SA-Search: a web tool for protein structure mining based on a Structural Alphabet

@article{Guyon2004SASearchAW,
  title={SA-Search: a web tool for protein structure mining based on a Structural Alphabet},
  author={Fr{\'e}d{\'e}ric Guyon and Anne-Claude Camproux and Jo{\"e}lle Hochez and Pierre Tuff{\'e}ry},
  journal={Nucleic acids research},
  year={2004},
  volume={32 Web Server issue},
  pages={
          W545-8
        }
}
SA-Search is a web tool that can be used to mine for protein structures and extract structural similarities. It is based on a hidden Markov model derived Structural Alphabet (SA) that allows the compression of three-dimensional (3D) protein conformations into a one-dimensional (1D) representation using a limited number of prototype conformations. Using such a representation, classical methods developed for amino acid sequences can be employed. Currently, SA-Search permits the performance of… 

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References

SHOWING 1-10 OF 22 REFERENCES
MATRAS: a program for protein 3D structure comparison
TLDR
A web server for comparing protein 3D structures using the program Matras, which employs the progressive alignment algorithm, in which pairwise 3D alignments are assembled in the proper order.
Protein structure alignment by incremental combinatorial extension (CE) of the optimal path.
A new algorithm is reported which builds an alignment between two protein structures. The algorithm involves a combinatorial extension (CE) of an alignment path defined by aligned fragment pairs
Protein structure alignment using a genetic algorithm
TLDR
A novel, fully automatic method for aligning the three‐dimensional structures of two proteins, which has applied to proteins from several well‐studied families: globins, immunoglobulins, serine proteases, dihydrofolate reductases, and DNA methyltransferases.
Hierarchical Protein Structure Superposition Using Both Secondary Structure and Atomic Representations
TLDR
A new algorithm for the comparison of proteins based on a hierarchy of structural representations, from the secondary structure level to the atomic level is presented, which was able to detect structural similarity at the same level as DALI.
PISCES: a protein sequence culling server
TLDR
PISCES is a public server for culling sets of protein sequences from the Protein Data Bank by sequence identity and structural quality criteria and provides better lists than servers that use BLAST, which is unable to identify many relationships below 40% sequence identity.
A hidden markov model derived structural alphabet for proteins.
Protein structure comparison
TLDR
The all-against-all comparison of known protein structures has allowed the structure of “fold-space” to be mapped, from broad general trends to specific clusters of proteins that have the same evolutionary origins.
LGA: a method for finding 3D similarities in protein structures
  • A. Zemla
  • Computer Science, Biology
    Nucleic Acids Res.
  • 2003
TLDR
Data generated by LGA can be successfully used in a scoring function to rank the level of similarity between two structures and to allow structure classification when many proteins are being analyzed.
Surprising similarities in structure comparison.
Protein structure comparison by alignment of distance matrices.
TLDR
A novel algorithm (DALI) for optimal pairwise alignment of protein structures that identifies structural resemblances and common structural cores accurately and sensitively, even in the presence of geometrical distortions is developed.
...
...