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Protein Networks02:26

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Proteins are the building block of life. They are also  the most abundant macromolecules with as many diverse roles in the body. They are part of many structural components that provide unique shapes and structures to animal cells, tissues, and organs. In addition, they also act as biological catalysts and carry out several anabolic and catabolic reactions. Notably, some proteins are chemical messengers and regulate many critical processes, such as metabolism, growth, and development. They...
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Protein domains are small structurally independent units that are part of a single amino acid chain.  Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
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Proteins are one of the most abundant organic molecules in living systems and have the most diverse range of functions of all macromolecules. Proteins may be structural, regulatory, contractile, or protective. They may serve in transport, storage, or membranes; or they may be toxins or enzymes. Their structures, like their functions, vary greatly. They are all, however, amino acid polymers arranged in a linear sequence.
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HYPO: A Database of Human Hypothetical Proteins.

Vijayaraghava S Sundararajan1,2, Girik Malik3, Johny Ijaq1,4

  • 1Bioclues.org, Kukatpally, Hyderabad 500072, India.

Protein and Peptide Letters
|August 29, 2018
PubMed
Summary

The HypoDB database now offers enhanced features for exploring human hypothetical proteins (HPs) and orphan genes. This updated resource provides crucial tools for researchers investigating unknown genomic regions and potential protein functions.

Keywords:
BLASTBioinformaticsapplication programming interfacesdatabasehypothetical proteinsorphan genes.

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Area of Science:

  • Genomics
  • Proteomics
  • Bioinformatics

Background:

  • Genes with unknown functions, termed orphan genes, and their encoded proteins, Hypothetical Proteins (HPs), represent a significant gap in genomic understanding.
  • These 'unknown' regions and proteins lack experimental validation, necessitating specialized databases for research.

Purpose of the Study:

  • To enhance the HypoDB database with improved annotation, application programming interfaces (APIs), and descriptive features for human hypothetical proteins.
  • To provide researchers with a manually curated resource of over 1000 human 'unknown' genomic regions and associated proteins.
  • To make the updated HypoDB, including BLAST and Match functionalities, freely accessible for scientific inquiry.

Main Methods:

  • Hypothetical proteins were curated and validated against experimental and non-experimental datasets from Swiss-Prot, TrEMBL, and UniProtKB.
  • The HypoDB backend was developed using Java, integrating data from EMBL, PIR, HPRD, and structural/interaction databases.

Main Results:

  • The enhanced HypoDB incorporates Application Programming Interfaces (APIs) for seamless resource searching and linking to external databases like NCBI Link-out.
  • Advanced search capabilities and integrated bioinformatics tools, including BLAST and Match, have been implemented.

Conclusions:

  • HypoDB stands as a unique open-source database for hypothetical proteins, offering comprehensive bioinformatics retrieval tools.
  • It serves as a vital reference for researchers seeking candidate sequences for experimental validation and functional studies.