Amino acid similarity matrices based on force fields

Z. Dosztányi, A. E. Torda

Research output: Contribution to journalArticle

18 Citations (Scopus)

Abstract

Motivation: We propose a general method for deriving amino acid substitution matrices from low resolution force fields. Unlike current popular methods, the approach does not rely on evolutionary arguments or alignment of sequences or structures. Instead, residues are computationally mutated and their contribution to the total energy/score is collected. The average of these values over each position within a set of proteins results in a substitution matrix. Results: Example substitution matrices have been calculated from force fields based on different philosophies and their performance compared with conventional substitution matrices. Although this can produce useful substitution matrices, the methodology highlights the virtues, deficiencies and biases of the source force fields. It also allows a rather direct comparison of sequence alignment methods with the score functions underlying protein sequence to structure threading.

Original languageEnglish
Pages (from-to)686-699
Number of pages14
JournalBioinformatics
Volume17
Issue number8
Publication statusPublished - 2001

Fingerprint

Force Field
Substitution
Amino Acids
Amino acids
Substitution reactions
Sequence Alignment
Amino Acid Substitution
Proteins
Score Function
Protein Sequence
Alignment
Similarity
Protein
Methodology
Energy

ASJC Scopus subject areas

  • Clinical Biochemistry
  • Computer Science Applications
  • Computational Theory and Mathematics

Cite this

Amino acid similarity matrices based on force fields. / Dosztányi, Z.; Torda, A. E.

In: Bioinformatics, Vol. 17, No. 8, 2001, p. 686-699.

Research output: Contribution to journalArticle

Dosztányi, Z & Torda, AE 2001, 'Amino acid similarity matrices based on force fields', Bioinformatics, vol. 17, no. 8, pp. 686-699.
Dosztányi, Z. ; Torda, A. E. / Amino acid similarity matrices based on force fields. In: Bioinformatics. 2001 ; Vol. 17, No. 8. pp. 686-699.
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