JOY statistics

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Citations per year

Number of citations per year for the bioinformatics software tool JOY
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Tool usage distribution map

This map represents all the scientific publications referring to JOY per scientific context
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Associated diseases

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Popular tool citations

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Protocols

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


No version available

Maintainers


  • person_outline Kenji Mizuguchi
  • person_outline Joy Team

Additional information


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

Publication for JOY

JOY citations

 (36)
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Structure Related Differences between Cytochrome Oxidase I Proteins in a Stable Heteroplasmic Mitochondrial System

2017
Genome Biol Evol
PMCID: 5726481
PMID: 29149282
DOI: 10.1093/gbe/evx235
call_split See protocol

[…] expected 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. Usin […]

call_split

Protein sites with more coevolutionary connections tend to evolve slower, while more variable protein families acquire higher coevolutionary connections

2017
F1000Res
PMCID: 5506539
PMID: 28751967
DOI: 10.5256/f1000research.12138.r21733
call_split See protocol

[…] tom 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 as solvent […]

library_books

Recognition of a structural domain (RWDBD) in Gcn1 proteins that interacts with the RWD domain containing proteins

2017
Biol Direct
PMCID: 5438488
PMID: 28526057
DOI: 10.1186/s13062-017-0184-3

[…] ional File which is a newly included Additional file. Kap121p is a hit with high reliability measures in many of the fold recognition methods used. Comment 4. Which manual adjustments were done with JOY (line 196)?Response: The manual adjustments were performed to disallow secondary structure breaks in the target-template alignment and also, as far as possible, the hydrophobic residues in the tar […]

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Less Empathic and More Reactive: The Different Impact of Childhood Maltreatment on Facial Mimicry and Vagal Regulation

2016
PLoS One
PMCID: 5042550
PMID: 27685802
DOI: 10.1371/journal.pone.0163853
call_split See protocol

[…] eriment consisted of four ‘‘condition-blocks” (each lasting 192 sec) and two ‘‘baseline blocks” (each lasting 120 sec). The four condition-blocks, one for each emotional condition (i.e., anger, fear, joy and sadness), were randomly presented. Inside each condition-block the sixteen stimuli, comprising the same emotion, were randomly presented three times (i.e., 48 trials at each block). Each stimu […]

library_books

Gelsolin Cu/ZnSOD interaction alters intracellular reactive oxygen species levels to promote cancer cell invasion

2016
Oncotarget
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. […]

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Examining the Conservation of Kinks in Alpha Helices

2016
PLoS One
PMCID: 4912094
PMID: 27314675
DOI: 10.1371/journal.pone.0157553
call_split See protocol

[…] 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 []. For membran […]


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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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