Velazquez-Muriel, J. A.; Sorzano, C. O. S.; Scheres, S. H. W. & Carazo, J. M. SPI-EM: Towards a tool for predicting CATH superfamilies in 3D-EM maps J. Molecular Biology, 2005, 345, 759-771
In this paper the theoretical framework used to build a superfamily probability in electron microscopy (SPI-EM) is presented. SPI-EM is a new tool for determining the homologous superfamily to which a protein domain belongs looking at its three-dimensional electron microscopy map. The homologous superfamily is assigned according to the domainarchitecture database CATH. Our method follows a probabilistic approach applied to the results of fitting protein domains into maps of proteins and the computation of local cross-correlation coefficient measures. The method has been tested and its usefulness proven with isolated domains at a resolution of 8A and 12A. Results obtained with simulated and experimental data at 10A suggest that it is also feasible to detect the correct superfamily of the domains when dealing with electron microscopy maps containing multi-domain proteins. The inherent difficulties and limitations that multi-domain proteins impose are discussed. Our procedure is complementary to other techniques existing in the field to detect structural elements in electron microscopy maps like a-helices and b-sheets. Based on the proposed methodology, a database of relevant distributions is being built to serve the community.
Fold recognition, fitting