PISCES protocols

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PISCES specifications

Information


Unique identifier OMICS_05153
Name PISCES
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Publication for PISCES

PISCES in pipelines

 (2)
2015
PMCID: 4394471
PMID: 25756377
DOI: 10.3390/ijms16035194

[…] subsequences of other proteins in a data set were eliminated. the frequently used clustering program contains blastclust (available from the national center for biotechnology information, ncbi), the pisces web server [], and the h-cd-hit program []. using the metadbsite method, the protein–dna complexes with a resolution better than 3.0 å were submitted to h-cd-hit to obtain a nonredundant data […]

2009
PMCID: 2795474
PMID: 19888216
DOI: 10.1038/msb.2009.80

[…] (%asas) were calculated with psaia ()., protein structures were downloaded from the protein data bank website (pdb, http://www.rcsb.org/pdb). removal of redundant structures was achieved using the pisces server () with the following criteria: x-ray structures only; no structure with cα only; resolution ⩽3 å; r-factor ⩽0.3; sequence length between 40 and 10 000 amino acids; and maximum 90% […]


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PISCES in publications

 (20)
PMCID: 5799304
PMID: 29402983
DOI: 10.1038/s41598-018-20819-x

[…] the swiss-prot (version 57.0) (http://www.uniprot.org/). this dataset contained 381 hiv-1 protein sequences and 109 hiv-2 protein sequences. the sequence identity was analyzed by a culling program pisces (http://dunbrack.fccc.edu/pisces.php),. the distribution of their sequence identity percentage was shown in table . in order to get enough number of protein sequences, hiv-1 dataset and hiv-2 […]

PMCID: 5517432
PMID: 28724993
DOI: 10.1038/s41598-017-06195-y

[…] generated by yang and li was used to estimate the effectiveness of the new prediction methods. the protein sequences in this dataset were downloaded from the animal toxin database (atdb), . the pisces, was used to cull the presynaptic and postsynaptic neurotoxin sequences where no two proteins in each dataset had more than 80% sequence identify. in the final dataset, presynaptic neurotoxin […]

PMCID: 5199198
PMID: 28025334
DOI: 10.1093/database/baw139

[…] our reference proteomes., there are a host of software programs and methods aimed at minimizing redundancy within protein sequence databases. these include skipredundant (), decrease redundancy (), pisces (), uniqueprot (), cd-hit (), fsa-blast (), blastclust (ftp://ftp.ncbi.nih.gov/blast/documents/blastclust.html), minset (), blastculler (), fastcluster (), leaf (), uclust () and compressive […]

PMCID: 4589334
PMID: 26422468
DOI: 10.1371/journal.pone.0139280

[…] not beta-hairpin) motifs information in archdb40 database [] were considered. thirdly, only proteins with six nuclei (c,c α,c β,h n,h α,n) assigned css were considered. finally, we utilized the pisces program [] to remove the highly similarity sequences. after strictly following the aforementioned procedures, 123 proteins were obtained. among 123 proteins, 87% (107 sequences) proteins […]

PMCID: 4394471
PMID: 25756377
DOI: 10.3390/ijms16035194

[…] subsequences of other proteins in a data set were eliminated. the frequently used clustering program contains blastclust (available from the national center for biotechnology information, ncbi), the pisces web server [], and the h-cd-hit program []. using the metadbsite method, the protein–dna complexes with a resolution better than 3.0 å were submitted to h-cd-hit to obtain a nonredundant data […]


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PISCES institution(s)
Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA, USA

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