PISCES: a protein sequence culling server.

Guoli Wang; Roland L Dunbrack

doi:10.1093/bioinformatics/btg224

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PISCES: a protein sequence culling server.

Guoli Wang·Roland L Dunbrack

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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.

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Algorithms Computing Methodologies Conserved Sequence Database Management Systems Databases, Protein Information Storage and Retrieval Sequence Alignment Sequence Analysis, Protein Sequence Homology, Amino Acid Software Comparative Study Festschrift Research Support, U.S. Gov't, P.H.S.

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Guoli Wang, Roland L Dunbrack. 2003-08-12. PISCES: a protein sequence culling server.. https://doi.org/10.1093/bioinformatics%2Fbtg224

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