PISCES: a protein sequence culling server.

by: G Wang, RL Dunbrack

Bioinformatics, Vol. 19, No. 12. (12 August 2003), pp. 1589-1591.

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Abstract

PISCES is a public server for culling sets of protein sequences from the Protein Data Bank (PDB) by sequence identity and structural quality criteria. PISCES can provide lists culled from the entire PDB or from lists of PDB entries or chains provided by the user. The sequence identities are obtained from PSI-BLAST alignments with position-specific substitution matrices derived from the non-redundant protein sequence database. PISCES therefore provides better lists than servers that use BLAST, which is unable to identify many relationships below 40% sequence identity and often overestimates sequence identity by aligning only well-conserved fragments. PDB sequences are updated weekly. PISCES can also cull non-PDB sequences provided by the user as a list of GenBank identifiers, a FASTA format file, or BLAST/PSI-BLAST output.

@article{citeulike:228639, abstract = {PISCES is a public server for culling sets of protein sequences from the Protein Data Bank (PDB) by sequence identity and structural quality criteria. PISCES can provide lists culled from the entire PDB or from lists of PDB entries or chains provided by the user. The sequence identities are obtained from PSI-BLAST alignments with position-specific substitution matrices derived from the non-redundant protein sequence database. PISCES therefore provides better lists than servers that use BLAST, which is unable to identify many relationships below 40\% sequence identity and often overestimates sequence identity by aligning only well-conserved fragments. PDB sequences are updated weekly. PISCES can also cull non-PDB sequences provided by the user as a list of GenBank identifiers, a FASTA format file, or BLAST/PSI-BLAST output.}, address = {Institute for Cancer Research, Fox Chase Cancer Center, 7701 Burholme Avenue, Philadelphia, PA 19111, USA.}, author = {Wang, G. and Dunbrack, R. L. }, citeulike-article-id = {228639}, doi = {10.1093/bioinformatics/btg224}, issn = {1367-4803}, journal = {Bioinformatics}, keywords = {database, protein-sequence}, month = {August}, number = {12}, pages = {1589--1591}, posted-at = {2008-03-26 14:57:26}, priority = {2}, title = {PISCES: a protein sequence culling server.}, url = {http://dx.doi.org/10.1093/bioinformatics/btg224}, volume = {19}, year = {2003} }

RIS record

TY - JOUR ID - citeulike:228639 L3 - citeulike-article-id:228639 TI - PISCES: a protein sequence culling server. JF - Bioinformatics VL - 19 IS - 12 SP - 1589 EP - 1591 AD - Institute for Cancer Research, Fox Chase Cancer Center, 7701 Burholme Avenue, Philadelphia, PA 19111, USA. SN - 1367-4803 N2 - PISCES is a public server for culling sets of protein sequences from the Protein Data Bank (PDB) by sequence identity and structural quality criteria. PISCES can provide lists culled from the entire PDB or from lists of PDB entries or chains provided by the user. The sequence identities are obtained from PSI-BLAST alignments with position-specific substitution matrices derived from the non-redundant protein sequence database. PISCES therefore provides better lists than servers that use BLAST, which is unable to identify many relationships below 40% sequence identity and often overestimates sequence identity by aligning only well-conserved fragments. PDB sequences are updated weekly. PISCES can also cull non-PDB sequences provided by the user as a list of GenBank identifiers, a FASTA format file, or BLAST/PSI-BLAST output. KW - database KW - protein-sequence AU - Wang, G AU - Dunbrack, RL PY - 2003/08/12/ UR - http://dx.doi.org/10.1093/bioinformatics/btg224 ER -

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