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 Jan 01 2019
Journal Name
Chemical Industry And Chemical Engineering Quarterly
Optimization of dye adsorption process for Albizia lebbeck pods as a biomass using central composite rotatable design model
...Show More Authors

Albizia lebbeck biomass was used as an adsorbent material in the present study to remove methyl red dye from an aqueous solution. A central composite rotatable design model was used to predict the dye removal efficiency. The optimization was accomplished under a temperature and mixing control system (37?C) with different particle size of 300 and 600 ?m. Highest adsorption efficiencies were obtained at lower dye concentrations and lower weight of adsorbent. The adsorption time, more than 48 h, was found to have a negative effect on the removal efficiency due to secondary metabolites compounds. However, the adsorption time was found to have a positive effect at high dye concentrations and high adsorbent weight. The colour removal effi

... Show More
View Publication
Scopus (14)
Crossref (12)
Scopus Clarivate Crossref
Publication Date
Tue Jan 01 2019
Journal Name
Chemical Industry And Chemical Engineering Quarterly
Optimization of dye adsorption process for Albizia lebbeck pods as a biomass using central composite rotatable design model
...Show More Authors

Albizia lebbeck biomass was used as an adsorbent material in the present study to remove methyl red dye from an aqueous solution. A central composite rotatable design model was used to predict the dye removal efficiency. The optimization was accomplished under a temperature and mixing control system (37?C) with different particle size of 300 and 600 ?m. Highest adsorption efficiencies were obtained at lower dye concentrations and lower weight of adsorbent. The adsorption time, more than 48 h, was found to have a negative effect on the removal efficiency due to secondary metabolites compounds. However, the adsorption time was found to have a positive effect at high dye concentrations and high adsorbent weight. The colour removal effi

... Show More
View Publication
Scopus (15)
Crossref (12)
Scopus Clarivate Crossref
Publication Date
Thu Feb 01 2024
Journal Name
Russian Journal Of Bioorganic Chemistry
Synthesis, Characterization of Formazan Derivatives from Isoniazid and Study Their Antioxidant Activity and Molecular Docking
...Show More Authors

Objective: Synthesis, Characterization of formazan derivatives and studies the antioxidant activity of prepared compounds and molecular docking. Methods: In this study, formazan compounds (III–XIV) were produced by combining Schiff base compounds (I), (II) with diazonium salts resulting from reactions of different aromatic amines with sodium nitrate in the presence of Con.HCl at 0–5°C. When isonicotinic acid hydrazide reacts with (N,N-dimethylbenzaldehyde, 4-hydroxy-3-methoxybenzaldehyde) in the presence glacial acetic acid as a solvent Schiff base compounds are created. Results: The prepared compounds were identified by FT-IR, 1H NMR, 13C NMR, then the antioxidant activity of the derivatives and molecular docking were studied. D

... Show More
View Publication
Scopus (7)
Crossref (1)
Scopus Clarivate Crossref
Publication Date
Sat May 30 2026
Journal Name
Iraqi Journal Of Science
Leucine-rich alpha-2-glycoprotein-1 as a Potential biomarker for polycystic ovary syndrome
...Show More Authors

     Polycystic ovary syndrome (PCOS) is a common endocrine disorder affecting women of reproductive age, characterized by anovulatory, infertility and metabolic disturbances. This study aimed to assess the diagnostic accuracy of Leucine-rich alpha-2-glycoprotein-1 (LRG1) and xanthine oxidase (XO) activity as novel biomarkers for PCOS, as well as to explore the relationship between LRG1 and XO activity across different groups. A total of 150 married women, aged 18-46 years were enrolled and divided into three groups: 50 with PCOS under treatment, 50 PCOS without treatment conditions shared by women with polycystic ovary conditions, and 50 healthy women. Serum samples were analysed to measure LRG1, xanthine oxidase (XO) activity,

... Show More
View Publication Preview PDF
Scopus Crossref
Publication Date
Sun May 15 2022
Journal Name
Al-kindy College Medical Journal
A serology conundrum – HIV infection in acute babesiosis infection could merely be a false positive result
...Show More Authors

Babesiosis is a tick-borne disease caused by Babesia microti. We present a case of false positive HIV in the setting of confirmed babesiosis infection. An understanding that patients with babesiosis can have a false positive HIV test result is important in management decisions.

 

View Publication Preview PDF
Crossref (2)
Crossref
Publication Date
Wed Jan 01 2020
Journal Name
2nd International Conference On Materials Engineering & Science (iconmeas 2019)
A kinetic model for prodigiosin production by Serratia marcescens as a bio-colorant in bioreactor
...Show More Authors

View Publication
Scopus (22)
Crossref (21)
Scopus Crossref
Publication Date
Tue Mar 20 2018
Journal Name
Mustansiria Dental Journal
A comparative Study in the Antibacterial effect of Eugenol as Hand Wash Material with two Types of Soap
...Show More Authors

Hands have consistently been an important vehicle in the transmission of disease (1). Thus, thorough hand-washing remains the single most important factor in preventing infection specially in hospitals and labs.Twenty-nine non-clinical volunteers (do not work or come in contact with a clinical or hospital setting) that lacked visible skin injuries, eczema or apparent skin disease were used, those subjects were all tested by a material of each of the three used in the study weekly and laboratory tests were done pre- and post washing.All three material were effective , Eugenol extract as effective as the bar and lotion soap. And this was confirmed statistically.Eugenol has a great antibacterial action even in small concentration and t

... Show More
View Publication
Crossref
Publication Date
Thu Aug 08 2024
Journal Name
Al-rafidain Journal Of Medical Sciences ( Issn 2789-3219 )
Novel Technique for Alveolar Ridge Expansion: A Comparative Clinical Study
...Show More Authors

Background: Piezosurgery improved the split approach by making it safer, easier, and less prone to complications when treating extremely atrophic crests. Densah drills, with their unique design, expand the ridge by densifying bone in a reverse, non-cutting mode. Objective: To assess the effectiveness of sagittal piezosurgery, which involves cutting bone to the full implant depth and then expanding it using osseodensification drills. We use this technique to expand narrow alveolar bones and simultaneously place dental implants in the maxillary and mandibular arches. Methods: Fourteen patients received 31 dental implants. The maxillary arch received 19, and the mandible received 12 dental implants. This study will include patients who

... Show More
View Publication Preview PDF
Crossref (1)
Scopus Crossref
Publication Date
Tue Jan 31 2023
Journal Name
Journal Of Legal Sciences
Compensation for Psychological Damage Caused by Negligence - A Comparative Study
...Show More Authors

Psychological damage is one of the damages that can be compensated under the fault of negligence in the framework of English law, where the latter intends to include an enumeration of civil errors on the basis of which liability can be determined, and aims under each of these errors to protect a specific interest (for example, defamation protects Among the damage to reputation and inconvenience are the rights contained on the land), and the same is true for the rest of the other errors. Compensation for psychological damage resulting from negligence has raised problems in cases where the psychological injury is "pure", that is, those that are not accompanied by a physical injury, which required subjecting them to special requirements by the

... Show More
View Publication
Publication Date
Sun Dec 09 2018
Journal Name
Baghdad Science Journal
A Comparative Study on the Electrical Characteristics of Generating Plasma by Using Different Target Sources
...Show More Authors

In this research, the electrical characteristics of glow discharge plasma were studied. Glow discharge plasma generated in a home-made DC magnetron sputtering system, and a DC-power supply of high voltage as input to the discharge electrodes were both utilized. The distance between two electrodes is 4cm. The gas used to produce plasma is argon gas which flows inside the chamber at a rate of 40 sccm. The influence of work function for different target materials (gold, copper, and silver), - 5cm in diameter and around 1mm thickness - different working pressures, and different applied voltages on electrical characteristics (discharge current, discharge potential, and Paschen’s curve) were studied. The results showed that the discharge cur

... Show More
View Publication Preview PDF
Scopus (22)
Crossref (14)
Scopus Clarivate Crossref