August 20, 2019: We were having problems with the server in the last month. They are fixed now (hopefully).
PISCES has several capabilities in producing subsets of sequences from larger sets:
subsets of sequences culled from the entire PDB according to structure
quality and maximum mutual sequence identity
subsets of sequences culled from a list of PDB chains or PDB entries input
by the user, according to structure quality and maximum mutual sequence identity
subsets of sequences from user-input lists of GenBank accession numbers,
according to maximum mutual sequence identity
subsets of sequences from user-input BLAST or PSI-BLAST output; the hits are
culled according to mutual sequence identity
Important features of this service:
sequence identities for PDB sequences are determined by creating a hidden Markov model
for every unique PDB sequence with the program HHblits (Söding et al.) and searching
the resulting collection of HMMs with each individual HMM with the program HHsearch.
PISCES can also therefore provide meaningful results at low sequence identity (15-30%).
non-PDB sequences are culled with sequence identities from PSI-BLAST. We do not search
the non-redundant sequence database, but rather use the user's input sequences as the
database. This server will usually be used to cull a related set of sequences, for instance
those from a PSI-BLAST search.
the server provides output lists of accession IDs and files of the sequences in FASTA
format on a webpage created for the user. The address is e-mailed to the user upon
completion of the calculation, and will be stored for one week.
PDB sequences are updated weekly from the PDB mmCIF files.
PISCES now correctly handles multi-character chain IDs, which are now used in very large
structures by the PDB