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September 1, 1998Protein Engineering Design and Selection

Protein structure alignment by incremental combinatorial extension (CE) of the optimal path

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Authors

ISIlya N. ShindyalovPBPhilip E. Bourne

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Overview

Algorithm builds protein structure alignments using aligned fragment pairs, revealing new similarities.

Key Points

  • The aim is to present a new algorithm for aligning protein structures more efficiently than traditional methods.
  • The algorithm uses a combinatorial extension of alignment paths defined by aligned fragment pairs (AFPs).
  • It extends or discards combinations of AFPs to derive a single optimal alignment.
  • The algorithm is tested against existing methods like Dali and VAST with a representative protein structure sample.
  • The new algorithm identifies several structural similarities missed by Dali and VAST.
  • It provides fast and accurate alignments suitable for database scanning.
  • Specific alignments can be performed against all structures in the Protein Data Bank (PDB).

Cite This Study

Shindyalov et al. (1998) studied this question.

synapsesocial.com/papers/69d6f19139aaaf0da5ab398bhttps://doi.org/10.1093/protein/11.9.739
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