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
Sun Feb 10 2019
Journal Name
Iraqi Journal Of Physics
Experimental study for the properties of Fe3O4 dusty plasma using the air in vacuum chamber system
...Show More Authors

In this work, we carried out an experimental study of thedusty
plasma by taking the dust material Fe3O4 with radius of the any grain
0.1μm - 0.5μm. In experiment we use air in the vacuum chamber
system under different low pressure (0.1-1) Torr. The results
illustrated that the present of dust particles in the air plasma did not
effect on Paschen minimum which is 0.5 without dust and with Fe3O4
dusty grains.
The effect of Fe3O4 dust particles on plasma parameters can be
notice in direct current system in glow discharge region. The plasma
parameters which were studied in this work represent plasma
potential, floating potential,electron saturation current, temperatu

... Show More
View Publication Preview PDF
Crossref
Publication Date
Thu Jun 28 2018
Journal Name
Journal Of The College Of Education For Women
The literature of the teacher and learner is a study in the light of “Holly Quran
...Show More Authors

Praise be to Allah, Lord of the Worlds, teach the pen, taught the human what he didn't know, Ihmad - Almighty - and thank him, and repent to him and ask forgiveness, which is the most forgiving, and bear witness that there is no god but Allah alone has no partner, gives and prevents, And I bear witness that Muhammad is  a slave to Allah  and his Messenger, who called for guidance and good speech and spoke, peace be upon him and his family and companions, and those who followed them until the Day of Judgment.

View Publication Preview PDF
Publication Date
Fri Jun 02 2023
Journal Name
East European Journal Of Physics
A Study of the Weakly Bound Structure of Nuclei Around the Magic Number N=50
...Show More Authors

An investigation of the quadrupole deformation of Kr, Sr, Zr, and Mo isotopes has been conducted using the HFB method and SLy4 Skyrme parameterization. The primary role of occupancy of single particle state 2d5/2 in the existence of the weakly bound structure around N=50 is probed. Shell gaps are performed using a few other calculations for the doubly magic number 100Sn using different Skyrme parameterizations. We explore the interplays among neutron pairing strength and neutron density profile in two dimensions, along with the deformations of 100Sn.

View Publication Preview PDF
Scopus (2)
Crossref (1)
Scopus Clarivate Crossref
Publication Date
Sun Jun 01 2014
Journal Name
Baghdad Science Journal
The role of TNF-? in the pathogenesis of multiple myeloma “a study in Iraqi patients”
...Show More Authors

During recent years, there has been an increasing interest in the investigation of the cytokines roles in pathogenesis of cancer, thus the study aimed at evaluating the level of tumor necrosis factor-alpha(TNF-?) in sera of Iraqi multiple myeloma (MM) patients. Beta 2-microglobulion (?2-m) was assessed to determine if there was any association between this cytokine and the level of ?2- m, as the latter is related to the stage of the disease. In addition, the age and gender were also taken into consideration. Furthermore, we investigated the relationship between IgG and TNF-? in sera of patients. 49 Iraqi patients (27 males and 22 females).The patients were also divided into two groups: the first group included (17) patients who were

... Show More
View Publication Preview PDF
Crossref
Publication Date
Thu Mar 09 2023
Journal Name
Tajseer Journal For Multidisciplinary Research And Studies
The General Principle Governing the Duty of Care – A Study in Light of English Law
...Show More Authors

The duty of care is the essence of the error of negligence under the English legal system, and without it, responsibility for negligence cannot be judged, regardless of the extent of the damage incurred. contained in English law. In view of the importance of proving the existence of the duty of care on the defendant so that it is possible to judge his responsibility for negligence, the need arises to find a general principle to which the defendant is subject in order to decide whether he owes the plaintiff with the duty of care and therefore responsible for the negligence, and this is what we will explain in the research topic the study.

View Publication
Publication Date
Fri Jan 01 2016
Journal Name
International Archives Of Medicine
The role of MRI in the diagnosis of intra articular knee derangement: A prospective study
...Show More Authors

View Publication Preview PDF
Crossref
Publication Date
Tue May 01 2018
Journal Name
Journal Of Physics: Conference Series
Performance of Case-Based Reasoning Retrieval Using Classification Based on Associations versus Jcolibri and FreeCBR: A Further Validation Study
...Show More Authors

View Publication Preview PDF
Scopus (5)
Crossref (1)
Scopus Clarivate Crossref
Publication Date
Mon Feb 01 2016
Journal Name
Journal Of Engineering
Deterioration Model for Sewer Network Asset Management in Baghdad City (case study Zeppelin line)
...Show More Authors

Asset management involves efficient planning of economic and technical performance characteristics of infrastructure systems. Managing a sewer network requires various types of activities so the network can be able to achieve a certain level of performance. During the lifetime of the network various components will start to deteriorate leading to bad performance and can damage the infrastructure. The main objective of this research is to develop deterioration models to provide an assessment tool for determining the serviceability of the sewer networks in Baghdad city the Zeppelin line was selected as a case study, as well as to give top management authorities the appropriate decision making. Different modeling techniques

... Show More
View Publication Preview PDF
Publication Date
Fri Jan 01 2016
Journal Name
Journal Of Cosmetics, Dermatological Sciences And Applications
Tuberculin as Intralesional Therapy for Viral Warts—Single-Blind, Split, Placebo, Controlled Study
...Show More Authors

View Publication
Crossref (3)
Crossref
Publication Date
Thu Jun 06 2013
Journal Name
Advances In Physics Theories And Applications
Adsorption study of Symmetrical schiff base ligand 4,4 -[hydrazine -1,2- diylidenebis ( methan-1-yl-1-ylidene) bis ( 2-methoxyphenol)] on Granulated Initiated calcined Iraqi …
...Show More Authors