The SIFTS database, maintained at the EBI, provides a mapping between PDB entries and a reference UniProt entry, as well as other datasources.
BLAST tool: NCBI BLAST Download, described here:
Camacho C., Coulouris G., Avagyan V., Ma N., Papadopoulos J., Bealer K., Madden T.L.. (2009) "BLAST+: architecture and applications." BMC Bioinformatics. 10:421.
The BLAST tool is used to search for related UniProt entries and to map features of these entries onto the reference entry. In addition the BLAST tool is used
to find UniProt entries in case the user provides a sequence. From these UniProt entries PDB entries are mapped.
JSMol visualization (version 14.4.2) is used for the
interactive visualization of the protein structure. It does not require a Java plugin.
BioJava version 4.2 is used for pairwise sequence alignment of similar sequences
found by blast. This alignment is done using a PAM250 substitution matrix, a gap opening penalty of 6 and a gap extension penalty of 1.