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Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
Published on: July 14, 2015
SISYPHUS--structural alignments for proteins with non-trivial relationships
Antonina Andreeva1, Andreas Prlić, Tim J P Hubbard
1MRC Centre for Protein Engineering, Hills Road, Cambridge CB2 2QH, UK. tony@mrc-lmb.cam.ac.uk
Nucleic Acids Research
|October 28, 2006
Summary
Identifying complex protein structures like circular permutations and segment-swapping is challenging. The SISYPHUS database offers manually curated alignments to aid in understanding these non-trivial protein relationships.
Area of Science:
- Structural bioinformatics
- Computational biology
- Protein structure analysis
Background:
- Homologous protein structures with topological irregularities, such as circular permutations and segment-swapping, are increasingly prevalent.
- Automatic identification of these non-trivial structural relationships is difficult with current computational tools.
- These complexities challenge multiple alignment algorithms, comparative modeling, and hierarchical protein structure classifications.
Purpose of the Study:
- To facilitate the understanding and annotation of proteins with non-trivial structural relationships.
- To introduce SISYPHUS, a compendium database for manually curated structural alignments.
- To address limitations in current computational tools for identifying complex protein folds.
Main Methods:
- Creation of SISYPHUS, a compendium database linked to the SCOP database.
- Manual curation of structural alignments for various protein regions (oligomeric units, domains, fragments).
- Integration with SPICE, a browser for viewing protein sequences, structures, and annotations.
Main Results:
- SISYPHUS provides manually curated structural alignments and inter-relationships for proteins with topological irregularities.
- The database includes alignments for diverse protein regions, from whole units to fragments.
- SPICE enables an integrated view of sequence, structure, and annotation data within SISYPHUS.
Conclusions:
- SISYPHUS aids in understanding and annotating proteins with complex and non-trivial structural features.
- The database supports research on evolutionary protein fold changes and hierarchical classifications.
- SISYPHUS offers a valuable resource for the structural biology community.
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