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
Tue Oct 01 2019
Journal Name
2019 12th International Conference On Developments In Esystems Engineering (dese)
Structural Rehabilitation on Continuous Post-Tensioned Prestressed Concrete Box-Girder Bridge Exposed to Explosion: A Case Study
...Show More Authors

View Publication
Crossref (1)
Scopus Clarivate Crossref
Publication Date
Sun Feb 22 2026
Journal Name
Discover Public Health
Patients’ lived experiences, attitudes, and skills on insulin self-administration among diabetic patients: a cross-sectional study
...Show More Authors

View Publication Preview PDF
Scopus Crossref
Publication Date
Tue Dec 29 2020
Journal Name
Iraqi Journal Of Pharmaceutical Sciences ( P-issn 1683 - 3597 E-issn 2521 - 3512)
Medication Safety in Patients under 18 Years Old; a Retrospective Study based on Iraqi Pharmacovigilance Center Database
...Show More Authors

Medication safety is an important part of the comprehensive patient safety term. Medication safety is gaining more attention as the World Health Organization set the goal of decreasing medication harm by (50%) for the next 5 years when launching the third global challenge. Studying medication safety in the risk groups such as young ages, children are crucial to learn more about the effect of medicines in this risk group since they are not included in the clinical trials. Adverse drug reaction is defined as any harm resulted from the drug itself during medical process journey, while medication errors are any harm resulted from the treatment process rather than the drug or it is the result of the failure in a step of the treatment process

... Show More
View Publication Preview PDF
Crossref (1)
Scopus Crossref
Publication Date
Sat Jun 01 2019
Journal Name
Collegian
Medication adherence and predictive factors in patients with cardiovascular disease: A comparison study between Australia and Iraq
...Show More Authors

View Publication
Scopus (17)
Crossref (14)
Scopus Clarivate Crossref
Publication Date
Sun Sep 01 2024
Journal Name
International Immunopharmacology
Evaluating treatment effect on interferon-alpha in female patients with systemic lupus erythematosus: a case-control study
...Show More Authors

Evaluating treatment effect on interferon-alpha in female patients with systemic lupus erythematosus: a case-control study

Preview PDF
Scopus (1)
Scopus
Publication Date
Wed Oct 05 2022
Journal Name
Journal Of Basic Science
Loss in the Translation of Colour Euphemstic Expressions in the Qur’an: A Pragmatic Analysis
...Show More Authors

Publication Date
Mon May 11 2026
Journal Name
Journal Of Studies And Researches Of Sport Education
The impact of the V-shape strategy on learning basic skills in a breaststroke
...Show More Authors

View Publication
Publication Date
Mon Aug 01 2011
Journal Name
Journal Of Peptide Science
Studies on the antileishmanial properties of the antimicrobial peptides temporin A, B and 1Sa
...Show More Authors

Given the paucity and toxicity of available drugs for leishmaniasis, coupled with the advent of drug resistance, the discovery of new therapies for this neglected tropical disease is recognised as being of the utmost urgency. As such antimicrobial peptides (AMPs) have been proposed as promising compounds against the causative Leishmania species, insect vector-borne protozoan parasites. Here the AMP temporins A, B and 1Sa have been synthesised and screened for activity against Leishmania mexicana insect stage promastigotes and mammalian stage amastigotes, a significant cause of human cutaneous disease. In contrast to previous studies with other species the activity of these AMPs against L. mexicana amastigotes was low. This suggests that ama

... Show More
View Publication
Scopus (29)
Crossref (28)
Scopus Clarivate Crossref
Publication Date
Wed Jun 03 2020
Journal Name
Political Sciences Journal
The presidential system in Turkey between reality and challenges: a vision of the future
...Show More Authors

The nature of the political system of any country in the international system must have an impact on the policy of the State, whether in the interior or exterior, both regional and international, Turkey is one of the most important countries in the Middle East, which have a place and effectiveness on the surrounding environment, hence the importance of research lies in its political system and the transfer of power in it and its transformation from the form of the parliamentary system to the presidential system of the repercussions of the task and mutual effects between Turkey and the countries of the surrounding region in terms of the extent of achieving political stability in the Turkish interior or not and how this can be refl

... Show More
View Publication Preview PDF
Crossref
Publication Date
Sun Feb 03 2019
Journal Name
Journal Of The College Of Education For Women
Analysis of the clause relations in the presidential presuasion in a war against Iraq
...Show More Authors

0

View Publication Preview PDF