The accuracy of protein structure alignment servers

Background: Protein structural alignment is one of the most fundamental and crucial areas of research in the domain of computational structural biology. Comparison of a protein structure with known structures helps to classify it as a new or belonging to a known group of proteins. This, in turn, is useful to determine the function of protein, its evolutionary relationship with other protein molecules and grasping principles underlying protein architecture and folding. Results: A large number of protein structure alignment methods are available. Each protein structure alignment tool has its own strengths andweaknesses that need to be highlighted.We compared and presented results of six most popular and publically available servers for protein structure comparison. These web-based servers were compared with the respect to functionality (features provided by these servers) and accuracy (how well the structural comparison is performed). The CATH was used as a reference. The results showed that overall CE was top performer. DALI and PhyreStorm showed similar results whereas PDBeFold showed the lowest performance. In case of few secondary structural elements, CE, DALI and PhyreStorm gave 100% success rate. Conclusion: Overall none of the structural alignment servers showed 100% success rate. Studies of overall performance, effect of mainly alpha and effect of mainly beta showed consistent performance. CE, DALI, FatCat and PhyreStorm showed more than 90% success rate

Enhancing the Resolution of Inkjet Printing Through Modification of Ink/Substrate Interaction

The focus of this research is on optimizing the performance of inkjet printing using the Meyer Burger PiXDRO LP50 printing platform and KM512-SH printhead with commercially available ink and substrates, focusing on print resolution to overcome one of the two main barriers that are currently preventing inkjet printing from being adopted for prototyping and volume manufacturing which are print reliability and print resolution. We would pursue three approaches to enhance inkjet printing resolution. In the first approach, we will study the properties of selected ink and substrates to understand their separate and combined influence on print resolution and we will try to find an optimized print setting based on the knowledge we gained from it. In the second and third approaches, we will physically and chemically modify the selected substrates using nanoimprint lithography (NIL), and Layer-by-layer Self-assembly (LbL) methods and we will study the effect of these surface modifications methods on print resolution

Investigating the Student Satisfaction of Combined Education Based on Learning Management System and Academic Participation

Aim and Purpose: Considering the importance of nursing education, especially the use of modern educational technology to meet existing educational needs, the present study aimed to investigating the satisfaction and academic participation of nursing students who use combination education based on learning management system (LMS) and studied their degree of satisfaction and academic participation. Method: This is a descriptive cross-sectional study in which 229 undergraduate nursing students. After obtaining permission from the university's ethics committee and informed consent, demographic data form, satisfaction of combined education questionnaire of Zolfaghari et al.'s, the educational participation scale questionnaire of Frederick et al.'s was completed as a tool for collecting data. Data were analyzed by SPSS software version 23 and significance level less than 0.05, descriptive statistics, independent t-test, one way ANOVA, and Scheffe post hoc test and Pearson correlation. Findings: The vast majority had a moderate or lower familiarity with the LMS system (75.5%). The majority did not easily access the LMS system (56.3%). Only 2.2% of the units had high satisfaction and 40.2% had relative satisfaction and 57.6% had low satisfaction from LMS-based combination training. The mean and standard deviation of the educational participation score was 51.16±14.86 and their behavioral subscale scores 69.68±16.48 and the emotional subscale was 49.56±20.53 and the cognitive subscale was 38.25±20.55%. Conclusion: According to the results of the study, most of the research units had low satisfaction with LMS-based combination training, which could increase student satisfaction by using all the capabilities of the learning management system and the more interactive design of the combination training, as the majority of previous studies have shown high satisfaction with combined training. &nbsp

Electronic Journal of Biotechnology The accuracy of protein structure alignment servers

Background: Protein structural alignment is one of the most fundamental and crucial areas of research in the domain of computational structural biology. Comparison of a protein structure with known structures helps to classify it as a new or belonging to a known group of proteins. This, in turn, is useful to determine the function of protein, its evolutionary relationship with other protein molecules and grasping principles underlying protein architecture and folding. Results: A large number of protein structure alignment methods are available. Each protein structure alignment tool has its own strengths and weaknesses that need to be highlighted. We compared and presented results of six most popular and publically available servers for protein structure comparison. These web-based servers were compared with the respect to functionality (features provided by these servers) and accuracy (how well the structural comparison is performed). The CATH was used as a reference. The results showed that overall CE was top performer. DALI and PhyreStorm showed similar results whereas PDBeFold showed the lowest performance. In case of few secondary structural elements, CE, DALI and PhyreStorm gave 100% success rate. Conclusion: Overall none of the structural alignment servers showed 100% success rate. Studies of overall performance, effect of mainly alpha and effect of mainly beta showed consistent performance. CE, DALI, FatCat and PhyreStorm showed more than 90% success rate

The accuracy of protein structure alignment servers

Background: Protein structural alignment is one of the most fundamental and crucial areas of research in the domain of computational structural biology. Comparison of a protein structure with known structures helps to classify it as a new or belonging to a known group of proteins. This, in turn, is useful to determine the function of protein, its evolutionary relationship with other protein molecules and grasping principles underlying protein architecture and folding. Results: A large number of protein structure alignment methods are available. Each protein structure alignment tool has its own strengths and weaknesses that need to be highlighted. We compared and presented results of six most popular and publically available servers for protein structure comparison. These web-based servers were compared with the respect to functionality (features provided by these servers) and accuracy (how well the structural comparison is performed). The CATH was used as a reference. The results showed that overall CE was top performer. DALI and PhyreStorm showed similar results whereas PDBeFold showed the lowest performance. In case of few secondary structural elements, CE, DALI and PhyreStorm gave 100% success rate. Conclusion: Overall none of the structural alignment servers showed 100% success rate. Studies of overall performance, effect of mainly alpha and effect of mainly beta showed consistent performance. CE, DALI, FatCat and PhyreStorm showed more than 90% success rate

IVisTMSA: Interactive Visual Tools for Multiple Sequence Alignments

IVisTMSA is a software package of seven graphical tools for multiple sequence alignments. MSApad is an editing and analysis tool. It can load 409% more data than Jalview, STRAP, CINEMA, and Base-by-Base. MSA comparator allows the user to visualize consistent and inconsistent regions of reference and test alignments of more than 21-MB size in less than 12 seconds. MSA comparator is 5,200% efficient and more than 40% efficient as compared to BALiBASE c program and FastSP, respectively. MSA reconstruction tool provides graphical user interfaces for four popular aligners and allows the user to load several sequence files at a time. FASTA generator converts seven formats of alignments of unlimited size into FASTA format in a few seconds. MSA ID calculator calculates identity matrix of more than 11,000 sequences with a sequence length of 2,696 base pairs in less than 100 seconds. Tree and Distance Matrix calculation tools generate phylogenetic tree and distance matrix, respectively, using neighbor joining% identity and BLOSUM 62 matrix

Stimulus-responsive liposomes as smart nanoplatforms for drug delivery applications

Liposomes are known to be promising nanoparticles (NPs) for drug delivery applications. Among the different types of self-assembled NPs, liposomes stand out for their non-toxic nature and their possession of dual hydrophilic-hydrophobic domains. The advantages of liposomes include the ability to solubilize hydrophobic drugs, the ability to incorporate different hydrophilic and lipophilic drugs at the same time, lessening the exposure of host organs to potentially toxic drugs and allowing modification of the surface by a variety of different chemical groups. This modification of the surface, or of the individual constituents, may be used to achieve two important goals. First, ligands for active targeting can be attached that are recognized by cognate receptors overexpressed on the target cells of tissues. Second, modification can be used to impart a stimulus-responsive or “smart” character to the liposomes, whereby the cargo is released on demand only when certain internal stimuli (pH, reducing agents, specific enzymes) or external stimuli [light, magnetic field, or ultrasound (US)] are present. Here, we review the field of smart liposomes for drug delivery applications

Evaluation of 2-Mercaptobenzimidazole Derivatives as Corrosion Inhibitors for Mild Steel in Hydrochloric Acid

This research aimed to develop a better understanding of the corrosion inhibition of the mild steel in acidic medium by new organic molecules. For this purpose, two new compounds namely, 2,3-dihydrobenzo[4,5]imidazo[2,1-b]thiazole (2-BIT) and 3,4-dihydro-2H-benzo[4,5]imidazo[2,1-b]thiazole (3-BIT) were synthesized and evaluated for mild steel (MS) corrosion in HCl. Analyses were carried out using weight loss measurements, electrochemical techniques, and scanning electron microscope (SEM). The adsorption of inhibitors onto the steel surface follows the Langmuir adsorption model. Generally, results showed that the corrosion inhibition efficiency of the investigated molecules was found to increase with increased concentration of inhibitors. Electrochemical tests, i.e., electrochemical impedance spectroscopy (EIS) and potentiodynamic polarization (PDP) techniques, showed that the addition of our investigated inhibitors decreases the dissolution of the metal and generally act as mixed-type inhibitors. In addition, the influence of temperature (from 303 to 333 K) on the corrosion inhibition was studied, and the results demonstrated that with an increase in temperature, the inhibition efficiency decrease. SEM results confirmed that the inhibition process is due to a protective film that prevents corrosion. Similarly, the results showed that the inhibitory efficiencies reach 93% at 5 × 10−3 M in the case of inhibitor 3-BIT. These results revealed that this compound could effectively control and reduce the corrosion rate of mild steel in the corrosion test solution