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

Background: The majority of residues in protein structures are involved in the formation of helices and -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 C coordinates and specifically addresses the requirements of vector-based protein similarity searches. Our program identifies two types of secondary structures: helix and -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 lin...

• Type: Journal
• Year: 2005
• Where: BMCBI
• Authors: Indraneel Majumdar, S. Sri Krishna, Nick V. Grishin
• Keywords: BMCBI 2005, Protein, Secondary Structure, Secondary Structure Elements