Improving consensus structure by eliminating averaging artifacts.

ABSTRACT:

Background

Common structural biology methods (i.e., NMR and molecular dynamics) often produce ensembles of molecular structures. Consequently, averaging of 3D coordinates of molecular structures (proteins and RNA) is a frequent approach to obtain a consensus structure that is representative of the ensemble. However, when the structures are averaged, artifacts can result in unrealistic local geometries, including unphysical bond lengths and angles.

Results

Herein, we describe a method to derive representative structures while limiting the number of artifacts. Our approach is based on a Monte Carlo simulation technique that drives a starting structure (an extended or a 'close-by' structure) towards the 'averaged structure' using a harmonic pseudo energy function. To assess the

SUBMITTER: Dukka BK 

PROVIDER: S-EPMC2662860 | biostudies-literature | 2009 Mar

REPOSITORIES: biostudies-literature