Abstract
BackgroundThe 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.ResultsWe 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.ConclusionPALSSE 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 .
Highlights
The majority of residues in protein structures are involved in the formation of αhelices and β-strands
A quadruplet is the smallest unit for defining potential β-sheets and is formed from a set of four Cα atoms that are linked with two covalent bonds and two pseudo-hydrogen bonds
Helices defined previously are split, using root mean square deviation (RMSD) of constituent residues about the helix axis, so that they can be represented as linear elements. β-strands are split using various geometrical criteria and pairing of neighboring residues
Summary
The majority of residues in protein structures are involved in the formation of αhelices and β-strands. The first algorithm for the automatic delineation of secondary structure was proposed by Levitt and Greer [7] They defined secondary structures based on peptide hydrogen bonds (using i, i+3 Cα distances and i, i+1, i+2, i+3 Cα torsion angles). A more comprehensive algorithm, DSSP, was subsequently developed and is based on a careful analysis of backbone-backbone hydrogen bond energies and geometrical features of the polypeptide chain [8] It is very accurate in its residue-based definition of the available coordinates and does not attempt to interpret the data in any predictive way. Xtlsstr defines secondary structure in the same way a person assigns secondary structure visually [10] It uses two angles and three distances computed from the protein backbone atoms. The P-Curve algorithm allows the helicoidal structure of a protein to be calculated starting from the atomic coordinates of its peptide backbone [11]
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