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Information


Unique identifier OMICS_20566
Name PPCheck
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Ramanathan Sowdhamini

Publication for PPCheck

PPCheck citations

 (5)
library_books

Bioinformatics comparisons of RNA binding proteins of pathogenic and non pathogenic Escherichia coli strains reveal novel virulence factors

2017
BMC Genomics
PMCID: 5571608
PMID: 28836963
DOI: 10.1186/s12864-017-4045-3

[…] active and the inactive hexamers of the protein for performing MD simulations, to save computational time. Various energy components of the dimer interface were measured using the in-house algorithm, PPCheck []. This algorithm identifies interface residues in protein-protein interactions on the basis of simple distance criteria, following which the strength of interactions at the interface are qua […]

library_books

Protein protein interfaces are vdW dominant with selective H bonds and (or) electrostatics towards broad functional specificity

2017
Bioinformation
PMCID: 5512853
PMID: 28729757
DOI: 10.6026/97320630013164

[…] anually curated non-redundant dataset of 278 heterodimer subunit interfaces as described elsewhere [] to relate interface size with vdW, H-bond and electrostatic energy to gain further insights using PPCheck (a robust tool for inter-atomic interface analysis) [, ]. This analysis is restricted to hetero complexes for the purpose of clarity and comparison with previously known information. It should […]

call_split

Integrative modelling of TIR domain containing adaptor molecule inducing interferon β (TRIF) provides insights into its autoinhibited state

2017
Biol Direct
PMCID: 5397763
PMID: 28427457
DOI: 10.1186/s13062-017-0179-0
call_split See protocol

[…] domain to guide the docking, the top poses were those in which the BB loop was present in the interface Docked poses were ranked using DockScore [] and interactions at the interface identified using PPCheck []. Both these softwares were developed in the lab. DockScore is a scoring scheme that utilizes various parameters such as the number of interfacial hydrophobic residues, spatial clustering of […]

call_split

PIMA: Protein Protein interactions in Macromolecular Assembly a web server for its Analysis and Visualization

2016
Bioinformation
PMCID: 4857458
PMID: 27212837
DOI: 10.6026/97320630012009
call_split See protocol

[…] PPCheck (a tool for quantifying protein-protein interactions) was used to identify interactions in macro-molecular assemblies. Residues within a Calpha - Calpha distance threshold of 10Å are initially […]

library_books

Energetic Calculations to Decipher pH Dependent Oligomerization and Domain Swapping of Proteins

2015
PLoS One
PMCID: 4456399
PMID: 26043007
DOI: 10.1371/journal.pone.0127716

[…] int near pH 10. At D-pH, the net charge on these basic amino acids is close to zero leading to weak salt bridge interactions at D-pH (). pH-dependent energy profile of NSI and detailed analysis using PPCheck server [] revealed unfavourable interactions between eight positively charged residues (). The magnitude of these unfavourable interactions drastically reduces at D-pH around 10, since net cha […]

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PPCheck institution(s)
National Centre for Biological Sciences, Bangalore, Karnataka, India; SASTRA University, Tirumalaisamudram, Thanjavur, Tamil Nadu, India
PPCheck funding source(s)
Supported by DBT-CoE grant (grant number: BT/01/COE/09/01).

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