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ArchDB specifications

Information


Unique identifier OMICS_08523
Name ArchDB
Restrictions to use None
Maintained Yes

Maintainer


  • person_outline Baldo Oliva

Publications for ArchDB

ArchDB citations

 (4)
library_books

Prediction and characterization of protein protein interaction network in Bacillus licheniformis WX 02

2016
Sci Rep
PMCID: 4726086
PMID: 26782814
DOI: 10.1038/srep19486

[…] we randomly selected 1,000 PPIs and submitted them to the PPI prediction web server (http://sbi.imim.es/iLoops.php). This web server, which defines protein structural features based on the loops from ArchDB and domains from SCOP, was used to validate the PPIs by evaluating whether loop or domain patterns from two input proteins had interaction signatures with random forest classifier.In addition, […]

library_books

The 2014 Nucleic Acids Research Database Issue and an updated NAR online Molecular Biology Database Collection

2013
Nucleic Acids Res
PMCID: 3965027
PMID: 24316579
DOI: 10.1093/nar/gkt1282

[…] e (NDB) and RNA Bricks, a new database of RNA 3D motifs and their contacts (,). The block of protein structure databases includes, among others, updates on Protein Data Bank in Europe (PDBe), PDBsum, ArchDB, Gene3D, ModBase, SCOP and the recently revived iPfam database. Diverse improvements at PDBe include comprehensive visualization and analysis of the rapidly growing collection of electron micro […]

library_books

Evolution of protein indels in plants, animals and fungi

2013
BMC Evol Biol
PMCID: 3706215
PMID: 23826714
DOI: 10.1186/1471-2148-13-140

[…] embrane depolarization rate and motility in sperm [].Much of the large scale study of indels has focused on improved structural modeling of protein loops often through indel databases such as LIP [], ArchDB [], PDBeFold [], IndelPDB [], SCINDEL [], and IndelFR []. Analyses of these data have confirmed earlier findings that indels are commonly found in loops and turns [,], and established that inde […]

library_books

A supersecondary structure library and search algorithm for modeling loops in protein structures

2006
Nucleic Acids Res
PMCID: 1440879
PMID: 16617149
DOI: 10.1093/nar/gkl156

[…] tructures benefit from the classification of loop conformations (,,). A recent work () described the advantage of using HMM sequence profiles in classifying and predicting loops that are derived from ArchDB database (). The good performance of database search methods is well established for cases when canonical loop conformations exist, as in the case of CDR loop predictions (,,) but their perform […]

Citations

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ArchDB institution(s)
Structural Bioinformatics Lab (GRIB-IMIM), Universitat Pompeu Fabra, Barcelona Research Park of Biomedicine (PRBB), Barcelona, Catalonia, Spain
ArchDB funding source(s)
Spanish Ministry of Science and Innovation (MICINN) [FEDER BIO2008-0205, FEDER BIO2011-22568, EUI2009-04018]; FI-DGR 2012 fellowship from ‘Generalitat de Catalunya’

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