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© Oxford University Press

PdbAlign, PdbDist and DistAlign: Tools to aid in relating sequence variability to structure

Roger Sayle , Saqi Mansoor 1, Malcolm Weir and Andrew Lyall

Bioinformatics Group, Department of Biomolecular Structure, Glaxo Medicines Research Centre Gunnels Wood Road, Stevenage, Herts SGI 2NY, UK

1To whom correspondence should be addressed Email mass15599{at}ggr.co.uk

Many sequence analysis problems involve consideration of a multiple sequence alignment where the 3-dimensional structure of one (or more) of the aligned sequences is known. In such cases, it is useful to map the sequence variability onto the atomic co-ordinates of known structure. If the structure also includes a bound ligand (or the location of the 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, provide additional insights into drug specificity, for example among viral mutants. This paper describes several useful programs that automate this analysis.

Received on June 13, 1995; revised on July 30, 1995; accepted on August 11, 1995

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