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Related Experiment Videos

An Integrated Sequence-Structure Database incorporating matching mRNA sequence, amino acid sequence and protein

I A Adzhubei1, A A Adzhubei, S Neidle

  • 1CRC Biomolecular Structure Unit, The Institute of Cancer Research, Sutton, Surrey SM2 5NG, UK.

Nucleic Acids Research
|February 21, 1998
PubMed
Summary

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The Integrated Sequence-Structure Database (ISSD) links gene sequences to protein structures. This resource aids in understanding codon usage and protein structure relationships.

Area of Science:

  • Bioinformatics
  • Structural Biology
  • Computational Biology

Background:

  • Integrating diverse biological data is crucial for comprehensive analysis.
  • Existing databases may lack integrated sequence and structure information for non-homologous proteins.
  • Understanding the relationship between nucleotide sequences and protein structures is fundamental.

Purpose of the Study:

  • To develop a comprehensive database (ISSD) integrating gene sequences, protein sequences, secondary structures, and 3D coordinates.
  • To provide a resource for analyzing the correlation between synonymous codon usage and protein structure.
  • To facilitate research in protein expression, structure prediction, and evolutionary analysis.

Main Methods:

  • Construction of a non-homologous database (ISSD) containing coding sequences, amino acid sequences, secondary structure assignments, and backbone coordinates.

Related Experiment Videos

  • Alignment of nucleotide sequences, amino acid sequences, and Protein Data Bank (PDB) 3D structure data for each protein entry.
  • Selection of sequences based on exact matches of source organism and cell environment.

    • Main Results:

    • The Integrated Sequence-Structure Database (ISSD) version 1.0 is available online.
    • The database currently includes 107 non-homologous mammalian proteins, with 80 human proteins.
    • Analysis revealed correlations between synonymous codon usage patterns in mRNA and 3D structure features of encoded proteins.

    Conclusions:

    • The ISSD provides a valuable resource for studying sequence-structure relationships.
    • The database can be applied to optimize protein expression and improve protein structure prediction.
    • ISSD facilitates the investigation of evolutionary aspects linking nucleotide sequences and protein structures.