MOTIVATION: Biological experimental approaches to protein-protein interaction (PPI) site prediction are critical for understanding the mechanisms of biochemical processes but are time-consuming and laborious. With the development of Deep Learning (DL...
The aim of the UniProt Knowledgebase is to provide users with a comprehensive, high-quality and freely accessible set of protein sequences annotated with functional information. In this publication we describe enhancements made to our data processing...
Methods in molecular biology (Clifton, N.J.)
Jan 1, 2023
Prediction of bacterial immunogens is a prerequisite for the process of vaccine development through reverse vaccinology. The application of in silico methods allows significant reduction in time and cost for the discovery of potential vaccine candida...
Recently, prediction of the structure and function of a protein from its sequence underwent a rapid increase in performance. It is primarily due to the application of machine learning methods, many of which rely on the predictive features supplied to...
MOTIVATION: Recent experimental evidence has shown that some long non-coding RNAs (lncRNAs) contain small open reading frames (sORFs) that are translated into functional micropeptides, suggesting that these lncRNAs are misannotated as non-coding. Cur...
MOTIVATION: To provide high quality, computationally tractable annotation of binding sites for biologically relevant (cognate) ligands in UniProtKB using the chemical ontology ChEBI (Chemical Entities of Biological Interest), to better support effort...
MOTIVATION: Protein essentiality is usually accepted to be a conditional trait and strongly affected by cellular environments. However, existing computational methods often do not take such characteristics into account, preferring to incorporate all ...
Protein science : a publication of the Protein Society
Jan 1, 2023
The availability of accurate and fast artificial intelligence (AI) solutions predicting aspects of proteins are revolutionizing experimental and computational molecular biology. The webserver LambdaPP aspires to supersede PredictProtein, the first in...
MOTIVATION: As more data of experimentally determined protein structures are becoming available, data-driven models to describe protein sequence-structure relationships become more feasible. Within this space, the amino acid sequence design of protei...