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 Jan 01 2023
Journal Name
Aip Conference Proceedings
Detection of human metapneumovirus RNA sequence in nasopharyngeal SWAP sample from children with acute respiratory tract infections in Najaf Province, Iraq
...Show More Authors

The purpose of this subject is to identify what is being studied in the article, which is the involvement of human Metapneumovirus in children with respiratory illnesses. During the period November 2020 to February 2021, 100 patients with respiratory tract infections were admitted to Al Zahra Teaching Hospital and AL-Forat AL-Awsat Teaching Hospital in Najaf Governorate. Nasopharyngeal swabs were collected from patients for molecular diagnosis of human metapneumovirus using Real-Time-PCR. The patients were distributed based on age into five groups as follows (Less than one, 1-2, 2-3, 3-4, and 4-5 years), and twenty samples of healthy individuals were approved as a control group without any clinical signs of infection. the children of age gr

... Show More
View Publication Preview PDF
Scopus Crossref
Publication Date
Wed May 10 2023
Journal Name
Journal Of Engineering
REMOVAL OF PHENOLIC COMPUNDS FROM AQUEOUS SOLUTIONS BY ADSOPTION ONTO ACTIVTED CARBONS PREPARED FROM DATE STONES BY CHEMICAL ACTIVATION WITH FeCl3
...Show More Authors

Activated carbon prepared from date stones by chemical activation with ferric chloride (FAC) was used an adsorbent to remove phenolic compounds such as phenol (Ph) and p-nitro phenol (PNPh) from aqueous solutions. The influence of process variables represented by solution pH value (2-12), adsorbent to adsorbate weight ratio (0.2-1.8), and contact time (30-150 min) on removal percentage and adsorbed amount of Ph and PNPh onto FAC was studied. For PNPh adsorption,( 97.43 %) maximum removal percentage and (48.71 mg/g) adsorbed amount was achieved at (5) solution pH,( 1) adsorbent to adsorbate weight ratio, and (90 min) contact time. While for Ph adsorption, at (4) solution pH, (1.4) absorbent to adsorbate weight ratio, and (120 min) contact

... Show More
View Publication Preview PDF
Crossref (3)
Crossref
Publication Date
Thu Jan 01 2015
Journal Name
Journal Of Plant Interactions
Photosynthetic and biochemical characterization of in vitro-derived African violet (<i>Saintpaulia ionantha</i>H. Wendl) plants to ex vitro conditions
...Show More Authors

View Publication
Scopus (19)
Crossref (19)
Scopus Clarivate Crossref
Publication Date
Sun Mar 13 2011
Journal Name
Baghdad Science Journal
Distribution Of Some Heavy Metals In Water,Sediment & Fish Cyprinus carpio in Euphrates River Near Al- Nassiriya City Center South Iraq .
...Show More Authors

The heavy metals Cd, Cu, Fe, pb, and Zn were determined in dissolved and particulate phases of the water,in addition to exchangeable and residual phases of the sediment and in the selected organs of the fish Cyprinus carpio collected from the Euphrates River near Al-Nassiriya city center south of Iraq during the summer period / 2009 .Also sediment texture and total organic carbon(TOC) were measured. Analysis emploing a flam Atomic Absorption Spectrophotometers . The mean regional concentrations of the heavy metals in dissolved (µg/l) and particulate phases (µg/gm) dry weight were Cd (0.15,16.13) ,Cu (0.59,24.48) ,Fe (726,909.4) ,Pb (0.20, 49.95) and Zn (2.5,35.62) respectively,and those for exchangeable and residual phases of the

... Show More
View Publication Preview PDF
Crossref
Publication Date
Sun Jun 05 2016
Journal Name
Baghdad Science Journal
Level and Statistical Distribution of Thyroid Peroxidase and Thyroid Hormones in Iraqi patients with Type1 Diabetes Mellitus at Al-Karkh Side
...Show More Authors

Type 1 diabetes mellitus (T1DM) is an autoimmune disease frequently associated with autoimmune thyroid disease (AITD). The study is conducted at the Specialized Center for Endocrinology and Diabetes-Baghdad at Al-karkh side, during December 2013 up to April 2014. In this study, we investigate the prevalence of anti-thyroid peroxidase (anti-TPO) antibody in(80) type1 diabetic patients with (AITD) and (30) healthy controls .Blood samples are taken for investigation of thyroid tests by using Vitek Immunodiagnstic Assay System (VIDAS).Enzeme Linked Immunosorbent Assay (ELISA) is used to detect anti-thyroid antibody(anti-TPO). The results show that age, gender and BMI (body mass index) are similar in both groups, p>0.05. Among 80 type1 diabetic

... Show More
View Publication Preview PDF
Crossref
Publication Date
Thu Sep 01 2022
Journal Name
Fuel
Experimental evaluation of Carbon Dioxide-Assisted Gravity Drainage process (CO2-AGD) to improve oil recovery in reservoirs with strong water drive
...Show More Authors

Crossref (24)
Crossref
Publication Date
Tue May 06 2014
Journal Name
Plos One
Gastroprotective Activity of Ethyl-4-[(3,5-di-tert-butyl-2-hydroxybenzylidene) Amino]benzoate against Ethanol-Induced Gastric Mucosal Ulcer in Rats
...Show More Authors

The study was carried out to determine the cytotoxic, antioxidant and gastro-protective effect of ethyl-4-[(3,5-di-tert-butyl-2-hydroxybenzylid ene)amino] benzoate (ETHAB) in rats.

View Publication
Scopus (40)
Crossref (37)
Scopus Clarivate Crossref
Publication Date
Sat Dec 11 2021
Journal Name
Iraqi Journal Of Pharmaceutical Sciences ( P-issn 1683 - 3597 E-issn 2521 - 3512)
Ameliorative Role of Nutraceutical Quercetin and its Derivatives Against Cognitive Impairment Process Induced by Lead Exposure in Drosophila melanogaster(Fruit Fly)
...Show More Authors

Cumulative lifetime lead (Pb) exposure has been associated with accelerated declines in cognition through the free radical generation and epigenetic effects. Several pieces of literature have identified a correlation between exposure to lead and neurodegenerative disorders. Harwich strain Drosophila melanogaster was exposed to lead acetate for two weeks, and changes in pulse transmission by acetylcholinesterase and systemic redox were evaluated. Besides, molecular docking studies of acetylcholinesterase against Quercetin and its most common derivatives contained in food have been performed. Pharmacokinetic studies on Quercetin and its derivatives have also been performed in silico toxicity. The data obtained showed alterations in antioxi

... Show More
View Publication Preview PDF
Scopus (3)
Crossref (3)
Scopus Crossref
Publication Date
Tue Aug 22 2023
Journal Name
Advances In Structural Engineering
Experimental and finite element analysis of reinforced concrete multi-cell box girders retrofitted with carbon fiber reinforced polymer strips under torsion
...Show More Authors

This study expands the state of the art in studies that assess torsional retrofit of reinforced concrete (RC) multi-cell box girders with carbon fiber reinforced polymer (CFRP) strips. The torsional behavior of non-damaged and pre-damaged RC multi-cell box girder specimens externally retrofitted by CFRP strips was investigated through a series of laboratory experiments. It was found that retrofitting the pre-damaged specimens with CFRP strips increased the ultimate torsional capacity by more than 50% as compared to the un-damaged specimens subjected to equivalent retrofitting. This indicated that the retrofit has been less effective for the girder specimen that did not develop distortion beforehand as a result of pre-loading. From

... Show More
Scopus (6)
Crossref (4)
Scopus Clarivate Crossref
Publication Date
Mon Sep 11 2023
Journal Name
Journal Of Chemical Technology &amp; Biotechnology
Modeling and optimization of biodiesel from high free‐fatty‐acid chicken fat by non‐catalytic esterification and mussel‐shell‐catalyzed transesterification
...Show More Authors
Abstract<sec><title>BACKGROUND

In this study, biodiesel was prepared from chicken fat via a transesterification reaction using Mussel shells as a catalyst. Pretreatment of chicken fat was carried out using non‐catalytic esterification to reduce the free fatty acid content from 36.28 to 0.96 mg KOH/g oil using an ethanol/ fat mole ratio equal to 115:1. In the transesterification reaction, the studied variables were methanol: oil mole ratio in the range of (6:1 ‐ 30:1), catalyst loading in the range of (9‐15) wt%, reaction temperature (55‐75 °C), and reaction time (1‐7) h. The heterogeneous alkaline catalyst was greenly synthesized from waste mussel shells throughout a calcin

... Show More
View Publication
Scopus (5)
Crossref (3)
Scopus Clarivate Crossref