WHAT_CHECK statistics

info info

Citations per year

Number of citations per year for the bioinformatics software tool WHAT_CHECK
info

Tool usage distribution map

This map represents all the scientific publications referring to WHAT_CHECK per scientific context
info info

Associated diseases

This word cloud represents WHAT_CHECK usage per disease context
info

Popular tool citations

chevron_left Structure validation chevron_right
Want to access the full stats & trends on this tool?

Protocols

WHAT_CHECK specifications

Information


Unique identifier OMICS_06364
Name WHAT_CHECK
Alternative name WHATCHECK
Software type Application/Script
Interface Command line interface
Restrictions to use Academic or non-commercial use
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

Download


download.png

Versioning


No version available

Maintainers


  • person_outline Gert Vriend
  • person_outline WHATCHECK Team

Additional information


http://servicesn.mbi.ucla.edu/WHATCHECK/

Information


Unique identifier OMICS_06364
Name WHAT_CHECK
Alternative name WHATCHECK
Interface Web user interface
Restrictions to use Academic or non-commercial use
Input data A structure file.
Computer skills Basic
Stability Stable
Maintained Yes

Maintainers


  • person_outline Gert Vriend
  • person_outline WHATCHECK Team

Additional information


http://servicesn.mbi.ucla.edu/WHATCHECK/

Publication for WHAT_CHECK

WHAT_CHECK citations

 (199)
library_books

Amino Terminal Processing of Helicobacter pylori Serine Protease HtrA: Role in Oligomerization and Activity Regulation

2018
Front Microbiol
PMCID: 5911493
PMID: 29713313
DOI: 10.3389/fmicb.2018.00642

[…] cted to amino acid residues 36–68 and 94–369. Modeller 9.16 () was used for modeling and RasMol for structure analysis and visualization (). The quality of the model was assessed using RAMPAGE () and WHATCHECK (). The resulting model exhibited a good backbone geometry (98% of all residues in the favored regions of the Ramachandran Plot) and no steric clashes larger 0.35 Å were observed. […]

library_books

Solution scattering study of the Bacillus subtilis PgdS enzyme involved in poly γ glutamic acids degradation

2018
PLoS One
PMCID: 5880399
PMID: 29608608
DOI: 10.1371/journal.pone.0195355

[…] secondary structure prediction of PgdS was performed using PsiPred server [], and the 3D model was generated by SWISS-MODEL[]. The structure validation and quality control was done by Procheck [] and WhatCheck module on WhatIf server []. […]

call_split

PhcrTx2, a New Crab Paralyzing Peptide Toxin from the Sea Anemone Phymanthus crucifer

2018
Toxins
PMCID: 5848173
PMID: 29414882
DOI: 10.3390/toxins10020072
call_split See protocol

[…] . Backbone conformation was evaluated by the inspection of the Psi/Phi Ramachandran plot obtained from PROCHECK analysis []. Packing quality of the 3D model was investigated by the calculation of the WHATCHECK Z-score value []. Lastly, sequence–structure compatibility was evaluated by VERIFY3D []. PROCHECK, WHATCHECK, and VERIFY3D were executed from the structure analysis and verification servers’ […]

library_books

Model validation: local diagnosis, correction and when to quit

2018
Acta Crystallogr D Struct Biol
PMCID: 5947777
PMID: 29533239
DOI: 10.1107/S2059798317009834

[…] with R free (Brünger, 1992), bond lengths and angles (Engh & Huber, 1991), twinning (Yeates, 1997), and the multi-criterion systems of PROCHECK (Laskowski et al., 1993), OOPS (Jones et al., 1991) and WHATCHECK (Hooft et al., 1996). Here, we will emphasize validation of the model, from physical principles and prior experience, always within the requirement for a good model-to-data fit.Finding probl […]

library_books

Mechanistic insights into the role of prenyl binding protein PrBP/δ in membrane dissociation of phosphodiesterase 6

2018
Nat Commun
PMCID: 5758567
PMID: 29311697
DOI: 10.1038/s41467-017-02569-y

[…] and displayed the results as “simulated annealing composite omit” maps of the apo-PrBP/δ cavity (Supplementary Fig. ). Structure validation was performed with the programs PHENIX, SFCHECK, PROCHECK, WHAT_CHECK, and RAMPAGE. Potential hydrogen bonds and van der Waals contacts were analyzed using the programs HBPLUS and LIGPLOT. All crystal structure superposition’s of backbone α-carbon traces were […]

library_books

Molecular basis for inner kinetochore configuration through RWD domain–peptide interactions

2017
PMCID: 5709738
PMID: 29046335
DOI: 10.15252/embj.201796636

[…] We evaluated our protein model coordinates with Molprobity (Chen et al, ) and WHATCHECK (Hooft et al, ). For pairwise superposition of structure coordinates, we used LSQKAB (Kabsch, ) or SSM (Krissinel & Henrick, ). We analysed protein interfaces with PISA (Krissinel & Henrick, […]


Want to access the full list of citations?
WHAT_CHECK institution(s)
EMBL, Heidelberg, Germany; EMBL-EBI, Cambridge, UK; Protein Data Ban, Brookhaven National Laboratory, Biology Department, New York, NY, USA

WHAT_CHECK reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review WHAT_CHECK