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
Thu May 02 2013
Journal Name
Al-mustansiriyah
Synthesis, Spectroscopic and Biological Studies of a New some Complexes with N-Pyridine-2-Y1 methyl-benzene-1, 2-diamine.
...Show More Authors

Publication Date
Sun Dec 01 2019
Journal Name
Baghdad Science Journal
Preparation and Characterization of (Hyacinth plant / Chitosan) Composite as a Heavy Metal Removal
...Show More Authors

In this study, the preparation and characterization of hyacinth plant /chitosan composite, as a heavy metal removal, were done. Water hyacinth plant (Eichhorniacrasspes) was collected from Tigris river in Baghdad. The root and shoot parts of plant were ground to powder. Composite materials were prepared at different ratios of plant part (from 2.9% to 30.3%, wt /wt) which corresponds to (30-500mg) of hyacinth plant (root and shoot) and chitosan. The results showed that all examined ratios of plant parts have an excellent absorption to copper (Cu (II)). Moreover, it was observed that 2.9% corresponds (30mg) of plant root revealed highest removal (82.7%) of Pb (II), while 20.23% of shoot removed 61% of Cd (II) within 24 hr

... Show More
View Publication Preview PDF
Scopus (9)
Crossref (6)
Scopus Clarivate Crossref
Publication Date
Thu Apr 20 2023
Journal Name
Ibn Al-haitham Journal For Pure And Applied Sciences
A Brief Review: Some Interesting Methods of Synthesis Chromene Derivatives as Bioactive Molecules
...Show More Authors

Chromene is considered a fused pyran ring with a benzene ring, which is found in many plants and is part of many important compounds such as anthocyanidins, anthocyanins, catechins, and flavanones. These compounds are included under the headings "flavonoids" and "isoflavonoids." These compounds are well known as bioactive molecules with wide medicinal uses. According to these pharmacokinetic characteristics, many researchers are giving more attention to this type of compound and its derivatives. Many chromene derivatives have been synthesized to study their biological effects for the treatment of many diseases. Furthermore, the researcher displayed wide interest in finding new methods for synthesizing chromene derivatives. These met

... Show More
Crossref (7)
Crossref
Publication Date
Tue Jun 01 2021
Journal Name
International Journal Of Aquatic Sience
Helminths and their fish hosts as bioindicators of heavy metal pollution: A review
...Show More Authors

View Publication Preview PDF
Publication Date
Wed Jun 28 2017
Journal Name
Proceedings Of The 2017 Acm Conference On Innovation And Technology In Computer Science Education
Media Literacy as a By-Product of Collaborative Video Production by CS Students
...Show More Authors

Understanding, promoting, and teaching media literacy is an important societal challenge. STEM educators are increasingly looking to incorporate 21st century skills such as media literacy into core subject education. In this paper we investigate how undergraduate Computer Science (CS) students can learn media literacy as a by-product of collaborative video tutorial production. The paper presents a study of 34 third-year CS undergraduates who, as part of their learning, were each asked to produce three video tutorials on Raspberry Pi programming, using a collaborative video production tool for mobile phones (Bootlegger). We provide results of both quantitative and qualitative analysis of the production process and resulting video tutorials,

... Show More
View Publication
Scopus (20)
Crossref (16)
Scopus Clarivate Crossref
Publication Date
Sun Aug 01 2021
Journal Name
Journal Of Engineering
Reuse of Glass waste as a partial replacement to fine aggregates in concrete
...Show More Authors

As human societies grow, the problem of waste management becomes one of the pressing issues that need to be addressed. Recycling and reuse of waste are effective waste management measures that prevent pollution and conserve natural resources. In this study, the possibility of using glass waste as an alternative was used as a partial weight substitute for fine aggregates with replacement ratios of 10, 20, 30, and 40% by the weight, and formed into test models (15 cm * 15 cm ) cube and (15 cm * 30 cm) cylinder, then matured and tested their strength compression and tensile strength at the age of 7 and 28 days and compared with a reference or conventional concrete with a mixing ratio (1: 1.5: 3) as well as testing its worka

... Show More
View Publication Preview PDF
Crossref (4)
Crossref
Publication Date
Thu Aug 11 2022
Journal Name
Arabian Journal For Science And Engineering
Synthesis and Characterization of Novel Nano Azo Compounds as a New pH Sensor
...Show More Authors

View Publication
Scopus (7)
Crossref (3)
Scopus Clarivate Crossref
Publication Date
Thu Mar 07 2024
Journal Name
Problems Of Endocrinology
KI-67 as a predictive indicator of papillary thyroid cancer in Iraqi patients
...Show More Authors

BACKGROUND. KI-67 (MKI-67 in humans) is a protein able to bind to DNA which contributes to cell growth and cell proliferation. KI-67 is currently considered as a biomarker that is widely utilized as prognostic indicator for evaluating cell proliferation, diagnosing diseases, and conducting research. Several different kinds of cancer have high Ki-67 expression, which simplifying the choice of treatment for individuals with various cancer types.AIM. The objective was to evaluate the expression of KI67 in patients suffering papillary thyroid cancer (PTC) also the association between patients age and gender and KI67 expression.MATERIALS AND METHODS. To undertake an in-

... Show More
View Publication
Scopus (1)
Scopus Crossref
Publication Date
Mon Jan 01 2018
Journal Name
Ibn Al-haitham J. For Pure & Appl. Sci
Comparative Anatomical Study between Typhadomengensis and Phragmites communis
...Show More Authors

Both of the species Typha domengensis and Phragmites communis among the most important plant endemic in flora of Iraq from monocotyledon. Due to the similarity of the two species with each other in many morphological characteristics such as the environment where they live and the form of leaves and type of leaf venation and type of stomata….ets, also both of species belong to monocots plant therefore this research work was conducted find anatomical differences that have the same as taxonomic value to help distinguishing between both species under study. Through this research, we found great importance to the anatomical characteristics which we reached by studying the roots, stems and leaves sections f

... Show More
Publication Date
Sat Oct 28 2023
Journal Name
Baghdad Science Journal
Experimental Investigation of the Mechanical and Structural Properties of a Functionally Graded Material by Adding Alumina Nanoparticles Using A Centrifugal Technique
...Show More Authors

In this work, functionally graded materials were synthesized by centrifugal technique at different
volume fractions 0.5, 1, 1.5, and 2% Vf with a rotation speed of 1200 rpm and a constant rotation time, T
= 6 min . The mechanical properties were characterized to study the graded and non-graded nanocomposites
and the pure epoxy material. The mechanical tests showed that graded and non-graded added alumina
(Al2O3) nanoparticles enhanced the effect more than pure epoxy. The maximum difference in impact strength
occurred at (FGM), which was loaded from the rich side of the nano-alumina where the maximum value was
at 1% Vf by 133.33% of the sample epoxy side. The flexural strength and Young modulus of the fu

... Show More
View Publication Preview PDF
Scopus (5)
Crossref (2)
Scopus Crossref