PdbAlign, PdbDist and DistAlign: tools to aid in relating sequence variability to structure.
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.
Sayle
R
R
Department of Biomolecular Structure, Glaxo Medicines Research Centre, Stevenage, Herts, UK.
Saqi
M
M
Weir
M
M
Lyall
A
A
D000595:Amino Acid Sequence; D001665:Binding Sites / Q000235:genetics; D014644:Genetic Variation; D016333:HIV Protease / Q000737:chemistry / Q000235:genetics; D008958:Models, Molecular; D008969:Molecular Sequence Data; D015394:Molecular Structure; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry / Q000235:genetics*; D016415:Sequence Alignment / Q000379:methods* / Q000706:statistics & numerical data; D017386:Sequence Homology, Amino Acid; D012984:Software
D011506:Proteins; D016333:HIV Protease