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
Wed Apr 01 2020
Journal Name
Civil Engineering Journal
Model Development for the Prediction of the Resilient Modulus of Warm Mix Asphalt
...Show More Authors

Increasing material prices coupled with the emission of hazardous gases through the production and construction of Hot Mix Asphalt (HMA) has driven a strong movement toward the adoption of sustainable construction technology. Warm Mix Asphalt (WMA) is considered relatively a new technology, which enables the production and compaction of asphalt concrete mixtures at temperatures 15-40 °C lower than that of traditional hot mix asphalt. The Resilient modulus (Mr) which can be defined as the ratio of axial pulsating stress to the corresponding recoverable strain, is used to evaluate the relative quality of materials as well as to generate input for pavement design or pavement evaluation and analysis. Based on the aforementioned preface, it is

... Show More
View Publication
Crossref (6)
Crossref
Publication Date
Sat Aug 01 2020
Journal Name
Journal Of Water Process Engineering
Humic acid coated sand as a novel sorbent in permeable reactive barrier for environmental remediation of groundwater polluted with copper and cadmium ions
...Show More Authors

Plantation of humic acid nanoparticles on the inert sand through simple impregnation to obtain the permeable reactive barrier (PRB) for treating of groundwater contaminated with copper and cadmium ions. The humic acid was extracted from sewage sludge which is byproduct of the wastewater treatment plant; so, this considers an application of sustainable development. Batch tests signified that the coated sand by humic acid (CSHA) had removal efficiencies exceeded 98 % at contact time, sorbent dosage, and initial pH of 1 h, 0.25 g/50 mL and 7, respectively for 10 mg/L initial concentration and 200 rpm agitation speed. Results proved that physicosorption was the predominant mechanism for metals-CSHA interaction because the sorption data followed

... Show More
View Publication
Crossref (34)
Crossref
Publication Date
Thu Mar 15 2018
Journal Name
Arab World English Journal
Pedagogical Stylistics as a Tool in the Classroom: An Investigation of EFL Undergraduate Students' Ability in Analyzing Poetic Language
...Show More Authors

View Publication
Crossref (1)
Crossref
Publication Date
Wed Jan 02 2019
Journal Name
Journal Of The College Of Languages (jcl)
Meanings of Colours as a Medium Reflecting the World Linguistic Image: Значение цветов как способ отражения языковой картины мира
...Show More Authors

 The paper sheds light on the meanings of colours as a significant  medium reflecting the world linguistic image which represents the culture of any country since language is closely related with culture. Language goes hand in hand with people's daily expressions, specifically those cultural ones. Language is a way to store historical and cultural information, and is a means of transferring the experience of a group to outside groups. 

The world linguistic image identifies the standards of human behavior in dependence upon the human view of the surrounding world, along with the type of behavior with which the world interacts and to whose challenges and effects it responds. So, multi-cultural people perceive the sam

... Show More
View Publication Preview PDF
Crossref
Publication Date
Thu Mar 01 2018
Journal Name
Arab World English Journal
Pedagogical Stylistics as a Tool in the Classroom: An Investigation of EFL Undergraduate Students' Ability in Analyzing Poetic Language
...Show More Authors

.

Publication Date
Wed Jan 30 2019
Journal Name
Journal Of The College Of Education For Women
The Impact of Applying Mind Mapping Technique as a Pre- Writing Tool on EFL College Students in Essay Writing
...Show More Authors

Based on the assumption that the more teachers know about brain science, the better
prepared they will be to make instructional decisions.
Mind Mapping is a powerful tool for assisting any form of writing. Language is an
important device and a very beneficial means for human being to communicate with other
people .Writing is one of the language skills that will never be left in education.
The study aims at investigating the Impact of applying mind mapping technique as a prewriting
tool on Iraqi EFL college students in essay writing. To do so, 60 EFL college students
were divided randomly selected and divided into two groups experimental and control. Prior
to treatment, participants of the both groups were given a

... Show More
View Publication Preview PDF
Publication Date
Mon Jan 01 2018
Journal Name
Journal Of Wildlife Diseases
MENINGEAL WORM (PARELAPHOSTRONGYLUS TENUIS) AS A CAUSE OF MORTALITY IN THE RESTORED ELK (CERVUS CANADENSIS) POPULATION IN MISSOURI, USA
...Show More Authors

View Publication Preview PDF
Scopus (10)
Crossref (9)
Scopus Clarivate Crossref
Publication Date
Sat Feb 01 2020
Journal Name
Iop Conference Series: Materials Science And Engineering
How geometric reverse engineering techniques can conserve our heritage; a case study in Iraq using 3D laser scanning
...Show More Authors
Abstract<p>Laser scanning has become a popular technique for the acquisition of digital models in the field of cultural heritage conservation and restoration nowadays. Many archaeological sites were lost, damaged, or faded, rather than being passed on to future generations due to many natural or human risks. It is still a challenge to accurately produce the digital and physical model of the missing regions or parts of our cultural heritage objects and restore damaged artefacts. The typical manual restoration can become a tedious and error-prone process; also can cause secondary damage to the relics. Therefore, in this paper, the automatic digital application process of 3D laser modelling of arte</p> ... Show More
View Publication
Scopus (9)
Crossref (5)
Scopus Clarivate Crossref
Publication Date
Fri Dec 01 2023
Journal Name
City And Environment Interactions
Towards local sustainability: A case study to evaluate outdoor urban spaces in Baghdad using physiological equivalent temperature index
...Show More Authors

View Publication
Scopus (8)
Crossref (8)
Scopus Clarivate Crossref
Publication Date
Sat Sep 30 2023
Journal Name
Iraqi Journal Of Chemical And Petroleum Engineering
Effect of Heterogeneity on Recovery Factor for Carbonate Reservoirs. A Case Study for Mishrif Formation in West Qurna Oilfield, Southern Iraq
...Show More Authors

Oil recovery could be impacted by the relation between vertical permeability (Kv) and horizontal permeability (Kh) (Kv/Kh). 4816 plugs that have been getting hold of 18 wells of Mishrif formation in the West Qurna oilfield were used. Kv/Kh data provided some scatter, but the mean is ~1. Kv/Kh =1 was used for the Petrel model before upscaling according to the heterogeneity of each layer.

Kv/Kh values for Mishrif Formation in West Qurna Oilfield are 0.8 for relatively homogeneous, 0.4 for heterogeneous rock, and 0.1 for cap rocks (CRII).

   Eclipse TM was used for reservoir simulation. PVT and SCAL data e

... Show More
View Publication Preview PDF
Crossref (16)
Crossref