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
Fri Nov 01 2013
Journal Name
Journal Of Cosmetics, Dermatological Sciences And Applications
Podophyllin (10%) Ointment: A New Therapeutic Modality for Psoriasis
...Show More Authors

KE Sharquie, AA Noaimi, WK Al-Janabi, Journal of Cosmetics, Dermatological Sciences and Applications, 2013

View Publication
Publication Date
Sat Oct 01 2016
Journal Name
International Journal Of Pure And Apllied Mathematics
A SEMI ANALYTICAL ITERATIVE TECHNIQUE FOR SOLVING DUFFING EQUATIONS
...Show More Authors

View Publication
Crossref (13)
Crossref
Publication Date
Tue Jun 08 2021
Journal Name
Biomolecules
A Pan-Inhibitor for Protein Arginine Methyltransferase Family Enzymes
...Show More Authors

Protein arginine methyltransferases (PRMTs) play important roles in transcription, splicing, DNA damage repair, RNA biology, and cellular metabolism. Thus, PRMTs have been attractive targets for various diseases. In this study, we reported the design and synthesis of a potent pan-inhibitor for PRMTs that tethers a thioadenosine and various substituted guanidino groups through a propyl linker. Compound II757 exhibits a half-maximal inhibition concentration (IC50) value of 5 to 555 nM for eight tested PRMTs, with the highest inhibition for PRMT4 (IC50 = 5 nM). The kinetic study demonstrated that II757 competitively binds at the SAM binding site of PRMT1. Notably, II757 is selective for PRMTs over a panel of other methyltransferases, w

... Show More
View Publication
Scopus (19)
Crossref (21)
Scopus Clarivate Crossref
Publication Date
Wed Mar 29 2023
Journal Name
Iraqi Journal Of Chemical And Petroleum Engineering
A Review on Models for Evaluating Rock Petrophysical Properties
...Show More Authors

The evaluation of subsurface formations as applied to oil well drilling started around 50 years ago. Generally, the curent review articule includes all methods for coring, logging, testing, and sampling. Also the methods for deciphering logs and laboratory tests that are relevant to assessing formations beneath the surface, including a look at the fluids they contain are discussed. Casing is occasionally set in order to more precisely evaluate the formations; as a result, this procedure is also taken into account while evaluating the formations. The petrophysics of reservoir rocks is the branch of science interested in studying chemical and physical properties of permeable media and the components of reservoir rocks which are associated

... Show More
View Publication Preview PDF
Crossref (4)
Crossref
Publication Date
Mon Dec 03 2018
Journal Name
Journal Of Engineering
Variable Structure Control Design for a Magnetic Levitation System
...Show More Authors

In this paper the variable structure control theory is utilized to derive a discontinuous controller to the magnetic levitation system. The magnetic levitation system model is considered uncertain, which subjected to the uncertainty in system parameters, also it is open-loop unstable and strongly nonlinear. The proposed variable structure control to magnetic levitation system is proved, and the area of attraction is determined. Additionally, the chattering, which induced due to the discontinuity in control law, is attenuated by using a non-smooth approximate. With this approximation the resulted controller is a continuous variable structure controller with a determined steady state error according to the selected control

... Show More
View Publication Preview PDF
Crossref (1)
Crossref
Publication Date
Sat Jul 31 2021
Journal Name
Iraqi Journal Of Science
A Decision Tree-Aware Genetic Algorithm for Botnet Detection
...Show More Authors

     In this paper, the botnet detection problem is defined as a feature selection problem and the genetic algorithm (GA) is used to search for the best significant combination of features from the entire search space of set of features. Furthermore, the Decision Tree (DT) classifier is used as an objective function to direct the ability of the proposed GA to locate the combination of features that can correctly classify the activities into normal traffics and botnet attacks. Two datasets  namely the UNSW-NB15 and the Canadian Institute for Cybersecurity Intrusion Detection System 2017 (CICIDS2017), are used as evaluation datasets. The results reveal that the proposed DT-aware GA can effectively find the relevant features from

... Show More
Scopus (6)
Crossref (2)
Scopus Crossref
Publication Date
Tue Jan 01 2008
Journal Name
2008 15th Asia-pacific Software Engineering Conference
G2Way A Backtracking Strategy for Pairwise Test Data Generation
...Show More Authors

View Publication
Scopus (16)
Crossref (30)
Scopus Clarivate Crossref
Publication Date
Sun Oct 15 2023
Journal Name
Journal Of Yarmouk
Artificial Intelligence Techniques for Colon Cancer Detection: A Review
...Show More Authors

Publication Date
Tue Mar 30 2021
Journal Name
Baghdad Science Journal
Variant Domination Types for a Complete h-ary Tree
...Show More Authors

Graph  is a tool that can be used to simplify and solve network problems. Domination is a typical network problem that graph theory is well suited for. A subset of nodes in any network is called dominating if every node is contained in this subset, or is connected to a node in it via an edge. Because of the importance of domination in different areas, variant types of domination have been introduced according to the purpose they are used for. In this paper, two domination parameters the first is the restrained and the second is secure domination have been chosn. The secure domination, and some types of restrained domination in one type of trees is called complete ary tree  are determined.

View Publication Preview PDF
Scopus (18)
Crossref (2)
Scopus Clarivate Crossref
Publication Date
Wed Jul 06 2022
Journal Name
Journal Of Al-qadisiyah For Computer Science And Mathematics
Pixel Based Techniques for Gray Image Compression: A review
...Show More Authors

Currently, with the huge increase in modern communication and network applications, the speed of transformation and storing data in compact forms are pressing issues. Daily an enormous amount of images are stored and shared among people every moment, especially in the social media realm, but unfortunately, even with these marvelous applications, the limited size of sent data is still the main restriction's, where essentially all these applications utilized the well-known Joint Photographic Experts Group (JPEG) standard techniques, in the same way, the need for construction of universally accepted standard compression systems urgently required to play a key role in the immense revolution. This review is concerned with Different

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