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
Mon Jan 13 2020
Journal Name
Day 3 Wed, January 15, 2020
Numerical Simulation of Gas Lift Optimization Using Genetic Algorithm for a Middle East Oil Field: Feasibility Study
...Show More Authors
<p>Gas-lift technique plays an important role in sustaining oil production, especially from a mature field when the reservoirs’ natural energy becomes insufficient. However, optimally allocation of the gas injection rate in a large field through its gas-lift network system towards maximization of oil production rate is a challenging task. The conventional gas-lift optimization problems may become inefficient and incapable of modelling the gas-lift optimization in a large network system with problems associated with multi-objective, multi-constrained, and limited gas injection rate. The key objective of this study is to assess the feasibility of utilizing the Genetic Algorithm (GA) technique to optimize t</p> ... Show More
View Publication
Scopus (15)
Crossref (8)
Scopus Crossref
Publication Date
Wed Apr 23 2025
Journal Name
Journal Of The College Of Basic Education
A historical study of Iraqi Olympic participation for the period (1929 - 2000)
...Show More Authors

The history of the Olympic movement in Iraq is a rich history that reflects the interest of Iraqi governments and society in sports, the social and economic conditions, and international relations, and highlights the intersection of sports and politics and the impact of global events on local sports development. Therefore, providing a valuable insight into the reality of the participation and results achieved by Iraq in the Olympic Games for the period under study helps in giving a broader understanding of Iraq’s position in the global sports community. The research aims to document the important events in the development of the Olympic movement in Iraq for the period (1929-2000) and explore the formation and development of the Iraqi Olym

... Show More
View Publication Preview PDF
Crossref
Publication Date
Sat Jul 20 2024
Journal Name
Ibn Al-haitham Journal For Pure And Applied Sciences
Polyacrylonitrile Nanofiber Composites as Efficient Removal of Pollutants for Wastewater: A Review Article
...Show More Authors

Polyacrylonitrile nanofiber (PANFS), a well-known polymers, has been extensively employed in the manufacturing of carbon nanofibers (CNFS), which have recently gained substantial attention due to their excellent features, such as spinnability, environmental friendliness, and commercial feasibility. Because of their high carbon yield and versatility in tailoring the final CNFS structure, In addition to the simple formation of ladder structures through nitrile polymerization to yield stable products, CNFS and PAN have been the focus of extensive research as potential production precursors. For instance, the development of biomedical and high-performance composites has now become achievable. PAN homopolymer or PAN-based precursor copolymer can

... Show More
Publication Date
Mon Jun 19 2023
Journal Name
Journal Of Polymer Research
Design, and synthesis of a plasticizer- Schiff’s bases complexes as additive for polystyrene
...Show More Authors

This work involved the successful synthesis of three new Schiff base complexes, including Ni(II), Mn(II), and Cu(II) complexes. The Schiff base ligand was created by reacting the malonyldihydrazide molecule with naphthaldehyde, and the final step involved reacting the ligand with the corresponding metallic chloride yielding pure target complexes. FTIR, 1 H NMR, 13 C NMR, mass, and UV/Vis spectroscopies were used to comprehensively characterize the produced complexes. These substances have been employed in this study to photo-stabilize polystyrene (PS) and lessen the photo-degradation of its polymeric chains. Several methods, including FTIR, weight loss, viscosity average molecular weight, light and atomic force microscopy, and energy disper

... Show More
Scopus (5)
Crossref (5)
Scopus Clarivate Crossref
Publication Date
Mon Sep 04 2017
Journal Name
International Journal Of Environmental Science And Technology
A review of permeable reactive barrier as passive sustainable technology for groundwater remediation
...Show More Authors

Scopus (145)
Crossref (134)
Scopus Clarivate Crossref
Publication Date
Tue Apr 25 2023
Journal Name
Journal Of Periodontal Research
Salivary E‐cadherin as a biomarker for diagnosis and predicting grade of periodontitis
...Show More Authors
Abstract<sec><title>Objectives

To determine the abilities of salivary E‐cadherin to differentiate between periodontal health and periodontitis and to discriminate grades of periodontitis.

Background

E‐cadherin is the main protein responsible for maintaining the integrity of epithelial‐barrier function. Disintegration of this protein is one of the events associated with the destructive forms of periodontal disease leading to increase concentration of E‐cadherin in the oral biofluids.

Materials and Methods

A total of 63 patients with periodontitis (case) and 35

... Show More
View Publication
Scopus (13)
Crossref (12)
Scopus Clarivate Crossref
Publication Date
Mon Dec 30 2019
Journal Name
Iraqi Journal Of Chemical And Petroleum Engineering
A Comparative Study of Pressure Losses and Hole Cleaning Efficiency of Water and Polymer solutions in Horizontal Wells
...Show More Authors

The main objective of this study is to experimentally investigate the effect of the CMC polymeric drag reducer on the pressure drop occurred along the annulus of the wellbore in drilling operation and investigate the optimum polymer concentration that give the minimum pressure drop. A flow loop was designed for this purpose consist from 14 m long with transparent test section and differential pressure transmitter that allows to sense and measure the pressure losses along the test section. The results from the experimental work show that increasing in polymer concentration help to reduce the pressure drop in annulus and the optimum polymer concentration with the maximum drag reducing is 0.8 kg/m3. Also increasing in flow rate a

... Show More
View Publication Preview PDF
Crossref
Publication Date
Thu Feb 01 2018
Journal Name
Journal Of Us-china Public Administration
Victims of Terrorism between Compensation and Loss of Rights: A Comparative Study between Iraqi Law and French Law
...Show More Authors

The problem of the damage caused by terrorist acts has raised many difficulties in many countries, including Iraq, which requires the existence of a law that sets out sufficient rules for compensating the victims of terrorist acts, in order to compensate them for the harm they have not suffered. It may be difficult or impossible for them to identify causing damage, and therefore unable to obtain compensation by applying the traditional rules of liability that require proof of fault and identify the culprit. The security funds come as an appropriate alternative that pays compensation in such cases for victims to reparation for the damage they suffered. Therefore, this problem remains one of the most problems that Iraq suffers from it, which

... Show More
View Publication
Publication Date
Thu Jun 16 2022
Journal Name
Comparative Parasitology
A Comparative Study of Some Intestinal Parasites in Fecal Samples of Domestic and Stray Cats in Baghdad, Iraq
...Show More Authors

Some feline intestinal parasites such as Toxocara, Giardia, and Cryptosporidium can spread to humans through feces. Therefore, it is important to prevent exposure of family members by screening cat fecal samples twice per year for potential treatment regimes. This study was initiated to compare and identify gastrointestinal parasites of domestic and stray cats (Felis domesticus) in Baghdad City, Iraq. Parasite eggs and oocysts were identified under light microscopy by applying standard laboratory techniques (flotation and sedimentation). Overall, 59 of 121 (48.7%) fecal samples were positive for intestinal parasites. The rate of infection by Toxoplasma gondii was (3.31%), Isospora spp. (6.61%), Cryptosporidium spp. (31.4%), and Toxocara spp

... Show More
View Publication Preview PDF
Scopus (6)
Crossref (1)
Scopus Crossref
Publication Date
Sun Jan 01 2023
Journal Name
Results In Chemistry
Synthesis and characterization of (E)-4-(((4-(5-mercapto-1, 3, 4-oxadiazol-2-yl) phenyl) amino) methyl)-2-methoxyphenol as a novel corrosion inhibitor for mild-steel in acidic medium
...Show More Authors

View Publication
Scopus (21)
Crossref (22)
Scopus Clarivate Crossref