out of 36(77.78%) showed an evidence of ovulation ovulation after 3 months of metformin therapy(p<0.01)

... Show More
View Publication Preview PDF
Publication Date
Mon Sep 30 2024
Journal Name
Iraqi Journal Of Chemical And Petroleum Engineering
Elimination of phenol by sonoelctrochemical process utilizing graphite, stainless steel, and titanium anodes: optimization by taguchi approach
...Show More Authors

   Phenol is one of the worst-damaging organic pollutants, and it produces a variety of very poisonous organic intermediates, thus it is important to find efficient ways to eliminate it. One of the promising techniques is sonoelectrochemical processing. However, the type of electrodes, removal efficiency, and process cost are the biggest challenges. The main goal of the present study is to investigate the removal of phenol by a sonoelectrochemical process with different anodes, such as graphite, stainless steel, and titanium. The best anode performance was optimized by using the Taguchi approach with an L16 orthogonal array. the degradation of phenol sonoelectrochemically was investigated with three process parameters: current de

... Show More
View Publication Preview PDF
Crossref
Publication Date
Sun Mar 17 2019
Journal Name
Baghdad Science Journal
Fabrication and Characterization of Gas Sensor from ZrO2: MgO Nanostructure Thin Films by R.F. Magnetron Sputtering Technique
...Show More Authors

Thin films ZrO2: MgO nanostructure have been synthesized by a radio frequency magnetron plasma sputtering technique at different ratios of MgO (0,6, 8 and  10)% percentage to be used as the gas sensor for nitrogen dioxide NO2. The samples were investigated by X-ray diffraction (XRD), atomic force microscopy (AFM), scanning electron microscopy (SEM), energy-dispersive X-ray (EDX) and sensing properties were also investigated. The average particle size of all prepared samples was found lower than 33.22nm and the structure was a monoclinic phase. The distribution of grain size was found lower than36.3 nm and uninformed particles on the surface. Finally, the data of sensing properties have been discussed, where the

... Show More
View Publication Preview PDF
Scopus (9)
Crossref (1)
Scopus Clarivate Crossref
Publication Date
Tue Mar 01 2016
Journal Name
Al-academy
Semantic Analogy of Quran Text Content Found in Ornamental Figures in Islamic Architecture: وسام كامل عبد الامير
...Show More Authors

This study aims at creating an analogy between Quran text Contents as meanings that have representations as visional shapes within ornamental figures in Islamic architecture. The theoretical framework of the study deals with the concept of semantics and its parts, artistic contents of Quran texts, and ornamental figures in Islamic architecture. The study procedures included a population of (69) figures, (5) of them were chosen deliberately for analysis in accordance with a form that had been presented to a number of experts to ensure its validity. The study reached a number of conclusions, the most significant among them are: adopting natural denotation of direct reference in order to link the ornamental figure to the source it was taken

... Show More
View Publication Preview PDF
Crossref
Publication Date
Thu Jan 13 2022
Journal Name
Journal Of Research In Medical And Dental Science
Impact of Bad Oral Habits on Dental Caries among 6-10 Years Old Children in Hilla City
...Show More Authors

Background: There is a clear debate about the role of bad oral habits (thumb-sucking and biting nails) and on oral health and the state of the dental caries, but there is no doubt that continuing these bad habits until advanced ages will lead to deep and difficult problems to solve. Objective: The purpose of study was to evaluate the effect of bad habits, include finger sucking and nail biting on dental caries among children aged from 6 to 10 years old. Subjects and methods: In Al-Hilla city, Iraq, a comparative study was conducted in which (200) primary school students aged between 6 to10 years old were involved. A questionnaire filled out by their parents was used to gather information related to the bad oral habit, and then all the stude

... Show More
Publication Date
Tue Jan 09 2018
Journal Name
Research Journal Of Pharmacy And Technology
Sequencing of Mitochondrial COI gene in new Iraqi record Paropeas achatinaceum L. P. Feiffer, 1846, Gastropoda: Subulinidea
...Show More Authors

Fifty snails of Paropeas achatinaceum specimens were collected and classified from four areas in Baghdad-Iraq from the period between June and July, 2017. The snails were divided into two groups (each group contain 25 snails). Two environment conditions were used in this study. Natural environment considered as control and experimental environment contains Citrus sinensis (L.) roots as snail’s source food. The comparison result between snail weights in the nature and experimental environment was not significant (0.497, 95% confidence interval [CI] 0.01209–0.02309). Also, the comparison between snail weights in the nature environment and the food mean weight was significant (0.014, 95% confidence interval [CI] 0.00591-0.04109), while the

... Show More
Preview PDF
Publication Date
Fri Nov 30 2018
Journal Name
Oriental Journal Of Chemistry
Viscosity and Density Studies of Drugs in Aqueous Solution and in Aqueous Threonine Solution at 298.15 K
...Show More Authors

Viscosities (η) and densities (ρ) of atenolol and propranolol hydrochloride in water and in concentrations (0.05 M) and (0.1 M) aqueous solution of threonine have been used to reform different important thermodynamic parameters like apparent molal volumes fv partial molal volumes at infinite dilution fvo , transfer volume fvo (tr), the slop Sv , Gibbs free energy of activation for viscous flow of solution ΔG*1,2 and the B-coefficient have been calculated using Jones-Dole equation. These thermodynamic parameters have been predicted in terms of solute-solute and solute-solvent interaction.

Publication Date
Mon Nov 14 2022
Journal Name
Biomedicine
Cytotoxic effect of cloned EGFP gene on NCI-H727 cell line via genetically engineered gene transfer system
...Show More Authors

Introduction and Aim: Cancers are a complex group of genetic illnesses that develop through multistep, mutagenic processes which can invade or spread throughout the body. Recent advances in cancer treatment involve oncolytic viruses to infect and destroy cancer cells. The Newcastle disease virus (NDV), an oncolytic virus has shown to have anti-cancer effects either directly by lysing cancer cells or indirectly by activating the immune system. The green fluorescent protein (GFP) has been widely used in studying the anti-tumor activity of oncolytic viruses. This study aimed to study the anticancer effect of a recombinant rNDV-GFP clone on NCI-H727 lung carcinoma cell line in vitro.   Materials and Methods: The GFP gene was inserted t

... Show More
View Publication
Scopus (25)
Crossref (3)
Scopus Crossref