PSIPRED pipeline

PSIPRED specifications

Information


Unique identifier OMICS_06088
Name PSIPRED
Alternative names Predict Secondary Structure, PSI-PRED
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Subtools


  • pGenTHREADER
  • BioSerf
  • FFPred
  • MEMPACK
  • DomSerf
  • DISOPRED
  • MEMSAT
  • DomPred
  • GenTHREADER
  • pDomTHREADER

Maintainer


  • person_outline PSIPRED Team <>

Additional information


All method contained in the software can be separately at http://bioinf.cs.ucl.ac.uk/software_downloads/

Publications for Predict Secondary Structure

PSIPRED citations

 (13)
2018
PMCID: 5880399

[…] the flexibility of proteins, program eom [22] was also used to analyze the pgds enzyme with assemblies of different conformers., the 2d secondary structure prediction of pgds was performed using psipred server [23], and the 3d model was generated by swiss-model[24]. the structure validation and quality control was done by procheck [25] and whatcheck module on whatif server [26]., pgds […]

2017
PMCID: 5874642

[…] half-life, instability index, aliphatic index, and grand average of hydropathicity (gravy) [16]. the secondary structure of mic-a was predicted using psi-blast-based secondary structure prediction (psipred, bioinf.cs.ucl.ac.uk/psipred/) which is a simple and precise method to predict the secondary structure of a protein [17,18]., homology modelling predicting the three-dimensional (3d) […]

2017
PMCID: 5535262

[…] within the surface loops of the protein (figure 4a). however, of these csis, the 2 aa insert also appears to extend a helix. the current model is in agreement with secondary structure analyses (psipred/concord), and yielded reassuring measurements by errat, verify3d, rampage and prosa. the locations of these csis in the structure of the b. longum nrde subunit indicate […]

2016
PMCID: 5171910

[…] mighty ta cloning kit (takara bio inc.)., multiple alignment of aprt was prepared using the clustalx software (thompson et al., 1997). the secondary structure of the l. sordida aprt was predicted by psipred v3.3 on the psipred server47. we predicted a protein structure of aprt in l. sordida using the swiss-model automated protein structure homology-modeling server with the template of the aprt […]

2016
PMCID: 4758718

[…] analyzed on a ltq velos (esi) (thermo) or protof (maldi-tof) (perkinelmer)., newly identified tbnups were analyzed for several secondary structure elements, including β-sheets and α-helices using psipred [134] and phyre2 [57], natively unfolded regions using disopred [135], trans-membrane helices using phobius [136], and coiled-coil regions using coils [137]., trypanosomes were cryoprotected […]

PSIPRED institution(s)
Department of Computer Science, University College London, Gower Street, London

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