MimoDB

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MimoDB 2.0
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Description mimotope database
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Research center University of Electronic Science and Technology of China
Laboratory Key Laboratory for Neuroinformation of Ministry of Education
Authors Jian Huang
Primary citationHuang & al. (2012) [1]
Release date2011
Access
Website http://immunet.cn/mimodb

MimoDB is a database of peptides that have been selected from random peptide libraries based on their ability to bind small compounds, nucleic acids, proteins, cells, tissues, ... through phage display. [1]

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An epitope, also known as antigenic determinant, is the part of an antigen that is recognized by the immune system, specifically by antibodies, B cells, or T cells. For example, the epitope is the specific piece of the antigen to which an antibody binds. The part of an antibody that binds to the epitope is called a paratope. Although epitopes are usually non-self proteins, sequences derived from the host that can be recognized are also epitopes.

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Peptidomimetic class of chemical compounds designed to mimic the characteristics of peptides

A peptidomimetic is a small protein-like chain designed to mimic a peptide. They typically arise either from modification of an existing peptide, or by designing similar systems that mimic peptides, such as peptoids and β-peptides. Irrespective of the approach, the altered chemical structure is designed to advantageously adjust the molecular properties such as, stability or biological activity. This can have a role in the development of drug-like compounds from existing peptides. These modifications involve changes to the peptide that will not occur naturally. Based on their similarity with the precursor peptide, peptidomimetics can be grouped into four classes where A features the most and D the least similarities. Classes A and B involve peptide-like scaffolds, while classes C and D include small molecules.

Phage display biological technique to evolve proteins using bacteriophages

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Aptamers are oligonucleotide or peptide molecules that bind to a specific target molecule. Aptamers are usually created by selecting them from a large random sequence pool, but natural aptamers also exist in riboswitches. Aptamers can be used for both basic research and clinical purposes as macromolecular drugs. Aptamers can be combined with ribozymes to self-cleave in the presence of their target molecule. These compound molecules have additional research, industrial and clinical applications.

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A mimotope is a macromolecule, often a peptide, which mimics the structure of an epitope. Because of this property it causes an antibody response similar to the one elicited by the epitope. An antibody for a given epitope antigen will recognize a mimotope which mimics that epitope. Mimotopes are commonly obtained from phage display libraries through biopanning. Vaccines utilizing mimotopes are being developed. Mimotopes are a kind of peptide Aptamers.

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mRNA display is a display technique used for in vitro protein, and/or peptide evolution to create molecules that can bind to a desired target. The process results in translated peptides or proteins that are associated with their mRNA progenitor via a puromycin linkage. The complex then binds to an immobilized target in a selection step. The mRNA-protein fusions that bind well are then reverse transcribed to cDNA and their sequence amplified via a polymerase chain reaction. The result is a nucleotide sequence that encodes a peptide with high affinity for the molecule of interest.

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The Actinobacteriophage database, more commonly known as PhagesDB, is a database-backed website that gathers and shares information related to the discovery, characterization and genomics of viruses that prefer to infect Actinobacterial hosts. It is a bioinformatics tool that is used worldwide to compare multiple phages and their genomic annotations. Up to recent dates, there have been more than 8,000 bacteriophages, including over 1,600 with already sequenced genomes, have been entered into the database. It is an addition to the wide range of priorly existing bioinformatic tools, like NCBI. It provides results of already sequenced phage genomes and aims to allow access to drafted phage genomes to provide a larger spectrum of information.

SEA-PHAGES stands for Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science; it was formerly called the National Genomics Research Initiative. This was the first initiative launched by the Howard Hughes Medical Institute (HHMI) Science Education Alliance (SEA) by their director Tuajuanda C. Jordan in 2008 to improve the retention of Science, technology, engineering, and mathematics (STEM) students. SEA-PHAGES is a two-semester undergraduate research program administered by the University of Pittsburgh's Graham Hatfull's group and the Howard Hughes Medical Institute's Science Education Division. Students from over 100 universities nationwide engage in authentic individual research that includes a wet-bench laboratory and a bioinformatics component.

References

  1. 1 2 Huang, Jian; Ru Beibei; Zhu Ping; Nie Fulei; Yang Jun; Wang Xuyang; Dai Ping; Lin Hao; Guo Feng-Biao; Rao Nini (Jan 2012). "MimoDB 2.0: a mimotope database and beyond". Nucleic Acids Res. England. 40 (1): D271-7. doi:10.1093/nar/gkr922. PMC   3245166 . PMID   22053087.