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 Jun 01 2016
Journal Name
Journal Of Engineering
A Novel Analytical Model to Design Piezoelectric Patches Used to Repair Cracked Beams
...Show More Authors

In this paper, an analytical solution describing the deflection of a cracked beam repaired with piezoelectric patch is introduced. The solution is derived using perturbation method. A novel analytical model to calculate the proper dimensions of piezoelectric patches used to repair cracked beams is also introduced. This model shows that the thickness of the piezoelectric patch depends mainly on the thickness of the cracked beam, the electro-mechanical properties of the patch material, the applied load and the crack location. Furthermore, the model shows that the length of the piezoelectric patches depends on the thickness of the patch as well as it depends on the length of the cracked beam and the crack depth. The additional flexibil

... Show More
View Publication Preview PDF
Crossref (6)
Crossref
Publication Date
Sat Jul 01 2023
Journal Name
Journal Of Engineering
Toward Improving BIM Acceptance in FM: A Conceptual Model Integrating TTF and TAM
...Show More Authors

Substantial research has been performed on Building Information Modeling (BIM) in various topics, for instance, the use and benefit of BIM in design, construction, sustainable environment building, and Facility assets over the past several years. Although there are various studies on these topics, Building Information Modeling (BIM) awareness through facilities management is still relatively poor. The researcher's interest is increased in BIM study is based heavily upon the perception that it can facilitate the exchange and reuse of information during various project phases. This property and others can be used in the Iraqi Construction industry to motivate the government to eliminate the change resistance to use innovat

... Show More
View Publication Preview PDF
Crossref (1)
Crossref
Publication Date
Tue Sep 10 2019
Journal Name
Periodicals Of Engineering And Natural Sciences (pen)
A classification model on tumor cancer disease based mutual information and firefly algorithm
...Show More Authors

View Publication
Scopus (15)
Crossref (6)
Scopus Crossref
Publication Date
Wed Jun 01 2016
Journal Name
Journal Of Engineering
A Novel Analytical Model to Design Piezoelectric Patches Used to Repair Cracked Beams
...Show More Authors

In this paper, an analytical solution describing the deflection of a cracked beam repaired with piezoelectric patch is introduced. The solution is derived using perturbation method. A novel analytical model to calculate the proper dimensions of piezoelectric patches used to repair cracked beams is also introduced. This model shows that the thickness of the piezoelectric patch depends mainly on the thickness of the cracked beam, the electro-mechanical properties of the patch material, the applied load and the crack location. Furthermore, the model shows that the length of the piezoelectric patches depends on the thickness of the patch as well as it depends on the length of the cracked beam and the crack depth. The additio

... Show More
View Publication Preview PDF
Publication Date
Sat Jun 04 2022
Journal Name
Al–bahith Al–a'alami
paratexte in specialized literary journals : AL ADEEB AL IRAQI magazine is a model
...Show More Authors

Post-structural critical studies highlighted the importance of studying the texts surrounding the text as an important part in the process of receiving and understanding texts, and although this topic was dealt with by the ancient Arabs and Europeans, interest in it appeared clearly after the appearance of Gerard Genet's book (SEUILS), which separated it Text Thresholds. Or what he called paratexte, and dealt with them with interest as he reads them on books. With the development of semiotic studies, interest in paratexte studies began in a broader way and in various literary and non-literary texts, including journalistic texts. And since specialized magazines are one of the press releases that enjoy their privacy in terms of topics and

... Show More
View Publication Preview PDF
Crossref
Publication Date
Wed Jun 03 2020
Journal Name
Journal Of Applied Mathematics
Order and Chaos in a Prey-Predator Model Incorporating Refuge, Disease, and Harvesting
...Show More Authors

In this paper, a mathematical model consisting of a prey-predator system incorporating infectious disease in the prey has been proposed and analyzed. It is assumed that the predator preys upon the nonrefugees prey only according to the modified Holling type-II functional response. There is a harvesting process from the predator. The existence and uniqueness of the solution in addition to their bounded are discussed. The stability analysis of the model around all possible equilibrium points is investigated. The persistence conditions of the system are established. Local bifurcation analysis in view of the Sotomayor theorem is carried out. Numerical simulation has been applied to investigate the global dynamics and specify the effect

... Show More
View Publication Preview PDF
Scopus (9)
Crossref (4)
Scopus Clarivate Crossref
Publication Date
Wed Jun 15 2022
Journal Name
Journal Of Sensors
A Modern Approach towards an Industry 4.0 Model: From Driving Technologies to Management
...Show More Authors

Every so often, a confluence of novel technologies emerges that radically transforms every aspect of the industry, the global economy, and finally, the way we live. These sharp leaps of human ingenuity are known as industrial revolutions, and we are currently in the midst of the fourth such revolution, coined Industry 4.0 by the World Economic Forum. Building on their guideline set of technologies that encompass Industry 4.0, we present a full set of pillar technologies on which Industry 4.0 project portfolio management rests as well as the foundation technologies that support these pillars. A complete model of an Industry 4.0 factory which relies on these pillar technologies is presented. The full set of pillars encompasses cyberph

... Show More
View Publication
Scopus (101)
Crossref (89)
Scopus Clarivate Crossref
Publication Date
Wed Aug 28 2024
Journal Name
Mesopotamian Journal Of Cybersecurity
A Novel Anomaly Intrusion Detection Method based on RNA Encoding and ResNet50 Model
...Show More Authors

Cybersecurity refers to the actions that are used by people and companies to protect themselves and their information from cyber threats. Different security methods have been proposed for detecting network abnormal behavior, but some effective attacks are still a major concern in the computer community. Many security gaps, like Denial of Service, spam, phishing, and other types of attacks, are reported daily, and the attack numbers are growing. Intrusion detection is a security protection method that is used to detect and report any abnormal traffic automatically that may affect network security, such as internal attacks, external attacks, and maloperations. This paper proposed an anomaly intrusion detection system method based on a

... Show More
View Publication
Scopus (5)
Scopus Crossref
Publication Date
Wed Aug 28 2024
Journal Name
Mesopotamian Journal Of Cybersecurity
A Novel Anomaly Intrusion Detection Method based on RNA Encoding and ResNet50 Model
...Show More Authors

Cybersecurity refers to the actions that are used by people and companies to protect themselves and their information from cyber threats. Different security methods have been proposed for detecting network abnormal behavior, but some effective attacks are still a major concern in the computer community. Many security gaps, like Denial of Service, spam, phishing, and other types of attacks, are reported daily, and the attack numbers are growing. Intrusion detection is a security protection method that is used to detect and report any abnormal traffic automatically that may affect network security, such as internal attacks, external attacks, and maloperations. This paper proposed an anomaly intrusion detection system method based on a

... Show More
View Publication
Scopus (5)
Scopus Crossref
Publication Date
Mon Oct 02 2023
Journal Name
Journal Of Engineering
Controlling the Unbalanced Voltages of a Series-Connected Lead-Acid Batteries in a PV Power Storage System using Dynamic Capacitor Technique
...Show More Authors

Lead-acid batteries have been used increasingly in recent years in solar power systems, especially in homes and small businesses, due to their cheapness and advanced development in manufacturing them. However, these batteries have low voltages and low capacities, to increase voltage and capacities, they need to be connected in series and parallel. Whether they are connected in series or parallel, their voltages and capacities must be equal otherwise the quality of service will be degraded. The fact that these different voltages are inherent in their manufacturing, but these unbalanced voltages can be controlled. Using a switched capacitor is a method that was used in many methods for balancing voltages, but their respons

... Show More
View Publication Preview PDF
Crossref