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ncIDP specifications

Information


Unique identifier OMICS_26275
Name ncIDP
Alternative name Neighbor Corrected IDP Library
Software type Framework/Library
Interface Web user interface
Restrictions to use None
Input data A protein sequence.
Input format FASTA
Computer skills Basic
Stability Stable
Maintained No

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Publication for Neighbor Corrected IDP Library

ncIDP citations

 (3)
library_books

Solution NMR structure of the TRIM21 B box2 and identification of residues involved in its interaction with the RING domain

2017
PLoS One
PMCID: 5533445
PMID: 28753623
DOI: 10.1371/journal.pone.0181551

[…] s as α-helices and β-sheets. Backbone chemical shifts and sequence data was used as input to the CSI 3.0 server in order to identify secondary structure []. Random coil shift were predicted using the ncIDP (Neighbor Corrected IDP Library) server [] based on the amino acid sequence of TRIM21 B-box286-130. The chemical shift values of the NH, H, Hα, CO, Cα and Cβ atoms of the assigned residues were […]

library_books

Probing Medin Monomer Structure and its Amyloid Nucleation Using 13C Direct Detection NMR in Combination with Structural Bioinformatics

2017
Sci Rep
PMCID: 5361114
PMID: 28327552
DOI: 10.1038/srep45224

[…] shifts (see BMRB ID: 27021). These shifts were used to probe secondary structure propensities using Secondary Structure Propensity (SSP), neighbour corrected Intrinsically Disordered Protein Library (ncIDP) and the Collaborative Computing Project for NMR (CCPN) software Analysis. SSP provides a score for secondary structure propensity for carbon shifts with negative values indicating β-strand and […]

library_books

Characterization of ERM transactivation domain binding to the ACID/PTOV domain of the Mediator subunit MED25

2015
Nucleic Acids Res
PMCID: 4538835
PMID: 26130716
DOI: 10.1093/nar/gkv650

[…] fts compiled from strictly disordered proteins. Secondary chemical shifts 13Cα–13Cβ were here calculated as indicators for residual local secondary structure based on the random coil values database (ncIDP) from Tamiola et al. () that are neighbour-corrected. The secondary structure propensity (SSP) analysis compares the Cα and Cβ values not only to the random coil values expected in a strictly di […]

Citations

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ncIDP institution(s)
Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
ncIDP funding source(s)
Supported by a VIDI Grant from The Netherlands Organization for Scientific Research (NWO).

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