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Literature DB >> 10964983

Structure-derived substitution matrices for alignment of distantly related sequences.

Abstract

Sequence alignment is a standard method to infer evolutionary, structural, and functional relationships among sequences. The quality of alignments depends on the substitution matrix used. Here we derive matrices based on superimpositions from protein pairs of similar structure, but of low or no sequence similarity. In a performance test the matrices are compared with 12 other previously published matrices. It is found that the structure-derived matrices are applicable for comparisons of distantly related sequences. We investigate the influence of evolutionary relationships of protein pairs on the alignment accuracy.

Mesh：

Year: 2000 PMID： 10964983 DOI： 10.1093/protein/13.8.545

Source DB: PubMed Journal: Protein Eng ISSN： 0269-2139

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Cited

33 in total

1. Persistently conserved positions in structurally similar, sequence dissimilar proteins: roles in preserving protein fold and function.

Authors: Iddo Friedberg; Hanah Margalit
Journal: Protein Sci Date: 2002-02 Impact factor: 6.725

Review 2. Structural genomics: computational methods for structure analysis.

Authors: Sharon Goldsmith-Fischman; Barry Honig
Journal: Protein Sci Date: 2003-09 Impact factor: 6.725

3. CONTSOR--a new knowledge-based fold recognition potential, based on side chain orientation and contacts between residue terminal groups.

Authors: Boris Vishnepolsky; Malak Pirtskhalava
Journal: Protein Sci Date: 2011-11-23 Impact factor: 6.725

4. Aligning protein sequence and analysing substitution pattern using a class-specific matrix.

Authors: Hai Song Xu; Wen Ke Ren; Xiao Hui Liu; Xiao Qin Li
Journal: J Biosci Date: 2010-06 Impact factor: 1.826

5. Systematic detection of internal symmetry in proteins using CE-Symm.

Authors: Douglas Myers-Turnbull; Spencer E Bliven; Peter W Rose; Zaid K Aziz; Philippe Youkharibache; Philip E Bourne; Andreas Prlić
Journal: J Mol Biol Date: 2014-03-26 Impact factor: 5.469

6. Fold recognition by combining sequence profiles derived from evolution and from depth-dependent structural alignment of fragments.

Authors: Hongyi Zhou; Yaoqi Zhou
Journal: Proteins Date: 2005-02-01

Structure-derived substitution matrices for alignment of distantly related sequences.

1. Persistently conserved positions in structurally similar, sequence dissimilar proteins: roles in preserving protein fold and function.

Review 2. Structural genomics: computational methods for structure analysis.

3. CONTSOR--a new knowledge-based fold recognition potential, based on side chain orientation and contacts between residue terminal groups.

4. Aligning protein sequence and analysing substitution pattern using a class-specific matrix.

5. Systematic detection of internal symmetry in proteins using CE-Symm.

6. Fold recognition by combining sequence profiles derived from evolution and from depth-dependent structural alignment of fragments.

7. Reduced amino acid alphabets exhibit an improved sensitivity and selectivity in fold assignment.

8. Fast and accurate methods for predicting short-range constraints in protein models.

9. Sequence alignment as hypothesis testing.

10. Low-homology protein threading.