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 Jan 01 2022
Journal Name
Journal Of Engineering
A Five Variable Refined Plate Theory For Thermal Buckling Analysis Uniform And Nonuniform Of Cross-Ply Laminated Plates
...Show More Authors

This research is devoted to investigating the thermal buckling analysis behaviour of laminated composite plates subjected to uniform and non-uniform temperature fields by applying an analytical model based on a refined plate theory (RPT) with five unknown independent variables. The theory accounts for the parabolic distribution of the transverse shear strains through the plate thickness and satisfies the zero-traction boundary condition on the surface without using shear correction factors; hence a shear correction factor is not required. The governing differential equations and associated boundary conditions are derived by using the virtual work principle and solved via Navier-type analytical procedure to obtain critica

... Show More
View Publication Preview PDF
Crossref
Publication Date
Mon Oct 01 2018
Journal Name
Journal Of Petroleum Science And Engineering
Operation of a MEG pilot regeneration system for organic acid and alkalinity removal during MDEA to FFCI switchover
...Show More Authors

View Publication
Scopus (14)
Crossref (13)
Scopus Clarivate Crossref
Publication Date
Wed Dec 13 2017
Journal Name
Al-khwarizmi Engineering Journal
Design of a Kinematic Neural Controller for Mobile Robots based on Enhanced Hybrid Firefly-Artificial Bee Colony Algorithm
...Show More Authors

The paper present design of a control structure that enables integration of a Kinematic neural controller for trajectory tracking of a nonholonomic differential two wheeled mobile robot, then  proposes a Kinematic neural controller to direct a National Instrument mobile robot (NI Mobile Robot). The controller is to make the actual velocity of the wheeled mobile robot close the required velocity by guarantees that the trajectory tracking mean squire error converges at minimum tracking error. The proposed tracking control system consists of two layers; The first layer is a multi-layer perceptron neural network system that controls the mobile robot to track the required path , The second layer is an optimization layer ,which is impleme

... Show More
View Publication Preview PDF
Publication Date
Mon Apr 13 2026
Journal Name
Innovative Infrastructure Solutions
Beyond empiricism: a unified physics-based framework for resonance avoidance and carbon-efficient mass optimization of machine foundations
...Show More Authors

Dynamic machine foundations can be considered as a necessary component of the industrial infrastructure. Design of the dynamic equipment foundations has, however, traditionally been grounded on a rule of thumb that is inaccurate and rigid to use at the discretion of the engineers. The conventional rule of thumb, which includes minimum weight ratios and resonance avoidance criteria, has been used singularly with two poles, which can be either conservatively designed systems that are too heavy, or systems that are going to experience too much vibration and fatigue. This paper presents a novel, analytical framework for the reinterpretation of traditional design practices, using a physics-based approach, and results in a single, unified overall

... Show More
View Publication
Scopus Crossref
Publication Date
Sat Jun 01 2024
Journal Name
Results In Engineering
Electrochemical preparation and characterization of a new configuration SnO2 anode and its application for treating petroleum refinery wastewater
...Show More Authors

View Publication
Scopus (8)
Crossref (6)
Scopus Clarivate Crossref
Publication Date
Sun Oct 29 2023
Journal Name
Iraqi National Journal Of Nursing Specialties
A Survey of Diabetes Mellitus in a Sample of Children below 15 Years Attending Child Welfare Hospital
...Show More Authors

Objectives: Determine the age and gender distribution of children who experience diabetes mellitus (DM) under
the age of 15 years and the presence of some associated factors that might be a predisposing factor for the
disease including obesity.
Methodology: A cross-sectional study was conducted at diabetic clinic in Children Welfare Teaching Hospital
in Baghdad City during 2006. The study sample included diabetic children less than 15 years of age. Data were
taken from the patients' record and by direct interview with the patients' parents. Information included
demographic data, as well as past history of the patient and his/her family relative to diabetes and other immune
diseases.
Results: Data analysis showed t

... Show More
View Publication Preview PDF
Publication Date
Sun Sep 01 2019
Journal Name
مجلة بحوث
The role of university in promoting the culture of volunteering among students (Mustansiriya University Model)
...Show More Authors

Abstract The aim of this study is to identify the role played by the university in reinforcing the culture of voluntary work in college students and sequencing these roles according to their priority. To achieve this aim, the researcher used the descriptive approach. After being informed of the literature background and of the previous studies related to the core aim of this recent study, the researcher has built up a questionnaire of (20) items investigating the role of university in reinforcing the culture of voluntary work in the college students. The standardized features of the questionnaire have been checked for the purpose of the questionnaire validity (virtual and constructive validity) and stability (reconstruction and Cronbach's A

... Show More
View Publication
Publication Date
Thu Dec 14 2023
Journal Name
Malaysian Journal Of Mathematical Sciences
The Effect of Alternative Resource and Refuge on the Dynamical Behavior of Food Chain Model
...Show More Authors

This article examines and proposes a dietary chain model with a prey shelter and alternative food sources. It is anticipated that mid-predators' availability is positively correlated with the number of refuges. The solution's existence and exclusivity are examined. It is established that the solution is bounded. It is explored whether all potential equilibrium points exist and are locally stable. The Lyapunov approach is used to investigate the equilibrium points' worldwide stability. Utilizing a Sotomayor theorem application, local bifurcation is studied. Numerical simulation is used to better comprehend the dynamics of the model and define the control set of parameters.

View Publication
Scopus (12)
Crossref (5)
Scopus Clarivate Crossref
Publication Date
Tue Sep 08 2020
Journal Name
Baghdad Science Journal
Radiological Impact Assessment of Farm Soils and Ofada rice (Oryza sativa japonica) from Three Areas in Nigeria
...Show More Authors

Oryza sativa japonica (ofada rice) is largely grown in Aramoko, Abakaliki and Ofada are communities and consumed by both the poor and rich in Nigeria. A total of twenty ofada rice farmlands were identified in each study area and rice samples were randomly collected, thoroughly mixed to make a representative sample from each farmland. Soil samples were collected in each farm to a depth of 5-15cm from at least eight different points and thoroughly mixed together to form a representative sample. The samples were thereafter taken to the laboratory for preparation and spectroscopic analysis. A well-calibrated NaI(Tl) gamma-ray detector was used in spectrometric analysis of the samples and descriptive statistics was used to analyze th

... Show More
View Publication Preview PDF
Scopus (10)
Crossref (6)
Scopus Clarivate Crossref
Publication Date
Fri Apr 19 2019
Journal Name
Plant Archives
NEW INTERESTING RECORDS OF THREE SPECIES FROM PEZIZACEAE AND PYRONEMATACEAE FAMILIES (PEZIZALEA, ASCOMYCOTA) TO KURDISTAN REGION – IRAQ
...Show More Authors

The survey was carried out From January to April of 2018 on macrofungi samples collected from different places in Halabja province located in north eastern parts of Iraq-Kurdistan region. This region is rich in forest trees and pasture lands with diversity of shrubs and herbs and is expected to support the growth of several macro fungal species. However, this part of Kurdistan in Iraq is still unexplored from macrofungal point of view. In this paper three species from Pezizaceae and Pyronemataceae families that belonging to (Pezizales, Ascomycota), were reported from Iraqi Kurdistan. These macrofungal species are recorded for the first time from Iraq. Also the species were identified and showing their locations distributed on a map prepared

... Show More