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
Sat May 01 2021
Journal Name
Journal Of Physics: Conference Series
Pretreated Fishbone as Low Cost-Adsorbent for Cationic Dye Adsorption from Aqueous Solutions: Equilibrium, Optimization, Kinetic and Thermodynamic Study
...Show More Authors
Abstract<p>The present study investigated the use of pretreated fish bone (PTFB) as a new surface, natural waste and low-cost adsorbent for the adsorption of Methyl green (MG, as model toxic basic dye) from aqueous solutions. The functional groups and surface morphology of the untreated fish bone (FB) and pretreated fish bone were characterized using Fourier transform infrared (FTIR), scanning electron microscopy (SEM) and Energy dispersive X-ray spectroscopy (EDS), respectively. The effect of operating parameters including contact time, pH, adsorbent dose, temperature, and inorganic salt was evaluated. Langmuir, Freundlich and Temkin adsorption isotherm models were studied and the results showe</p> ... Show More
View Publication
Scopus (7)
Crossref (4)
Scopus Crossref
Publication Date
Fri Jun 01 2012
Journal Name
The Journal Of Engineering Research [tjer]
Thermal Performance of Solar Hot Water Systems Using a Flat Plate Collector of Accelerated Risers
...Show More Authors

 This study focuses on a comparison of the performance of two similar locally-fabricated solar water heaters. One of the collectors features a new design for accelerated absorber; its risers are made of converging ducts whose exit area is half that of the entrance. The other collector is a conventional absorber, with risers of the same cross sectional area along its length. Each collector is the primary part of an indirect thermosyphon circulation solar hot water system. Both collectors face south with a fixed tilt angle of 33.3

View Publication
Scopus (10)
Crossref (4)
Scopus Crossref
Publication Date
Mon Jul 01 2019
Journal Name
Iop Conference Series: Materials Science And Engineering
Study of different geostatistical methods to model formation porosity (Cast study of Zubair formation in Luhais oil field)
...Show More Authors
Abstract<p>This study is concerned with making comparison in using different geostatistical methods for porosity distribution of upper shale member - Zubair formation in Luhais oil field which was chosen to study.</p><p>Kriging, Gaussian random function simulation and sequential Gaussian simulation geostatistical methods were adopted in this study. After preparing all needed data which are contour map, well heads of 12 wells, well tops and porosity from CPI log. Petrel software 2009 was used for porosity distribution of mentioned formation in methods that are showed above. Comparisons were made among these three methods in order to choose the best one, the comparing cri</p> ... Show More
View Publication
Scopus (4)
Crossref (1)
Scopus Crossref
Publication Date
Wed Dec 12 2018
Journal Name
Iraqi National Journal Of Nursing Specialties
Relationship between General and Spinal Anesthesia and Its Impact upon Breast Feeding: Comparative Study
...Show More Authors

Objective: To identified the relationship between general and spinal Anesthesia upon breastfeeding and (demographic &reproductive) : Comparative Study. Methodology: The present study employs a descriptive comparative design held at the labor and delivery room , operational room for cesarean section and maternity word in maternity department at Al Emamain Al Kadhamain Medical City in Baghdad city. Data collection was initiated on 2nd January to end of March /2014. Purposive sample consisted of (150) mother and her neonate, The study sample divided into three groups:(50) under general anesthesia , (50) under

... Show More
View Publication Preview PDF
Publication Date
Thu Jun 29 2023
Journal Name
Iraqi Journal Of Chemical And Petroleum Engineering
Comparative Study between Different Oil Production Enhancement Scenarios in an Iraqi Tight Oil Reservoir
...Show More Authors

This paper presents a comparative study between different oil production enhancement scenarios in the Saadi tight oil reservoir located in the Halfaya Iraqi oil field. The reservoir exhibits poor petrophysical characteristics, including medium pore size, low permeability (reaching zero in some areas), and high porosity of up to 25%. Previous stimulation techniques such as acid fracturing and matrix acidizing have yielded low oil production in this reservoir. Therefore, the feasibility of hydraulic fracturing stimulation and/or horizontal well drilling scenarios was assessed to increase the production rate. While horizontal drilling and hydraulic fracturing can improve well performance, they come with high costs, often accounting for up t

... Show More
View Publication Preview PDF
Crossref
Publication Date
Mon Oct 02 2023
Journal Name
Journal Of Engineering
Comparative Study between Recycled Fine and Coarse Aggregate Used in Roller Compacted Concrete Pavement
...Show More Authors

To decrease the impact on the environment of building waste, the recycled aggregate may be used in various sustainable engineering applications, such as roller compacted concrete pavement (RCCP). This research examined how using recycled aggregate as a partial replacement for natural aggregate as coarse or fine affected the mechanical properties of roller-compacted concrete pavement. The recycled aggregate was crushed and sieved to coarse and fine aggregate before being used in the roller-compacted concrete pavement. Compressive strength, splitting tensile strength, and flexural strength were all evaluated after the samples were prepared at 28 and 90 days of curing. According to the study's findings, the partial replacem

... Show More
View Publication Preview PDF
Crossref (1)
Crossref
Publication Date
Sat Mar 02 2019
Journal Name
World Heart Journal
The Effects of Chronic Cigarette Smoking on the Right Ventricular Functions in Healthy Young Male Subjects: A Speckle Tracking Echocardiographic Study
...Show More Authors

Background: Chronic cigarette smoking is one of the major risk factors for coronary artery disease. However, it has additional cardiac adverse effects independent of coronary atherosclerosis. Patient and Methods: After informed consent and perm- ission from the review board of the hospital, 80 healthy subjects who were classified as smokers or non-smokers were included in the study. They were examined by standard echocardiography protocol which was followed by two-dimensional speckle tracking to assess the functions of the right ventricle. Results: The tricuspid annular plane systolic excursion (TAPSE) was significantly reduced in smokers as compared to non-smokers (P < 0.05). The tricuspid flow peak late diastolic velocity (A wave) was sig

... Show More
Scopus (1)
Scopus
Publication Date
Sat Oct 01 2022
Journal Name
Al–bahith Al–a'alami
Language communication, and the impact of journalism after 2003 AD (a study in the two newspapers, Al-Takahi and Al-Sabah)
...Show More Authors

The methods used by the print media (press) is varied in conveying its messages and its orientations to the readers. But language takes the leading method among these methods, or a real competitor - so far - due to the characteristics and advantages of languages, including: ease, abbreviation, and development, etc.

In the midst of such events, political tensions, and what they carry of the global developments, and among which was the most important the fall of the former Iraqi regime in the spring of 2003, the press had the greatest share, and a large portion on the level of monitoring, analyzing, and interpreting the various consequences of the event. The interpreting of the news varies according to the evolving political trends

... Show More
View Publication Preview PDF
Crossref
Publication Date
Tue Aug 01 2023
Journal Name
Journal Of Engineering
Comparative Analysis of H2 and H∞ Robust Control Design Approaches for Dynamic Control Systems
...Show More Authors

This paper discusses using H2 and H∞ robust control approaches for designing control systems. These approaches are applied to elementary control system designs, and their respective implementation and pros and cons are introduced. The H∞ control synthesis mainly enforces closed-loop stability, covering some physical constraints and limitations. While noise rejection and disturbance attenuation are more naturally expressed in performance optimization, which can represent the H2 control synthesis problem. The paper also applies these two methodologies to multi-plant systems to study the stability and performance of the designed controllers. Simulation results show that the H2 controller tracks a desirable cl

... Show More
View Publication Preview PDF
Crossref (3)
Crossref
Publication Date
Fri Jan 01 2021
Journal Name
Aip Conference Proceedings
Fabrication and characterization of zinc oxide nanorods coated by graphene oxide ZnO-NR@GO as a potential hybrid material photocatalyst
...Show More Authors

Hybrid architecture of ZnO nanorods/graphene oxide ZnO-NRs@GO synthesized by electrostatic self-assembly methods. The morphological, optical and luminescence characteristics of ZnO-NRs@GO and ZnO-NRs thin films have been described by FESEM, TEM, HRTEM, and AFM, which refers to graphene oxide have been coated ZnO-NRs with five layers. Here we synthesis ZnO-NRs@GO by simple, cheap and environmentally friendly method, which made it favorable for huge -scale preparation in many applications such as photocatalyst. ZnO-NRs@GO was applied as a photocatalyst Rodamin 6 G (R6G) dye from water using 532 nm diode laser-induced photocatalytic process. Overall degradation of R6G/ ZnO-NRs@GO was achieved after 90 minutes of laser irradiation while it ne

... Show More
View Publication
Scopus (4)
Scopus Crossref