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 Mar 01 2023
Journal Name
Iraqi Journal Of Physics
Theoretical Computation of Electron Density in Laser-Induced Carbon Plasma using Anisimov Model
...Show More Authors

In this work, electron number density calculated using Matlab program code with the writing algorithm of the program. Electron density was calculated using Anisimov model in a vacuum environment. The effect of spatial coordinates on the electron density was investigated in this study. It was found that the Z axis distance direction affects the electron number density (ne). There are many processes such as excitation; ionization and recombination within the plasma that possible affect the density of electrons. The results show that as Z axis distance increases electron number density decreases because of the recombination of electrons and ions at large distances from the target and the loss of thermal energy of the electrons in

... Show More
View Publication Preview PDF
Crossref (1)
Crossref
Publication Date
Sun May 11 2025
Journal Name
Iraqi Statisticians Journal
Estimating General Linear Regression Model of Big Data by Using Multiple Test Technique
...Show More Authors

View Publication
Crossref
Publication Date
Wed Mar 01 2023
Journal Name
Iraqi Journal Of Physics
Theoretical Computation of Electron Density in Laser-Induced Carbon Plasma using Anisimov Model
...Show More Authors

In this work, electron number density calculated using Matlab program code with the writing algorithm of the program. Electron density was calculated using Anisimov model in a vacuum environment. The effect of spatial coordinates on the electron density was investigated in this study. It was found that the Z axis distance direction affects the electron number density (ne). There are many processes such as excitation; ionization and recombination within the plasma that possible affect the density of electrons. The results show that as Z axis distance increases electron number density decreases because of the recombination of electrons and ions at large distances from the target and the loss of thermal energy of the electrons in high distance

... Show More
Publication Date
Tue Sep 30 2025
Journal Name
Iraqi Journal Of Chemical And Petroleum Engineering
Oxidation desulfurization of model oil using carbon composite derived from peach stone waste
...Show More Authors

     In this study, oxidative desulfurization of dibenzothiophene (DBT) with H2O2 as an oxidant was studied, whereas the catalyst used was zirconium oxide supported on Activated carbon (AC). Zirconium oxide (ZrO2) was impregnated over prepared activated carbon (AC) and characterized by various techniques such as XRD, FTIR, BET, SEM, and EDX. This composite was used as a heterogeneous catalyst for oxidation desulfurization of simulated oil. The results of this study showed that ZrO2/AC composite exhibited significant catalytic activity and stability, effectively lowering sulfur content under mild conditions. Factors such as reaction temperature (30, 40, 50, 60°C), time (5, 10, 15,20,30,60, 80 100 min), catalyst dose (0.3, 0.5,

... Show More
View Publication
Crossref
Publication Date
Wed Jul 04 2018
Journal Name
Civil Engineering Journal
Finite Element Analysis of Concrete Beam under Flexural Stresses Using Meso-Scale Model
...Show More Authors

Two dimensional meso-scale concrete modeling was used in finite element analysis of plain concrete beam subjected to bending. The plane stress 4-noded quadrilateral elements were utilized to model coarse aggregate, cement mortar. The effect of aggregate fraction distribution, and pores percent of the total area – resulting from air voids entrapped in concrete during placement on the behavior of plain concrete beam in flexural was detected. Aggregate size fractions were randomly distributed across the profile area of the beam. Extended Finite Element Method (XFEM) was employed to treat the discontinuities problems result from double phases of concrete and cracking that faced during the finite element analysis of concrete beam. Crac

... Show More
Crossref (6)
Clarivate Crossref
Publication Date
Tue Sep 27 2022
Journal Name
Al–bahith Al–a'alami
POLITICAL DEBATES AND THEIR ARTISTIC CONSTRUCTION IN IRAQI SATELLITE CHANNELS ( AN ANALYTICAL STUDY ) : (A research drawn from a Master Thesis)
...Show More Authors

The problem of research on the study of political debate programs in the Iraqi satellite channels, in the "People decide" program by Afaq channel and " electoral competition " by Fallujah channel), and its importance for the community and researchers in the scientific field, as new programs to enter the Iraqi media after we have been the world media a lot in this area at the academic and practical levels (The field), and seeks to find out what the technical construction of the programs of political debates in Iraqi satellite channels and methods of construction and methods of employment used by the technical elements in the presentation of the programs and The study adopted the surve

... Show More
View Publication Preview PDF
Crossref
Publication Date
Sat Apr 01 2023
Journal Name
Alexandria Engineering Journal
Employing Sisko non-Newtonian model to investigate the thermal behavior of blood flow in a stenosis artery: Effects of heat flux, different severities of stenosis, and different radii of the artery
...Show More Authors

View Publication
Scopus (28)
Crossref (30)
Scopus Clarivate Crossref
Publication Date
Fri Aug 02 2024
Journal Name
Quantum Studies: Mathematics And Foundations
Implementation of a modified noise-free and noisy multistage quantum cryptography protocol using QISKIT
...Show More Authors

Classical cryptography systems exhibit major vulnerabilities because of the rapid development of quan tum computing algorithms and devices. These vulnerabilities were mitigated utilizing quantum key distribution (QKD), which is based on a quantum no-cloning algorithm that assures the safe generation and transmission of the encryption keys. A quantum computing platform, named Qiskit, was utilized by many recent researchers to analyze the security of several QKD protocols, such as BB84 and B92. In this paper, we demonstrate the simulation and implementation of a modified multistage QKD protocol by Qiskit. The simulation and implementation studies were based on the “local_qasm” simulator and the “FakeVigo” backend, respectively. T

... Show More
View Publication
Scopus (2)
Crossref (1)
Scopus Clarivate Crossref
Publication Date
Thu Jun 23 2022
Journal Name
American Scientific Research Journal For Engineering, Technology, And Sciences
A Review of TCP Congestion Control Using Artificial Intelligence in 4G and 5G Networks
...Show More Authors

In recent years, the field of research around the congestion problem of 4G and 5G networks has grown, especially those based on artificial intelligence (AI). Although 4G with LTE is seen as a mature technology, there is a continuous improvement in the infrastructure that led to the emergence of 5G networks. As a result of the large services provided in industries, Internet of Things (IoT) applications and smart cities, which have a large amount of exchanged data, a large number of connected devices per area, and high data rates, have brought their own problems and challenges, especially the problem of congestion. In this context, artificial intelligence (AI) models can be considered as one of the main techniques that can be used to solve ne

... Show More
View Publication
Publication Date
Fri Apr 29 2022
Journal Name
Iraqi Journal Of Agricultural Sciences
EFFECT OF SUPPLEMENTARY IRRIGATION SYSTEM ON WHEAT PRODUCTION EFFICIENCY USING A STOCHASTIC FRONTIER ANALYSIS
...Show More Authors

This study was aimed to director wheat production's technical efficiency grown under two irrigation systems(fixed and pivot sprinkler irrigation systems)using random border analysis.Samples were collected randomly from267farmers from Salah Al-Din Governorate/Iraq.The samples were divided into two groups;187farmers used a pivot sprinkler irrigation system with three categories of possession(80,60and120dunums),while the other group used a fixed sprinkler irrigation system with four categories of possession(40,30,20and10dunums).Transcendent production function was used to study the effect of production factors on wheat yield. The results indicated that the mechanization work and the amount of added irrigation water increased by 1% whil

... Show More
View Publication
Scopus (6)
Crossref (4)
Scopus Crossref