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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 citations

 (31)
library_books

Minimizing proteome redundancy in the UniProt Knowledgebase

2016
PMCID: 5199198
PMID: 28025334
DOI: 10.1093/database/baw139

[…] of 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 ge […]

call_split

Implication of Terminal Residues at Protein Protein and Protein DNA Interfaces

2016
PLoS One
PMCID: 5017611
PMID: 27611671
DOI: 10.1371/journal.pone.0162143
call_split See protocol

[…] (dimers) and those extracted from higher order complexes (K-mers), from information available in the PDB.We filtered the DIMER70 list in order to reduce the redundancy between monomers to 25%, using PISCES (http://dunbrack.fccc.edu/PISCES.php) [] with the following input parameters: sequence percentage identity <25%, resolution <3Å, R-factor <0.3, sequence length between 40 and 10,000, include no […]

library_books

A novel secondary structure based on fused five membered rings motif

2016
Sci Rep
PMCID: 4980606
PMID: 27511362
DOI: 10.1038/srep31483

[…] A non-redundant dataset of 4114 protein chains present in 3976 PDB (Protein Data Bank), files were selected using PISCES server, such that the resolution ≤2 Å, R-factor is ≤0.2, and the sequence identity between any two protein sequences is ≤25%. The files used are given in. REDUCE was used to fix the hydrogen po […]

call_split

Ab Initio Coordination Chemistry for Nickel Chelation Motifs

2015
PLoS One
PMCID: 4435748
PMID: 25985439
DOI: 10.1371/journal.pone.0126787
call_split See protocol

[…] uctures were considered and all NMR and theoretical models were excluded. The initial dataset comprised about 928 crystal structures. The dataset was further was culled at 40% sequence identity using PISCES server [] to remove redundant structures due to homodimers and identical entries. Other threshold parameters employed included resolution between 0.0–3.0Å and R value of 0.3. The resulting cull […]

library_books

Briefing in Application of Machine Learning Methods in Ion Channel Prediction

2015
Sci World J
PMCID: 4415473
PMID: 25961077
DOI: 10.1155/2015/945927

[…] y, because the high similarity data will lead to overestimating the performance of the proposed predictors.In order to exclude highly similar sequences from these datasets, BLASTClust, CD-HIT [], and PISCES [] have been developed and could be freely obtained at the addresses listed in . BLASTClust is a program that can be used to cluster either protein or nucleotide sequences. However, since it re […]

library_books

An Overview of the Prediction of Protein DNA Binding Sites

2015
Int J Mol Sci
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 s […]

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

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