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 Oct 02 2024
Journal Name
International Development Planning Review
THE EFFECT OF EXERCISES USING A MINI SQUASH COURT ON IMPROVING SOME MOTOR ABILITIES AND LEARNING SOME BASIC SKILLS FOR PLAYERS AGED 10-12 YEARS
...Show More Authors

Publication Date
Sat Feb 01 2020
Journal Name
Physics Of Fluids
Modeling the effects of slip on dipole–wall collision problems using a lattice Boltzmann equation method
...Show More Authors

We study the physics of flow due to the interaction between a viscous dipole and boundaries that permit slip. This includes partial and free slip, and interactions near corners. The problem is investigated by using a two relaxation time lattice Boltzmann equation with moment-based boundary conditions. Navier-slip conditions, which involve gradients of the velocity, are formulated and applied locally. The implementation of free-slip conditions with the moment-based approach is discussed. Collision angles of 0°, 30°, and 45° are investigated. Stable simulations are shown for Reynolds numbers between 625 and 10 000 and various slip lengths. Vorticity generation on the wall is shown to be affected by slip length, angle of incidence,

... Show More
View Publication
Scopus (14)
Crossref (13)
Scopus Clarivate Crossref
Publication Date
Thu Mar 01 2018
Journal Name
Case Studies In Thermal Engineering
The temperatures distributions of a single-disc clutches using heat partitioning and total heat generated approaches
...Show More Authors

View Publication
Scopus (40)
Crossref (37)
Scopus Clarivate Crossref
Publication Date
Sun Mar 17 2019
Journal Name
Baghdad Science Journal
Study of Aerodynamic Surface Roughness for Baghdad City Using Signal-Level Measurements
...Show More Authors

Roughness length is one of the key variables in micrometeorological studies and environmental studies in regards to describing development of cities and urban environments. By utilizing the three dimensions ultrasonic anemometer installed at Mustansiriyah university, we determined the rate of the height of the rough elements (trees, buildings and bridges) to the surrounding area of the university for a radius of 1 km. After this, we calculated the zero-plane displacement length of eight sections and calculated the length of surface roughness. The results proved that the ranges of the variables above are ZH (9.2-13.8) m, Zd (4.3-8.1) m and Zo (0.24-0.48) m.

View Publication Preview PDF
Scopus (11)
Crossref (3)
Scopus Clarivate Crossref
Publication Date
Tue Feb 10 2026
Journal Name
Journal Of Baghdad College Of Dentistry
Evaluation of the Efficiency of Three Different Obturation Techniques to Obturate the Isthmus Area of Roots Canals Prepared by Two Different Instrumentation Techniques (An In Vitro Study)
...Show More Authors

Background: The isthmus is a difficult area in the root canal complex to manage. The research aimed to evaluate the efficiency of three different obturation techniques (lateral condensation, EandQ (thermoplasticized gutta percha system) and Soft Core (thermoplasticized core carrier gutta percha system)) to obturate the isthmus area of roots prepared by two different instrumentation techniques (rotary ProTaper universal and ProTaper Next systems). Material and method: Sixty freshly extracted teeth were randomly divided into two main groups (A and B) of 30 teeth each. Group A was prepared by rotary ProTaper Universal whereas group B was prepared by ProTaper Next system. Each main group was then randomly subdivided into three subgroups of 10 t

... Show More
View Publication Preview PDF
Crossref
Publication Date
Tue Sep 08 2020
Journal Name
Baghdad Science Journal
Convergence Analysis for the Homotopy Perturbation Method for a Linear System of Mixed Volterra-Fredholm Integral Equations
...Show More Authors

           In this paper, the homotopy perturbation method (HPM) is presented for treating a linear system of second-kind mixed Volterra-Fredholm integral equations. The method is based on constructing the series whose summation is the solution of the considered system. Convergence of constructed series is discussed and its proof is given; also, the error estimation is obtained. Algorithm is suggested and applied on several examples and the results are computed by using MATLAB (R2015a). To show the accuracy of the results and the effectiveness of the method, the approximate solutions of some examples are compared with the exact solution by computing the absolute errors.

View Publication Preview PDF
Scopus (5)
Crossref (2)
Scopus Clarivate Crossref
Publication Date
Sun Sep 01 2013
Journal Name
Journal Of Economics And Administrative Sciences
Measurement of economic returns and environmental and social for green sector trade A prospective study in institutions of Basra to focus on the electricity sector
...Show More Authors

        Environmental risk growing Become challenge "and a matter of controversy and concern to many of those concerned with environment, social, economic, and the same happens with the administrative rather than in isolation for this movement, as the issues of climate change Disturbed and troubled him, especially after what caused the risk of destruction, and irresponsibility , chaos, and the futility of resources, crops, fields,  nature and homes and reactors, and after what happened in Japan from the scourge of "Hurricane tsunami " and earthquakes successive accompanied him and what became of him by surprise catastrophic affected the economy and the univ

... Show More
View Publication Preview PDF
Crossref
Publication Date
Mon Apr 04 2022
Journal Name
Journal Of Educational And Psychological Researches
The Role of a University Professor in the Development of Democracy with the Contents of a University Student in the Light of a Democratic Society
...Show More Authors

The current research aims to answer the following questions: what is the substance of democracy? What is the content of a democratic society? What is the role of university professor in the democratic development of the student university in light of the new Iraqi society? In order to achieve the goals of the research, the researcher developed an a questionnaire based on literature, Iraq's draft constitution in 2005, and his experience of the field of teaching human rights and public freedoms and the teaching of democracy. It was applied to a sample of faculty members in Department of Education and Psychology / College of Education / University Baghdad for the year 20014 were obtained their answers were then processed statistically. Henc

... Show More
View Publication Preview PDF
Publication Date
Sun May 02 2021
Journal Name
Journal Of Accounting And Financial Studies ( Jafs )
Application of banking institutions' governance variables and their impact on financial performance as measured by (ROA & ROE): an applied study on a sample of local Islamic banks listed on the Iraq Stock Exchange
...Show More Authors

The research seeks to achieve its goal of demonstrating the impact of applying banking governance variables on the financial performance of Islamic banks, and the independent research variables are represented by (X) by (the number of independent members in the board (X1), the number of directors in the board (X2), the number of committees emanating from the board ( X3), the percentage of shares owned by major shareholders in the board (X4), the number of members of the Sharia supervisory board (X5)), and the dependent variable (Y) is represented by (rate of return on assets (Y1), rate of return on equity (Y2)).

The research sample included (4) Islamic banks, namely (Iraqi Islamic Bank, National Islamic Bank, Jihan Islamic Bank,

... Show More
View Publication Preview PDF
Publication Date
Mon Mar 11 2019
Journal Name
Al-khwarizmi Engineering Journal
An Investigation Study of Tool Geometry in Single Point Incremental Forming (SPIF) and their effect on Residual Stresses Using ANOVA Model
...Show More Authors

Incremental forming is a flexible sheet metal forming process which is performed by utilizing simple tools to locally deform a sheet of metal along a predefined tool path without using of dies. This work presents the single point incremental forming process for producing pyramid geometry and studies the effect of tool geometry, tool diameter, and spindle speed on the residual stresses. The residual stresses were measured by ORIONRKS 6000 test measuring instrument. This instrument was used with four angles of (0º,15º,30º, and 45º) and the average value of residual stresses was determined, the value of the residual stress in the original blanks was (10.626 MPa). The X-ray diffraction technology was used to measure the residual stresses

... Show More
View Publication Preview PDF
Crossref (1)
Crossref