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Interactome3D specifications

Information


Unique identifier OMICS_07963
Name Interactome3D
Interface Web user interface
Restrictions to use None
Computer skills Basic
Version 2015_02
Stability Stable
Maintained Yes

Maintainer


  • person_outline Patrick Aloy <>

Publication for Interactome3D

Interactome3D in publications

 (15)
PMCID: 5866917
PMID: 29572294
DOI: 10.15252/msb.20177974

[…] pvclust dendrogram. r packages gplots and rcolorbrewer were used for the heatmap drawing., we obtained a representative dataset of stable human protein interactors with a structural support from the interactome3d database version 2016_06 (mosca et al, ). the interactome3d database contains experimentally observed protein interaction partners for which either a pdb structure exists or a homology […]

PMCID: 5840819
PMID: 29510740
DOI: 10.1186/s13071-018-2745-4

[…] databases: intact [], string [], bioplex [], biogrid []. the resulting interacting pairs were used as input for obtaining the experimental and homology modelled structure interactions using interactome3d []. all experimental and modelled interactions were used to model potential rfg14-3-3e-host interactions using foldx []. the alignment of the human ywhae with rfg14-3-3e was done using […]

PMCID: 5571743
PMID: 28777078
DOI: 10.1107/S2059798317008920

[…] in modelling binary protein–protein interactions (i.e. complexes) using modeller. to perform this, we used query sequences from a publicly available benchmark data set of structures used by the interactome3d resource to provide complexes for their november 2011 release (mosca et al., 2013), which could be mapped to cath. this allowed us to compare our results with those reported in mosca et […]

PMCID: 5514078
PMID: 28717235
DOI: 10.1038/s41598-017-05686-2

[…] sequence there is no guarantee of an interaction. stein et al., using known ppis from six organisms including humans, estimated that less than 30% have a template for comparative modeling. the interactome3d approach uses several criteria to improve accuracy in predicting binding interfaces, but recovered acceptable models for only ~64% of interactions in their database. homology modeling […]

PMCID: 5490940
PMID: 28662117
DOI: 10.1371/journal.pcbi.1005522

[…] that efforts put on fast and automated protocols will be key to finally shift pharmacology to the systems level., we collected experimental protein structures from the human interactome available in interactome3d [], considering each chain separately. then, we used biogps to perform the structural analysis of putative binding pockets. biogps has three steps: (1) cavity search using flapsite, (2) […]


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Interactome3D institution(s)
Joint IRB-BSC Program in Computational Biology, Institute for Research in Biomedicine, Barcelona, Spain

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