Title :
Extending the incorporation of superfamily structural information in the process of flexible fitting in 3D-EM
Author :
Velázquez-Muriel, J.A. ; Carazo, J.M.
Author_Institution :
Centro Nacional de Biotecnologia, Campus Univ., Madrid, Spain
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.
Keywords :
biochemistry; biology computing; electron microscopy; molecular biophysics; organic compounds; principal component analysis; proteins; singular value decomposition; 3D-EM; aminoacids; flexible fitting process; incremental singular value decomposition; principal components; regular SVD; structural alignment core; superfamily structural information; three-dimensional electron microscopy; variational information; Atomic measurements; Biological system modeling; Bonding; Chemical elements; Crystallography; Deformable models; Electron microscopy; Matrix decomposition; Proteins; Singular value decomposition;
Conference_Titel :
Computational Systems Bioinformatics Conference, 2005. Workshops and Poster Abstracts. IEEE
Print_ISBN :
0-7695-2442-7
DOI :
10.1109/CSBW.2005.65
