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 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
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
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 (8)
Crossref
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 (17)
Scopus Clarivate Crossref
Publication Date
Sun Dec 01 2024
Journal Name
Journal Of Economics And Administrative Sciences
Nadaraya-Watson Estimation of a Circular Regression Model on Peak Systolic Blood Pressure Data
...Show More Authors

Purpose: The research aims to estimate models representing phenomena that follow the logic of circular (angular) data, accounting for the 24-hour periodicity in measurement. Theoretical framework: The regression model is developed to account for the periodic nature of the circular scale, considering the periodicity in the dependent variable y, the explanatory variables x, or both. Design/methodology/approach: Two estimation methods were applied: a parametric model, represented by the Simple Circular Regression (SCR) model, and a nonparametric model, represented by the Nadaraya-Watson Circular Regression (NW) model. The analysis used real data from 50 patients at Al-Kindi Teaching Hospital in Baghdad. Findings: The Mean Circular Erro

... Show More
View Publication Preview PDF
Crossref
Publication Date
Mon Feb 01 2021
Journal Name
Iop Conference Series: Materials Science And Engineering
On modelling and adaptive control of a linear smart beam model interacting with fluid
...Show More Authors
Abstract<p>This paper deals with modelling and control of Euler-Bernoulli smart beam interacting with a fluid medium. Several distributed piezo-patches (actuators and/or sensors) are bonded on the surface of the target beam. To model the vibrating beam properly, the effect of the piezo-patches and the hydrodynamic loads should be taken into account carefully. The partial differential equation PDE for the target oscillating beam is derived considering the piezo-actuators as input controls. Fluid forces are decomposed into two components: 1) hydrodynamic forces due to the beam oscillations, and 2) external (disturbance) hydrodynamic loads independent of beam motion. Then the PDE is discretized usi</p> ... Show More
View Publication
Crossref
Publication Date
Sun Sep 01 2019
Journal Name
Baghdad Science Journal
An Analysis of a Partial Temporary Immunity SIR Epidemic Model with Nonlinear Treatment Rate
...Show More Authors

     A partial temporary immunity SIR epidemic model involv nonlinear treatment rate is proposed and studied. The basic reproduction number  is determined. The local and global stability of all equilibria of the model are analyzed. The conditions for occurrence of local bifurcation in the proposed epidemic model are established. Finally, numerical simulation is used to confirm our obtained analytical results and specify the control set of parameters that affect the dynamics of the model.

View Publication Preview PDF
Scopus (11)
Crossref (4)
Scopus Clarivate Crossref
Publication Date
Mon Nov 06 2023
Journal Name
Communications In Mathematical Biology And Neuroscience
Effect of hunting cooperation and fear in a food chain model with intraspecific competition
...Show More Authors

Taking into account the significance of food chains in the environment, it demonstrates the interdependence of all living things and has economic implications for people. Hunting cooperation, fear, and intraspecific competition are all included in a food chain model that has been developed and researched. The study tries to comprehend how these elements affect the behavior of species along the food chain. We first examined the suggested model's solution properties before calculating every potential equilibrium point and examining the stability and bifurcation nearby. We have identified the factors that guarantee the global stability of the positive equilibrium point using the geometric approach. Additionally, the circumstances that would gu

... Show More
View Publication Preview PDF
Scopus (7)
Scopus Clarivate Crossref