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- person_outline Baldo Oliva
Publications for ArchDB
Prediction and characterization of protein protein interaction network in Bacillus licheniformis WX 02
[…] 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, […]
The 2014 Nucleic Acids Research Database Issue and an updated NAR online Molecular Biology Database Collection
[…] 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 […]
Evolution of protein indels in plants, animals and fungi
[…] 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 […]
A supersecondary structure library and search algorithm for modeling loops in protein structures
[…] 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 […]
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