Protein structure comparison by alignment of distance matrices.

  title={Protein structure comparison by alignment of distance matrices.},
  author={L. Holm and Chris Sander},
  journal={Journal of molecular biology},
  volume={233 1},
With a rapidly growing pool of known tertiary structures, the importance of protein structure comparison parallels that of sequence alignment. We have developed a novel algorithm (DALI) for optimal pairwise alignment of protein structures. The three-dimensional co-ordinates of each protein are used to calculate residue-residue (C alpha-C alpha) distance matrices. The distance matrices are first decomposed into elementary contact patterns, e.g. hexapeptide-hexapeptide submatrices. Then, similar… 
CAALIGN: a program for pairwise and multiple protein-structure alignment.
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Connectivity independent protein-structure alignment: a hierarchical approach
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Protein structure alignment using environmental profiles.
A new protein structure alignment procedure is described, which is fast enough to do all-against-all structural comparisons routinely and sometimes finds an alignment that suggests an evolutionary relationship and which is not normally obtained if only geometry is considered.
Hierarchical Protein Structure Superposition Using Both Secondary Structure and Atomic Representations
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.
A substitution matrix for structural alphabet based on structural alignment of homologous proteins and its applications
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Dali: a network tool for protein structure comparison.
Protein Structure Comparison by alignment of distance matrices
  • Protein Structure Comparison by alignment of distance matrices
  • 1993