Simple alignment

From Proteinfunction.net

Well-formed concave surface regions in the form of pockets and voids are examined to identify similarity relationship that might be directly related to protein function. They first exhaustively identify and measure analytically all 910,379 surface pockets and interior voids on 12,177 protein structures from the Protein Data Bank. The similarity of patterns of residues forming pockets and voids are then assessed in sequence, in spatial arrangement, and in orientational arrangement. Statistical significance in the form of E and p-values is then estimated for each of the three types of similarity measurements.



Reference

---

Binkowski, T., Adamian, L. and Liang, J., Infering Functional Relationships of Proteins from Local Sequence and Spatial Surface Patterns. J. Mol. Biol., 332:505-526, 2003