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 Jun 28 2025
Journal Name
Journal Of Physical Education
The effect of using the strategy Learning by playing for some skills handball patting According to the curriculum for female students Second stage, College of Physical Education and Sports Sciences, University of Baghdad
...Show More Authors

The aim of the research was to identify  On the effect of the learning-by-play strategy on learning some handball skills among second-stage female students,Comparing the results of students' performance before and after implementing the learning by playing strategy,Providing development proposals for teaching handball skills in light of the research results.,I dependresearcherCurriculumexperimentalIn research procedures as an appropriate approach to achieving research objectives,For two groups, one experimental and the other control,Community of female studentsSecondFor the academic year 2024-2025, consisting of (4Female people (numbering)151) StudentChosen.Research sample30 female students from Section (B) were selected and (4) fe

... Show More
View Publication
Crossref
Publication Date
Sat Feb 01 2014
Journal Name
Journal Of Economics And Administrative Sciences
Distribution of Municipal Services and Some Factors Affecting Them (A survey in a sample of districts from Rushed municipal in Baghdad)
...Show More Authors

s The study aims to identify the fairness in the distribution of municipal services between  municipal districts and areas, from point of view  of municipal chamber staff and from the point of view of the citizen. It also aims to identify factors affecting the fairness of the distribution of municipal services. Municipal services were being studied : hygiene and waste, water supply, sewer, creating gardens,  and street paving .Factors which  examined its impact on municipal services are: resources available to municipal chamber, the managerial  process at municipal chamber,  and factors in the external environment surrounding  municipal chamber.The results of the study showed that level of the e

... Show More
View Publication Preview PDF
Crossref (1)
Crossref
Publication Date
Wed Nov 24 2021
Journal Name
International Journal Of Differential Equations
The Impact of Media Coverage and Curfew on the Outbreak of Coronavirus Disease 2019 Model: Stability and Bifurcation
...Show More Authors

In this study, the spreading of the pandemic coronavirus disease (COVID-19) is formulated mathematically. The objective of this study is to stop or slow the spread of COVID-19. In fact, to stop the spread of COVID-19, the vaccine of the disease is needed. However, in the absence of the vaccine, people must have to obey curfew and social distancing and follow the media alert coverage rule. In order to maintain these alternative factors, we must obey the modeling rule. Therefore, the impact of curfew, media alert coverage, and social distance between the individuals on the outbreak of disease is considered. Five ordinary differential equations of the first-order are used to represent the model. The solution properties of the system ar

... Show More
View Publication
Scopus (7)
Crossref (2)
Scopus Clarivate Crossref
Publication Date
Sun Jul 01 2018
Journal Name
Journal Of Educational And Psychological Researches
The effect of constructivist model of yager in acquiring the geographical concepts among first intermediate students in geography
...Show More Authors

The purpose of the study is to investigate the effect of the constructivist model of yager in acquiring the geographical concepts among first intermediate students in geography. The study was carried on based on the null hypothesis, which states, there is no significant difference at the level of (0.05) between the experimental group that follows yager model in learning the principles of geography, and the control group that studies the same subject considering the traditional methods of learning, the. To do so, a sample of (70) first-intermediate student were chosen purposefully from two random class for the academic year (2016-2017) divided into two groups. The selected schools located at Al-rusafa side in the city of Baghdad, as well

... Show More
View Publication Preview PDF
Publication Date
Sun Sep 03 2017
Journal Name
Baghdad Science Journal
Synthesis, Spectroscopic Studies and Biological Activities of Mixed Metal (III) Complexes of Uracil with 1, 10-Phenanthroline
...Show More Authors

New complexes of the [M(Ura)(Phen)(OH2)Cl2]Cl.2H2O type, where (Ura) uracil ; (Phen) 1,10-phenanthroline hydrate; M (Cr+3 , Fe+3 and La+3) were synthesized from mix ligand and characterized . These complexes have been characterized by the elemental micro analysis, spectral (FT-IR., UV-Vis, 1HNMR, 13CNMR and Mass) and magnetic susceptibility as well the molar conductive mensuration. Cr+3, Fe+3 and La+3- complexes of six–coordinated were proposed for the insulated for three metal(III) complexes for molecular formulas following into uracil property and 1,10-phenanthroline hydrate present . The proposed molecular structure for all metal (III) complexes is octahedral geometries .The biological activity was tested of metal(III) salts, liga

... Show More
View Publication Preview PDF
Scopus (4)
Crossref (1)
Scopus Crossref
Publication Date
Sun Sep 03 2017
Journal Name
Baghdad Science Journal
Synthesis, Spectroscopic Studies and Biological Activities of Mixed Metal (III) Complexes of Uracil with 1, 10-Phenanthroline
...Show More Authors

New complexes of the [M(Ura)(Phen)(OH2)Cl2]Cl.2H2O type, where (Ura) uracil ; (Phen) 1,10-phenanthroline hydrate; M (Cr+3 , Fe+3 and La+3) were synthesized from mix ligand and characterized . These complexes have been characterized by the elemental micro analysis, spectral (FT-IR., UV-Vis, 1HNMR, 13CNMR and Mass) and magnetic susceptibility as well the molar conductive mensuration. Cr+3, Fe+3 and La+3- complexes of six–coordinated were proposed for the insulated for three metal(III) complexes for molecular formulas following into uracil property and 1,10-phenanthroline hydrate present . The proposed molecular structure for all metal (III) complexes is octahedral geometries .The biological activity was tested of metal(III) salts, ligands

... Show More
Scopus (4)
Crossref (1)
Scopus Crossref
Publication Date
Sat Oct 01 2022
Journal Name
Baghdad Science Journal
The Role of Serum Chitinase-3-Like 1 Protein (YKL-40) Level and its Correlation with Proinflammatory Cytokine in Patients with Rheumatoid Arthritis
...Show More Authors

Chitinase-3-like 1 protein (YKL-40) is a glycoprotein primarily produced in the arthritic joint and plays a crucial role in inflammatory processes. The aim of the study is to establish the role of YKL-40 as a biomarker for rheumatoid arthritis (RA) compared to proinflammatory biomarkers and disease activity. The study included 58 patients and 18 control. Diseases activity score (DAS-28) and clinical disease activity index (CDAI) were measured. Serum level of YKL-40, tumor necrosis factor-α (TNF-α), interleukin-1B (IL-1β), erythrocyte sedimentation (ESR), rheumatoid factor (RF), C-reactive protein (CRP), and anti-citrullinated protein antibody (ACPA) were assessed. The results showed that the median serum YKL-40 level which was 5.42 

... Show More
View Publication Preview PDF
Scopus (15)
Crossref (8)
Scopus Clarivate Crossref
Publication Date
Tue Jul 01 2025
Journal Name
Journal Of Studies In Humanities And Educational Sciences
The Effect of the Needham Constructivist Model on the Achievement of Third Year Biology Department Students in the Subject of Teaching Methods
...Show More Authors

The current research aims to know the effect of Needham's constructivist model on the achievement of third-year students in the Life Sciences Department in the teaching methods subject. To achieve the research objectives, the experimental method was followed for the experimental and control groups with dimensional measurement of the achievement variable of the teaching methods subject. The research sample included (62) students in the third year of the Life Sciences Department, distributed into two equal groups in the variables (self-assessment of learning methods - chronological age in years - intelligence level - previous information). To measure the level of students' achievement, an achievement test was constructed consisting of (40) te

... Show More
Publication Date
Sun Jun 05 2016
Journal Name
Baghdad Science Journal
Synthesis, Characterization of some New 1, 3, 4-Oxadiazole derivatives based on 4- amino benzoic acid
...Show More Authors

In this research various of 2,5-disubstituted 1,3,4-oxadiazole (Schiff base, oxo-thiazolidine , and other compounds) were synthesized from 2,5-di(4,4?- amino-1,3,4-oxadiazole ) which use quently synthesized from mixture of 4-amino benzoic acid and hydrazine in the presence of polyphosphorus acid. The synthesized compounds were characterized by using some Spectral data (UV, FT-IR, and 1H-NMR).

View Publication Preview PDF
Crossref
Publication Date
Fri Jan 01 2016
Journal Name
The Journal Of The College Of Basic Education
Polymorphism of IL-4 -590 (C>T) gene in Iraqi children with Type 1 Diabetes Mellitus
...Show More Authors

This study included 50 blood serum samples that collected from children with age ranged between 7-12 years. Thirty five samples collected from children with Type 1 Diabetes Mellitus (T1D), and 15 blood serum samples collected from healthy children as a control sample. The polymorphism of IL-4 -590 (C>T) gene, which amplified by using amplification refractory mutation system (ARMS-PCR) was showed high percentage of C allele frequency in T1D patients sample in comparison with T allele frequency, and the C allele revealed as etiological faction with risk by having T1D disease, whereas the T allele showed high frequency from the C allele frequency in control sample, and the T allele revealed as preventive faction from infection by this disease.

... Show More
Preview PDF