Extending the incorporation of superfamily structural information in the process of flexible fitting in 3D-EM

Abstract

A new procedure to increase the number of aminoacids that are taken into account in the structural alignment core when performing flexible fitting with superfamily information in three-dimensional electron microscopy (3D-EM) is described. We propose to use incremental singular value decomposition (ISVD) instead of regular SVD to compute the principal components of the alignment core, in this way allowing to add new data and to estimate missing values. The results proof that positions of the alignment with gaps contain variational information that improves the models built for the fitting step of the procedure.