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Open Access Methodology article

PALSSE: A program to delineate linear secondary structural elements from protein structures

Indraneel Majumdar2, S Sri Krishna2 and Nick V Grishin12*

Author Affiliations

1 Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd. Dallas, TX 75390, USA

2 Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390, USA

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BMC Bioinformatics 2005, 6:202  doi:10.1186/1471-2105-6-202

Published: 11 August 2005

Abstract

Background

The majority of residues in protein structures are involved in the formation of α-helices and β-strands. These distinctive secondary structure patterns can be used to represent a protein for visual inspection and in vector-based protein structure comparison. Success of such structural comparison methods depends crucially on the accurate identification and delineation of secondary structure elements.

Results

We have developed a method PALSSE (Predictive Assignment of Linear Secondary Structure Elements) that delineates secondary structure elements (SSEs) from protein Cα coordinates and specifically addresses the requirements of vector-based protein similarity searches. Our program identifies two types of secondary structures: helix and β-strand, typically those that can be well approximated by vectors. In contrast to traditional secondary structure algorithms, which identify a secondary structure state for every residue in a protein chain, our program attributes residues to linear SSEs. Consecutive elements may overlap, thus allowing residues located at the overlapping region to have more than one secondary structure type.

Conclusion

PALSSE is predictive in nature and can assign about 80% of the protein chain to SSEs as compared to 53% by DSSP and 57% by P-SEA. Such a generous assignment ensures almost every residue is part of an element and is used in structural comparisons. Our results are in agreement with human judgment and DSSP. The method is robust to coordinate errors and can be used to define SSEs even in poorly refined and low-resolution structures. The program and results are available at http://prodata.swmed.edu/palsse/ webcite.