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Protocols

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


  • BioSerf
  • DomPred
  • DomSerf
  • GenTHREADER
  • pDomTHREADER
  • pGenTHREADER

Maintainers


  • person_outline David Jones
  • person_outline PSIPRED Team
  • person_outline Daniel Buchan

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

 (1206)
library_books

Identification and characterization of smallest pore forming protein in the cell wall of pathogenic Corynebacterium urealyticum DSM 7109

2018
BMC Biochem
PMCID: 5944148
PMID: 29743008
DOI: 10.1186/s12858-018-0093-9

[…] spatial arrangements of secondary structures of potential C. urealyticum porins (hypothetical protein CUR_1714 and hypothetical protein CUR_1715) sequences were submitted to different servers such as PSIPRED (http://bioinf.cs.ucl.ac.uk/psipred), MINNOU (http://minnou.cchmc.org/), PredictProtein (http://www.predictprotein.org/), TMRPres2D (http://bioinformatics.biol.uoa.gr/TMRPres2D/) and PORTER (h […]

library_books

Identification and Functional Characterization of Sugarcane Invertase Inhibitor (ShINH1): A Potential Candidate for Reducing Pre and Post harvest Loss of Sucrose in Sugarcane

2018
Front Plant Sci
PMCID: 5944049
PMID: 29774044
DOI: 10.3389/fpls.2018.00598

[…] g CLC Genomics Workbench. A phylogenetic tree was constructed with the neighbor-joining method using Mega 7.0 software (Kumar et al., ). Secondary structure prediction of ShINH1 was carried out using PSIPRED (http://bioinf.cs.ucl.ac.uk/psipred/) (Jones, ). […]

library_books

Investigation of immunogenic properties of Hemolin from silkworm, Bombyx mori as carrier protein: an immunoinformatic approach

2018
Sci Rep
PMCID: 5934409
PMID: 29725106
DOI: 10.1038/s41598-018-25374-z

[…] The secondary structure prediction using PSIPRED server for Hemolin revealed the existence of 58% β sheet and 41% coils. The β sheets and coils are the classic structure of Ig like domains which validates the SMART tool analysis result. This […]

library_books

Interaction of the GntR family transcription factor Sll1961 with thioredoxin in the cyanobacterium Synechocystis sp. PCC 6803

2018
Sci Rep
PMCID: 5923263
PMID: 29703909
DOI: 10.1038/s41598-018-25077-5

[…] ounded by α-helices,,.Sll1961 belongs to the PlmA subfamily, which is specific to cyanobacteria and shares very limited sequence homology with the other subfamilies. Secondary structure prediction by PSIPRED showed that Sll1961 has 44% α-helices, 16% β-sheets, and 40% coils (Supplementary Fig. ), consistent with the CD results. The prediction indicated that residues 13–78 have propensities toward […]

call_split

The polymorphisms of LCR, E6, and E7 of HPV 58 isolates in Yunnan, Southwest China

2018
Virol J
PMCID: 5918753
PMID: 29695285
DOI: 10.1186/s12985-018-0986-7
call_split See protocol

[…] E6/E7 sequences were aligned to the HPV-58 prototype sequence (GenBank: D90400.1) by MEGA (version 7.0) [] after sequencing.The secondary structures of the HPV-58 E6 and E7 proteins were predicted by PSIPRED v3.3 (http://bioinf.cs.ucl.ac.uk/psipred/) using the default parameters [].The neighbor-joining phylogenetic tree based on the HPV-58 LCR/E6/E7 was constructed by MEGA software (version 7.0) u […]

library_books

An ecoimmunological approach to study evolutionary and ancient links between coagulation, complement and Innate immunity

2018
PMCID: 5955456
PMID: 29473457
DOI: 10.1080/21505594.2018.1441589

[…] al modifications. To predict the structure of GGL27 when released from TFPI-1, the C-terminal peptide was analyzed by web-based PSIPRED and JPred4 software (secondary structure prediction tools). The PSIPRED results for the peptide alone suggest that there are two helical sequence stretches (residues 4-12 and 14-25) in the peptide. This result was also confirmed by the JPred4 tool that predicted i […]

Citations

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

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