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
Sat Aug 01 2020
Journal Name
International Journal Of Psychosocial Rehabilitation
Building and legalizing a test for evaluating the tactical learning of the footwork for the foil fencer in the fencing game
...Show More Authors

AA wahid, journal mustansiriyah of sports science, 2023

View Publication
Publication Date
Sun Dec 01 2019
Journal Name
Computers And Electronics In Agriculture
Meteorological data mining and hybrid data-intelligence models for reference evaporation simulation: A case study in Iraq
...Show More Authors

View Publication
Crossref (112)
Crossref
Publication Date
Thu Jun 26 2025
Journal Name
Plos One
Neurologists’ perspectives on management challenges and mitigation strategies for Parkinson’s disease patients: A qualitative study in Iraq
...Show More Authors

Background Parkinson’s disease (PD) is currently the fastest-growing neurological disorder in the world. Patients with PD face numerous challenges in managing their chronic condition, particularly in countries with scarce healthcare infrastructure. Objective This qualitative study aimed to delve into neurologists’ perspectives on challenges and gaps in the Iraqi healthcare system that influence the management of PD, as well as strategies to mitigate these obstacles. Method Semi-structured interviews were conducted with neurologists from five different Iraqi provinces, working in both hospitals and private neurology clinics, between November 2024 and January 2025. A thematic analysis approach was employed to identify the main challenge

... Show More
View Publication Preview PDF
Scopus Clarivate Crossref
Publication Date
Thu Sep 18 2025
Journal Name
Sustainable Engineering And Innovation
Using fruit fly and dragonfly optimization algorithms to estimate the Fama-MacBeth model
...Show More Authors

This research proposes the application of the dragonfly and fruit fly algorithms to enhance estimates generated by the Fama-MacBeth model and compares their performance in this context for the first time. To specifically improve the dragonfly algorithm's effectiveness, three parameter tuning approaches are investigated: manual parameter tuning (MPT), adaptive tuning by methodology (ATY), and a novel technique called adaptive tuning by performance (APT). Additionally, the study evaluates the estimation performance using kernel weighted regression (KWR) and explores how the dragonfly and fruit fly algorithms can be employed to enhance KWR. All methods are tested using data from the Iraq Stock Exchange, based on the Fama-French three-f

... Show More
View Publication
Crossref
Publication Date
Thu Apr 01 2021
Journal Name
Biochemical And Cellular Archives
STUDY OF LYSYL OXIDASE-1 AND KIDNEY FUNCTION IN SERA OF IRAQI PATIENTS WITH DIABETIC NEPHROPATHY
...Show More Authors

This study aimed to compare lysyl oxidase-1 level in diabetic patients with and without renal dysfunction, that LOX-1 may be an indicator for the early stage of diabetic nephropathy (DN). In addition to finding it is a relationship with kidney functions in Iraqi diabetic patients with and without renal dysfunction. Blood was obtained from 25 healthy individuals as a control group (G1), 25 diabetic patients with renal dysfunction, and 25 diabetic patients without renal dysfunction. Age range 40-60 years for all subjects. BMI (25-27) Kg/m2 . The serum was used for the analysis of LOX-1, FBG, urea, creatinine and uric acid. Whole blood is used for the determination of HbA1C. Results of FBG and HbA1C revealed a significant increase in G2 and G

... Show More
Publication Date
Wed Jan 13 2021
Journal Name
Palarch's Journal Of Archaeology Of Egypt / Egyptology
A WEIGHTED MEASUREMENT TO DIAGNOSED REASONS OF THE LOW SUCCESS RATIOS IN MATHEMATIC SUBJECT FOR THE THIRD INTERMEDIATE SCHOOLS AMONG A SAMPLE IN IRAQ
...Show More Authors

Objective: To suggest a weighted measure to diagnose the reasons for the low student success ratios in mathematics concerning the third grade of intermediate schools in light of components educational system represented by: [Students, Teachers, Curriculum, and Environmental reasons (others reasons)] assuming differentiated and interrelated components, Also the effectiveness forming of these components according to the gender variable. Methods: Data collection tools were prepared by constructing two questionnaires for each of (Students and Teachers), which included a number of items that involved some domains for studied components of educational system, which demonstrated a high level of validity and reliability in the pilot study, in addi

... Show More
View Publication Preview PDF
Publication Date
Wed Jul 01 2015
Journal Name
Journal Of Saudi Chemical Society
Synthesis, characterization and comparative study the microbial activity of some heterocyclic compounds containing oxazole and benzothiazole moieties
...Show More Authors

View Publication
Scopus (52)
Crossref (38)
Scopus Clarivate Crossref
Publication Date
Sun Jan 14 2024
Journal Name
Journal Of Al-rafidain University College For Sciences ( Print Issn: 1681-6870 ,online Issn: 2790-2293 )
Using Nonparametric Procedure to Develop an OCMT Estimator for Big Data Linear Regression Model with Application Chemical Pollution in the Tigris River
...Show More Authors

Chemical pollution is a very important issue that people suffer from and it often affects the nature of health of society and the future of the health of future generations. Consequently, it must be considered in order to discover suitable models and find descriptions to predict the performance of it in the forthcoming years. Chemical pollution data in Iraq take a great scope and manifold sources and kinds, which brands it as Big Data that need to be studied using novel statistical methods. The research object on using Proposed Nonparametric Procedure NP Method to develop an (OCMT) test procedure to estimate parameters of linear regression model with large size of data (Big Data) which comprises many indicators associated with chemi

... Show More
View Publication
Crossref
Publication Date
Sun Aug 13 2023
Journal Name
Arpn Journal Of Engineering And Applied Sciences
A NEW APPROACH FOR MODELLING THE VIBRATION OF BEAMS UNDER MOVING LOAD EFFECT
...Show More Authors

In this paper, a new equivalent lumped parameter model is proposed for describing the vibration of beams under the moving load effect. Also, an analytical formula for calculating such vibration for low-speed loads is presented. Furthermore, a MATLAB/Simulink model is introduced to give a simple and accurate solution that can be used to design beams subjected to any moving loads, i.e., loads of any magnitude and speed. In general, the proposed Simulink model can be used much easier than the alternative FEM software, which is usually used in designing such beams. The obtained results from the analytical formula and the proposed Simulink model were compared with those obtained from Ansys R19.0, and very good agreement has been shown. I

... Show More
View Publication Preview PDF
Scopus (1)
Scopus Crossref
Publication Date
Mon Aug 01 2011
Journal Name
Journal Of Engineering
DESIGN OF A CONTINUOUS SLIDING MODE CONTROLLER FOR THE ELECTRONIC THROTTLE VALVE SYSTEM
...Show More Authors

Lowering the emission, fuel economy and torque management are the essential
requirements in the recent development in the automobile industry. The main engine control
input that satisfies the above requirements is the throttling angle which adjusts the air mass
flow rate to the engine port. Due to the uncertainty and the presence of the nonlinear
components in its dynamical model, the sliding mode control theory is utilized in this work
for the throttle valve angle control system to design a robust controller for this system in the
presence of a nonlinear spring and Coulomb friction. A continuous sliding mode control law
which consists of a saturation function, instead of a signum function, and the integral of
ano

... Show More
View Publication Preview PDF
Crossref (2)
Crossref