Links

Structure based sequence alignment

Dali: compare the coordinates of query protein structure against those in the PDB.

TCoffee: tools for evaluating and making alignments of DNA and protein. For structures use 3Dcoffee align, the output file that can be read into ESPript to make figures with secondary structure elements.

Structure analysis

PISA: tool for looking at protein, DNA/RNA and ligand interfaces, possible quaternary structures.