PISCES: recent improvements to a PDB sequence culling server

By Guoli Wang, Roland L. Dunbrack. 2005

359 citations recorded by the source corpus.

PISCES is a database server for producing lists of sequences from the Protein Data Bank (PDB) using a number of entry- and chain-specific criteria and mutual sequence identity. Our goal in culling the PDB is to provide the longest list possible of the highest resolution structures that fulfill the sequence identity and structural quality cut-offs. The new PISCES server uses a combination of PSI-BLAST and structure-based alignments to determine sequence identities. Structure alignment produces more complete alignments and therefore more accurate sequence identities than PSI-BLAST. PISCES now allows a user to cull the PDB by-entry in addition to the standard culling by individual chains. In this scenario, a list will contain only entries that do not have a chain that has a sequence identity to any chain in any other entry in the list over the sequence identity cut-off. PISCES also provides fully annotated sequences including gene name and species. The server allows a user to cull an input list of entries or chains, so that other criteria, such as function, can be used. Results from a search on the re-engineered RCSB's site for the PDB can be entered into the PISCES server by a single click, combining the powerful searching abilities of the PDB with PISCES's utilities for sequence culling. The server's data are updated weekly. The server is available at .

Subfields: Materials Chemistry, Molecular Biology, Spectroscopy

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Materials Chemistry

In Molecular Biology

In Spectroscopy

Citations in the corpus

Defining and searching for structural motifs using DeepView/Swiss-PdbViewer (2012, methodology): “A search for the generated motif specification was performed across a collection of pdb structures (13180 90% non-redundant X-ray structures having a resolution of 3.0 Å or better obtained by using the PISCES sequence culling server [38,39]).”
DISOPRED3: precise disordered region predictions with annotated protein-binding activity (2014, methodology): “Our understanding of the biological importance and of the widespread occurrence of this phenomenon is gradually expanding, thanks to the fine-tuning of experimental techniques and to computational genome-wide surveys.”
Contact Potential for Structure Prediction of Proteins and Protein Complexes from Potts Model. (2018, methodology): “To calculate the Potts parameters ~ h and J , a nonredundant training set of 6338 protein chains was collected by the Protein Sequence Culling Server (58).”
AMPLE: a cluster-and-truncate approach to solve the crystal structures of small proteins using rapidly computed ab initio models. (2012, methodology): “This set was further filtered using PISCES (Wang & Dunbrack, 2005) to eliminate sequence redundancy to a 5% level.”
MetaDisorder: a meta-server for the prediction of intrinsic disorder in proteins (2012, methodology): “Representative structures were extracted using the PISCES server [43] and filtered according to the following criteria: experimental technique: X-ray crystallography, resolution 2 Å, R-factor 0.2, length 50 – 1000 aa residues, and mutual sequence similarity 20%.”
Solvent accessible surface area approximations for rapid and accurate protein structure prediction (2009, methodology): “The complete list of proteins from the PDB was submitted to the PISCES server [54, 55] to identify proteins with low sequence similarity.”
Sequence-similar, structure-dissimilar protein pairs in the PDB (2007, background): “(5) ‘‘Intra-chain (18 structure)’’—the presence/absence of part of a protein chain in one of the structures, a point mutation (combined with an additional cause), or in two instances, oxidized versus reduced intra-chain S S bonds.”
LYRA, a webserver for lymphocyte receptor structural modeling (2015, methodology): “PDB codes of all BCR and TCR structures present in the IMGT/3Dstructure-DB (16) were retrieved and culled using the Pisces web server (17) to remove all redundant structures.”
Minimizing proteome redundancy in the UniProt Knowledgebase (2016, background): “These include SkipRedundant (10), Decrease Redundancy (11), Pisces (12), UniqueProt (13), CD-HIT (14), FSA-BLAST (15), BlastClust (ftp://ftp.ncbi.nih.gov/ blast/documents/blastclust.html), MinSet (16), BlastCuller (17), FastCluster (18), Leaf (6), UCLUST (19) and Compressive genomics (20).”
A new clustering of antibody CDR loop conformations (2010, neutral): “1“ 1GGIM(31) 1GGCL(30) “40±50“ 1IBGL(36) L1-6 1 L1-12-3 “1F7” 1FIGL(52, Resol=3Å) L1-1 2 L1-13-1 2FB4L 2RHEA L1-2 1 L1-14-2 7FABL(43) L1-3 A 2 L1-14-1 1INDL 1GIGL(9) L1-3 B 1 L1-14-1 1MFAL L1-4 1 L1-11-3 8FABA (Chothia length incorrect) L2-1 16 L2-8-1 1FGVL 1FLRL 1HILA 1IGML 1INDL 1MFAL 2FB4L 2IMMA ”
SCWRL and MolIDE: computer programs for side-chain conformation prediction and homology modeling (2008, background): “However, a list of sequences of proteins in the PDB, such that no two sequences are more than 20% identical to each other, contains only about 4,000 sequence”
Comparison of multiple Amber force fields and development of improved protein backbone parameters (2006, background): “40,41 Dihe-dral plots based on this statistical survey of the PDB provide experimental indication of the values of backbone torsions that are commonly found in proteins.”
Rapid Sampling of Hydrogen Bond Networks for Computational Protein Design (2018, methodology): “A library of native protein crystal structures was generated by providing the Pisces web server 34,35 with the following conditions: Sequence percentage identity ≤ 60; Resolution ≤ 2.0 Å; R-factor ≤ 0.3, Sequence Length 40 – 10000; Non X-ray entries excluded; CA-only entries excluded; Cull PDB by…”