Amino acid similarity matrices based on force fields | Zendy

Zsuzsanna Dosztányi | Zendy; Andrew E. Torda | Zendy

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Amino acid similarity matrices based on force fields

Author(s) -

Zsuzsanna Dosztányi,

Andrew E. Torda

Publication year - 2001

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/17.8.686

Subject(s) - substitution (logic) , force field (fiction) , matrix (chemical analysis) , similarity (geometry) , threading (protein sequence) , sequence (biology) , set (abstract data type) , substitution method , computer science , amino acid substitution , sequence alignment , position (finance) , algorithm , protein structure , peptide sequence , chemistry , artificial intelligence , image (mathematics) , mutation , telecommunications , biochemistry , finance , chromatography , economics , gene , programming language

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.

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