PISCES: a protein sequence culling server

PISCES: a protein sequence culling server

Received on October 4, 2002; revised on January 30, 2003; accepted on March 18, 2003 | Guoli Wang and Roland L. Dunbrack Jr*
PISCES is a public server designed to cull sets of protein sequences from the Protein Data Bank (PDB) based on sequence identity and structural quality criteria. It offers several functionalities, including culling the entire PDB, culling a list of user-provided PDB chain identifiers, and culling any set of sequences provided by the user in FASTA format, GenBank identifiers, or BLAST/PSI-BLAST output. PISCES uses PSI-BLAST to calculate sequence identities, which provides better estimates at longer evolutionary distances compared to BLAST. The server updates sequences in the PDB weekly and applies criteria such as resolution, R-value, sequence length, and Cα-only status. PISCES aims to provide the longest lists of high-resolution structures that meet the specified criteria. The server is available at http://www.fccc.edu/research/labs/dunbrack/pisces and can be contacted at rl.dunbrack@fcc.edu.PISCES is a public server designed to cull sets of protein sequences from the Protein Data Bank (PDB) based on sequence identity and structural quality criteria. It offers several functionalities, including culling the entire PDB, culling a list of user-provided PDB chain identifiers, and culling any set of sequences provided by the user in FASTA format, GenBank identifiers, or BLAST/PSI-BLAST output. PISCES uses PSI-BLAST to calculate sequence identities, which provides better estimates at longer evolutionary distances compared to BLAST. The server updates sequences in the PDB weekly and applies criteria such as resolution, R-value, sequence length, and Cα-only status. PISCES aims to provide the longest lists of high-resolution structures that meet the specified criteria. The server is available at http://www.fccc.edu/research/labs/dunbrack/pisces and can be contacted at rl.dunbrack@fcc.edu.
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