Defining linear segments in protein structure

The analysis of protein structure using secondary structure line segments h as been widely used in many structure analysis and prediction methods over the past 20 years. Its use in methods that compare protein structures at th is level of representation is becoming more important as an increasing numb er of protein structures become determined through structural genomic progr ammes. The standard method used to define line segments is to fit an axis t hrough each secondary structure element. This approach has difficulties, ho wever, both with inconsistent definitions of secondary structure and the pr oblem of fitting a single straight line to a bent structure. The procedure described here avoids these problems by finding a set of line segments inde pendently of any external secondary structure definition. This allows the s egments to be used as a novel basis for secondary structure definition by t aking the average rise/residue along each axis to characterise the segment. This practice has the advantage that secondary structures are described by a single (continuous) value that is not restricted to the conventional cla sses of alpha -helix, 3(10) and beta -strand. This latter property allows s tructures without "classic" secondary structures to be encoded as line segm ents that can be used in comparison algorithms. When compared over a large number of pairs of homologous proteins, the current method was found to be slightly more consistent than a widely used method based on hydrogen bonds. (C) 2001 Academic Press.