PDIdb specifications


Unique identifier OMICS_03023
Name PDIdb
Alternative name Protein-DNA Interface database
Restrictions to use None
Maintained Yes

Publication for Protein-DNA Interface database

PDIdb citations


Protein flexibility in the light of structural alphabets

Front Mol Biosci
PMCID: 4445325
PMID: 26075209
DOI: 10.3389/fmolb.2015.00020

[…] but most studies focused on the protein side. Most of protein/DNA interfaces only extend the classical approaches to analyze protein/protein interfaces or protein/ligands interface. For instance, in PDIdb (Ferrada and Melo, ) or Biswas and coworkers studies, the interface is classified into core and rim regions, the first one being more sequentially conserved. Biswas and coworkers proposed a new […]


Computer Based Annotation of Putative AraC/XylS Family Transcription Factors of Known Structure but Unknown Function

PMCID: 3312330
PMID: 22505803
DOI: 10.1155/2012/103132

[…] h varied sequence while at the same time retaining the helical parameters of the original DNA structure. For each initial model, 10,000 models with randomized DNA sequences were built. Next, from the Protein-DNA Interface database [], a nonredundant set of 208 protein-DNA complexes was obtained. This set was used to derive statistical distance-dependent pairwise potentials at the protein-DNA inter […]

PDIdb institution(s)
Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile

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