DSC: public domain protein secondary structure predication.
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Amino Acid Sequence↗
Biomedical subjects
R Sayle
Publications and source records attributed to R Sayle.
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.
Amino Acid Sequence↗
PdbMotif--a tool for the automatic identification and display of motifs in protein structures.
A program PdbMotif, which automatically identifies protein motifs in a protein data bank file and generates a script file which can be read directly by the molecular rendering program RasMol, is described. PdbMotif accepts the standard PROSITE pattern syntax and will scan the PROSITE pattern database or a set of user defined patterns. Any motifs detected are automatically highlighted in the RasMol image.
Algorithms↗