The GO-Cellular Component (GO-CC) ontology provides a controlled vocabulary for the consistent description of the subcellular compartments or macromolecular complexes where proteins may act. Current machine learning-based methods used for the automat...
Percolator is an important tool for greatly improving the results of a database search and subsequent downstream analysis. Using support vector machines (SVMs), Percolator recalibrates peptide-spectrum matches based on the learned decision boundary b...
BACKGROUND: Protein superfamilies can be divided into subfamilies of proteins with different functional characteristics. Their sequences can be classified hierarchically, which is part of sequence function assignation. Typically, there are no clear s...
The existing protein complex detection methods can be broadly divided into two categories: unsupervised and supervised learning methods. Most of the unsupervised learning methods assume that protein complexes are in dense regions of protein-protein i...
The plant apoplast is integral to intercellular signalling, transport and plant-pathogen interactions. Plant pathogens deliver effectors both into the apoplast and inside host cells, but no computational method currently exists to discriminate betwee...
Recent advances in computing power and machine learning empower functional annotation of protein sequences and their transcript variations. Here, we present an automated prediction system UniGOPred, for GO annotations and a database of GO term predic...
The objective of this research was to identify and characterize the encoded peptides present in nut storage proteins of . It was found, through in silico prediction, proteomic analysis, and MS spectrometry, that bioactive peptides were mainly found i...
In tandem mass spectrometry (MS/MS)-based proteomics, search engines rely on comparison between an experimental MS/MS spectrum and the theoretical spectra of the candidate peptides. Hence, accurate prediction of the theoretical spectra of peptides ap...
Here we present a free interactive web tool to process and visualize proteomics data sets with a single click. GiaPronto can process all proteomics quantification methods, label-free, SILAC and isobaric labeling, and analyze post-translational modif...
Various 1,3,4-oxadiazole thioether derivatives containing 2-chloro-5-methylene pyridine, 2-chloro-5-methylene thiazole, 3,4-dimethoxy-2-methylene pyridine, and N,N-dimethyl-2-ethylamino moieties were designed, synthesized, and assessed for their anti...
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