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
Mon Jul 01 2019
Journal Name
Journal Of Educational And Psychological Researches
The Impact of Strategy 3-2-1 in acquiring Concepts of Sociology of fourth grade students: The Impact of Strategy 3-2-1 in acquiring Concepts of Sociology of fourth grade students
...Show More Authors

 

Abstract

The current research aims to identify the impact of triangular bridging strategy in the acquisition of sociology of fourth-stage students. To achieve the research objective, the following null hypotheses were adopted: there are no statistically significant differences at a significance level (0, 05) between the average grades of the experimental group students who studied the triangular bridging strategy in acquiring concepts of sociology and average grades of the control group. The researcher has selected the fourth-stage students from Alexandronah School for girls that s related to the Directorate General of Baghdad the sample consisted of (87) students at litera

... Show More
View Publication 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
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
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
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 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 Aug 30 2016
Journal Name
Mechanical Engineering
The Effect of Different Furrow Depths and Speeds of Machinary Units Using A Locally Assembled Combine Implement on Planting Maize
...Show More Authors

View Publication
Publication Date
Thu Aug 04 2022
Journal Name
Journal Of Nanomaterials
Thermal Management of the Melting Process in a Latent Heat Triplex Tube Storage System Using Different Configurations of Frustum Tubes
...Show More Authors

In this study, the energy charging mechanism is mathematically modeled to determine the impact of design modifications on the thermofluidic behavior of a phase change material (PCM) filled in a triplex tube containment geometry. The surface area of the middle tube, where the PCM is placed, is supported by single or multi-internal frustum tubes in vertical triplex tubes to increase the performance of the heating and cooling of the system. In addition to the ordinary straight triplex tubes, three more scenarios are considered: (1) changing the middle tube to the frustum tube, (2) changing the inner tube to the frustum tube, and (3) changing both the internal and central tubes to the frustum tubes. The impact of adopting the tube desig

... Show More
View Publication
Scopus (52)
Crossref (48)
Scopus Clarivate Crossref
Publication Date
Sun Nov 23 2025
Journal Name
Journal Of Physical Education
The effect of special exercises using a designer device and added relative weights to develop some of the physical abilities of volleyball players
...Show More Authors

View Publication
Publication Date
Sun Dec 31 2023
Journal Name
Sumer Journal For Pure Science
COVID-19Disease Diagnosis using Artificial Intelligence based on Gene Expression: A Review
...Show More Authors