NMRDSP: an accurate prediction of protein shape strings from NMR chemical shifts and sequence data.

ABSTRACT: Shape string is structural sequence and is an extremely important structure representation of protein backbone conformations. Nuclear magnetic resonance chemical shifts give a strong correlation with the local protein structure, and are exploited to predict protein structures in conjunction with computational approaches. Here we demonstrate a novel approach, NMRDSP, which can accurately predict the protein shape string based on nuclear magnetic resonance chemical shifts and structural profiles obtained from sequence data. The NMRDSP uses six chemical shifts (HA, H, N, CA, CB and C) and eight elements of structure profiles as features, a non-redundant set (1,003 entries) as the training set, and a conditional random field as a classification algorithm. For an independent testing set (203 en

SUBMITTER: Mao W 

PROVIDER: S-EPMC3871590 | biostudies-literature | 2013

REPOSITORIES: biostudies-literature