Amplitude spectrum distance: measuring the global shape divergence of protein fragments.

ABSTRACT:

Background

In structural bioinformatics, there is an increasing interest in identifying and understanding the evolution of local protein structures regarded as key structural or functional protein building blocks. A central need is then to compare these, possibly short, fragments by measuring efficiently and accurately their (dis)similarity. Progress towards this goal has given rise to scores enabling to assess the strong similarity of fragments. Yet, there is still a lack of more progressive scores, with meaningful intermediate values, for the comparison, retrieval or clustering of distantly related fragments.

Results

We introduce here the Amplitude Spectrum Distance (ASD), a novel way of comparing protein fragments based on the discrete Fourier transform of their C(α) dist

SUBMITTER: Galiez C 

PROVIDER: S-EPMC4535829 | biostudies-literature | 2015 Aug

REPOSITORIES: biostudies-literature