JOY statistics

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Citations per year

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JOY specifications

Information


Unique identifier OMICS_29243
Name JOY
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Subtools


  • hydrogen bonding patterns (HBOND)
  • secondary structures (SSTRUC)
  • Solvent accessibility (PSA)

Maintainers


  • person_outline Kenji Mizuguchi <>
  • person_outline Joy Team <>

Additional information


http://mizuguchilab.org/joy/joyman.htm

Information


Unique identifier OMICS_29243
Name JOY
Software type Application/Script
Interface Graphical user interface
Restrictions to use Academic or non-commercial use
Operating system Unix/Linux
Programming languages Fortran
Computer skills Medium
Version 5.0
Stability Stable
Maintained Yes

Subtools


  • hydrogen bonding patterns (HBOND)
  • secondary structures (SSTRUC)
  • Solvent accessibility (PSA)

Versioning


Add your version

Maintainers


  • person_outline Kenji Mizuguchi <>
  • person_outline Joy Team <>

Additional information


http://mizuguchilab.org/joy/joyman.htm

Publication for JOY

JOY in pipeline

2012
PMCID: 3306375
PMID: 22438895
DOI: 10.1371/journal.pone.0033138

[…] tree was generated using a neighbor-joining (nj) method . the mega program (version 4.0) was used to draw the tree . the tree was annotated with bootstrap values (1000 iterations). the program joy was used for displaying the three-dimensional structural features of the human dohh and leishmania dohh protein sequences with respect to the crystal structure of the e. coli yiba protein., […]


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JOY in publications

 (28)
PMCID: 5726481
PMID: 29149282
DOI: 10.1093/gbe/evx235

[…] to reflect functional differences. because the structures of the bivalve proteins are unknown, structural environment was estimated for coi using the known bovine structure 1v54. the program joy () was used for this purpose, partitioning coi into categories for 11 structural environments. for illustration, consider an environment relating to main chain to main chain hydrogen bonding. […]

PMCID: 5506539
PMID: 28751967
DOI: 10.5256/f1000research.12138.r21733

[…] coordinates supplied in the individual pdb file. structural properties, such as solvent accessibility, secondary structures, and hydrogen bonds, were computed from the protein structure using the joy package ( http://mizuguchilab.org/joy/) solvent accessibility was measured using the psa program from the joy package, and residues that had an accessible surface area <7% were treated […]

PMCID: 5438488
PMID: 28526057
DOI: 10.1186/s13062-017-0184-3

[…] aligning the multiple sequence alignment of gcn1 (previous step) to its template, a kap121p protein, a karyopherin (pdb id: 3w3w) using hhpred []. finally this alignment was manually adjusted using joy [] and used to generate 3-d models using modeller 9v12 [] for the gcn1 region 2207–2602. manual adjustments in the alignment were made to disallow secondary structure breaks and, as far […]

PMCID: 5288152
PMID: 27391159
DOI: 10.18632/oncotarget.10451

[…] identified using a distance cut off of 5 angstrom between apolar groups in the apolar side chains []. the hydrogen bonds formed between subunits are identified using hbond program which is a part of joy suite []. the interactions that exist in at least 60% of the simulated structures were considered as dynamically stable and used for the interpretation of stability., gene expression microarray […]

PMCID: 4912094
PMID: 27314675
DOI: 10.1371/journal.pone.0157553

[…] measured by kink finder is shown in fig f in . a list of pdb codes in each set is available in ., for the sets of soluble, membrane, and redundant membrane chains, helices were annotated using joy []. any helical segments separated by only one or two residues were combined. the ends of helices were trimmed until they satisfied the criteria for a helical seed used by mc-helan []. […]


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JOY institution(s)
Department of Biochemistry, University of Cambridge, Cambridge, UK; Department of Biochemistry, University of Turku, Turku, Finland; Computational Chemistry and Protein Crystallography, Pfizer Central Research, Kent, UK
JOY funding source(s)
Supported by Pfizer Central Research, the SERC, the Imperial Cancer Research Fund, Long Term Fellowship of the International Human Frontier Science Program Organization and the Wellcome Trust.

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