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 Dec 27 2023
Journal Name
Journal Of Planner And Development
Priorities for the reconstruction of religious buildings in the old city of Mosul using Expert Choice program
...Show More Authors

This paper attempts to shed light on the most influential factors in the importance of religious buildings were destroyed because of the recent war due to the control of terrorist gangs of ISIS over the city of Mosul, and to prioritize their reconstruction and their role in reviving the historical center of Mosul.

The research’s problem emerged in the lack of knowledge about the identifying the most influential factors in the importance of religious buildings and utilizing them to prioritize their reconstruction. This study aims to analyze the factors influencing the importance of religious buildings using the Expert Choice software through the Analytic Hierarchy Process (AHP) to reach an analysis of their weights and propose p

... Show More
View Publication Preview PDF
Publication Date
Tue May 01 2018
Journal Name
Iop Conference Series: Materials Science And Engineering
Evaluation of Electromagnetic Near-Field Measurement Technique as Non-Destructive Testing for Composite Structures
...Show More Authors

View Publication
Scopus (3)
Crossref (3)
Scopus Clarivate Crossref
Publication Date
Thu Feb 15 2018
Journal Name
International Journal Of Architectural Heritage
Active use of panoramic mobile mapping systems for as built surveying and heritage documentation
...Show More Authors

View Publication
Scopus (11)
Crossref (9)
Scopus Clarivate Crossref
Publication Date
Sun Dec 06 2009
Journal Name
Baghdad Science Journal
Mean-field Solution of the mixed spin-1 and spin-5/2Ising system with different single-ion anisotropies
...Show More Authors

The mixed-spin ferrimagnetic Ising system consists of two-dimensional sublattices A and B with spin values and respectively .By used the mean-field approximation MFA of Ising model to find magnetism( ).In order to determined the best stabile magnetism , Gibbs free energy employ a variational method based on the Bogoliubov inequality .The ground-state (Phase diagram) structure of our system can easily be determined at , we find six phases with different spins values depend on the effect of a single-ion anisotropies .these lead to determined the second , first orders transition ,and the tricritical points as well as the compensation phenomenon .

View Publication Preview PDF
Crossref
Publication Date
Fri Aug 30 2024
Journal Name
Iraqi Journal Of Science
The Migration Effect on an Eco-toxicant Model
...Show More Authors

This paper proposes and studies an ecotoxicant system with Lotka-Volterra functional response for predation including prey protective region. The equilibrium points and the stability of this model have been investigated analytically both locally and globally. Finally, numerical simulations and graphical representations have been utilized to support our analytical findings

Scopus (2)
Scopus Crossref
Publication Date
Wed Jan 01 2020
Journal Name
Proceedings Of The 2020 2nd International Conference On Sustainable Manufacturing, Materials And Technologies
The food web prey-predator model with toxin
...Show More Authors

View Publication
Crossref (5)
Crossref
Publication Date
Wed Jul 13 2022
Journal Name
International Journal Of Health Sciences
Study of the reliability of serum vascular endothelial growth factor and its soluble receptor as markers of diabetic nephropathy in type 2 diabetes patients
...Show More Authors

The levels of circulating angiogenic and anti-angiogenic factors, namely vascular endothelial growth factor–A (VEGF-A) and soluble vascular endothelial growth factor receptor-1 (sVEGFR-1), have been linked to the development of renal dysfunction due to the proliferation of microvasculature within the kidneys of type 2 diabetic (T2DM) patients. The study aims to scrutinize serum levels of VEGF and sVEGFR-1 in a sample of Iraqi diabetic nephropathy patients to support their reliability as markers for the prediction of nephropathy in type 2 diabetes mellitus patients as well as to assess the ACE inhibitor’s effect on the levels of these two markers. Method: The ninety participants of this case-control study were split into three gr

... Show More
View Publication
Crossref
Publication Date
Fri May 31 2019
Journal Name
Journal Of Engineering
Geological Model of the Tight Reservoir (Sadi Reservoir-Southern of Iraq)
...Show More Authors

A3D geological model was constructed for Al-Sadi reservoir/ Halfaya Oil Field which is discovered in 1976 and located 35 km from Amara city, southern of Iraq towards the Iraqi/ Iranian borders.

Petrel 2014 was used to build the geological model. This model was created depending on the available information about the reservoir under study such as 2D seismic map, top and bottom of wells, geological data & well log analysis (CPI). However, the reservoir was sub-divided into 132x117x80 grid cells in the X, Y&Z directions respectively, in order to well represent the entire Al-Sadi reservoir.

Well log interpretation (CPI) and core data for the existing 6 wells were the basis of the petrophysical model (

... Show More
View Publication Preview PDF
Crossref (2)
Crossref
Publication Date
Tue Feb 16 2021
Journal Name
Applied Physics A
Widening of the optical band gap of CdO2(1-X)Al(X) thin films prepared by pulsed laser deposition
...Show More Authors

In this study, doped thin cadmium peroxide films were prepared by pulsed laser deposition with different doping concentrations of aluminium of 0.0, 0.1, 0.3, and 0.5 wt.% for CdO2(1-X)Al(X) and thicknesses in the range of 200 nm. XRD patterns suggest the presence of cubic CdO2 and the texture factor confirms that the (111) plane was the preferential growth plane, where the texture factor and the grain size decreased from 2.02 to 9.75 nm, respectively, in the pure sample to 1.88 and 5.65 nm, respectively, at a concentration of 0.5 wt%. For the predominant growth plane, the deviation of the diffraction angle Δθ and interplanar distance Δd from the standard magnitudes was 2.774° and 0.318 Å, respectively, for the pure sample decreased to

... Show More
View Publication
Scopus (3)
Crossref (2)
Scopus Clarivate Crossref
Publication Date
Wed Jun 24 2020
Journal Name
Systematic Reviews In Pharmacy
Studies on the Photostability of Polystyrene Films with New Metals Complex of 1, 2, 4-triazole-3-thione Derivate
...Show More Authors

The new complexes including Cu(II), Co(II), Ni(II), Pt(IV), and Pd(II) metals with 4,4'-(((1E,1'E)-1,4-phenylenebis(methaneylylidene))bis(azaneylylidene))bis(5-(4-chlorophenyl)-4H-1,2,4-triazole-3-thione) have been synthesized of utilizing us polystyrene (PS) photostability. The supplement (0,5 w / v%) was for the production of polystyrene ( PS) in the form of tetrahydrofuran (THF). Polystyrene films were exposing irradiation (250 – 380 nm) absorption light intensity of 6.02 x 10-9 ein dm-3 s-1 at room temperature, through the changes that occur to each of viscosity average molecular weight (Mv), main chain scission (S), degree of polymerization (DPn), weight loss %, hydroxyl index (lOH), carbonyl index (ICo) determined the photo stabiliz

... Show More
View Publication Preview PDF
Scopus (19)
Scopus