PDBALIGN, PDBDIST AND DISTALIGN - TOOLS TO AID IN RELATING SEQUENCE VARIABILITY TO STRUCTURE

Many sequence analysis problems involve consideration of a multiple se quence alignment where the 3-dimensional structure of one (or more) of the aligned sequences is known. In such cases, it is useful to map th e sequence variability onto the atomic co-ordinates of known structure . If the structure also includes a bound ligand (or the location of th e active site is known), each column position in the multiple sequence alignment may be annotated with its 'distance' from the binding site. These annotations, together with a measure of sequence variability, p rovide additional insights into drug specificity, for example among vi ral mutants. This paper describes several useful programs that automat e this analysis.