Combined Experimental and Computational Approach for Rational Design of Bio-Nano Interfaces

2015 ◽  
Keyword(s):  
Rational Design ◽  
Computational Approach

scholarly journals Computational approach for selection of epitope-based dengue vaccine targets

2018 ◽  
Vol 14 (4) ◽  
pp. 605-618
Author(s):  
Phuc Nguyen ◽  
Ly Le
Keyword(s):  
Amino Acids ◽  
T Cell ◽  
Dengue Virus ◽  
Rational Design ◽  
Protein Sequences ◽  
Computational Approach ◽  
Amino Acid Sequences ◽  
Universal Vaccine ◽  
E Protein

High antigenic variability in the envelope (E) protein of different virus strains has been a major obstacle in designing effective vaccines for Dengue virus (DENV). To maintain their biological function, some parts of viral proteins remain stable during evolution thus one possible approach to solve this problem is to recognize specific regions within different protein sequences of E that have the tendency to stay constant through evolution. These regions may possess some special attributes to become a vaccine candidate against dengue virus. In this study, a computational approach was utilized to identify and analyze highly conserved amino acid sequences of the DENV E protein. Sequences of 9 amino acids or more were specifically focused due to their immune-relevant as T-cell determinants. Different bioinformatics tools were responsible for revealing conserved regions in the DENV E protein and constructing the phylogenetic tree from the sequence database. The tools also predicted immunogenicity of the identified vaccine targets. Ultimately, two peptide regions of at least 9 amino acids were chosen due to their high conserved attribute in more than 95% of all collected DENV sequences. Moreover, both of them was found to be immune-relevant by their correspondence to known or putative HLA-restricted T cell determinants. The conserved attribute of these sequences through the entire analysis of this study supports their potential as candidates for further in vitro experiments for rational design a universal vaccine which has longer and broader impact.

Towards the rational design of palladium-N-heterocyclic carbene catalysts by a combined experimental and computational approach

Tetrahedron ◽  
2005 ◽  
Vol 61 (41) ◽  
pp. 9723-9735 ◽  
Author(s):  
Christopher J. O'Brien ◽  
Eric Assen B. Kantchev ◽  
Gregory A. Chass ◽  
Niloufar Hadei ◽  
Alan C. Hopkinson ◽  
...  
Keyword(s):  
Rational Design ◽  
Computational Approach

scholarly journals Computational design of single-stranded DNA hairpin aptamers immobilized on a biosensor substrate

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Iman Jeddi ◽  
Leonor Saiz
Keyword(s):  
Rational Design ◽  
High Surface ◽  
Computational Design ◽  
Computational Approach ◽  
Nacl Solution ◽  
Dna Hairpin ◽  
Analysis Techniques ◽  
And Performance ◽  
Muc1 Aptamer ◽  
System Designs

AbstractAptamer interactions with a surface of attachment are central to the design and performance of aptamer-based biosensors. We have developed a computational modeling approach to study different system designs—including different aptamer-attachment ends, aptamer surface densities, aptamer orientations, and solvent solutions—and applied it to an anti MUC1 aptamer tethered to a silica biosensor substrate. Amongst all the system designs explored, we found that attaching the anti MUC1 aptamer through the 5′ terminal end, in a high surface density configuration, and solvated in a 0.8 M NaCl solution provided the best exposure of the aptamer MUC1 binding regions and resulted in the least amount of aptamer backbone fluctuations. Many of the other designs led to non-functional systems, with the aptamer collapsing onto the surface. The computational approach we have developed and the resulting analysis techniques can be employed for the rational design of aptamer-based biosensors and provide a valuable tool for improving biosensor performance and repeatability.

Computational Approach to the Rational Design of Molecularly Imprinted Polymers for Voltammetric Sensing of Homovanillic Acid

2005 ◽  
Vol 77 (20) ◽  
pp. 6741-6746 ◽  
Author(s):  
Yolanda Diñeiro ◽  
M. Isabel Menéndez ◽  
M. Carmen Blanco-López ◽  
M. Jesús Lobo-Castañón ◽  
Arturo J. Miranda-Ordieres ◽  
...  
Keyword(s):  
Molecularly Imprinted Polymers ◽  
Rational Design ◽  
Homovanillic Acid ◽  
Computational Approach ◽  
Molecularly Imprinted ◽  
Imprinted Polymers ◽  
Voltammetric Sensing
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