SUMMARY: Evolutionary information in the form of a Position-Specific Scoring Matrix (PSSM) is a widely used and highly informative representation of protein sequences. Accordingly, PSSM-based feature descriptors have been successfully applied to impr...
Predicting the subcellular localization of proteins is an important and challenging problem. Traditional experimental approaches are often expensive and time-consuming. Consequently, a growing number of research efforts employ a series of machine lea...
MOTIVATION: The importance of RNA protein-coding gene regulation is by now well appreciated. Non-coding RNAs (ncRNAs) are known to regulate gene expression at practically every stage, ranging from chromatin packaging to mRNA translation. However the ...
SUMMARY: We have implemented the lecular esign aboratory's nti icrobial eptides package ( ), a Python-based software package for the design, classification and visual representation of peptide data. modlAMP offers functions for molecular descriptor c...
MOTIVATION: Residue-residue contacts are of great value for protein structure prediction, since contact information, especially from those long-range residue pairs, can significantly reduce the complexity of conformational sampling for protein struct...
MOTIVATION: Biological data and knowledge bases increasingly rely on Semantic Web technologies and the use of knowledge graphs for data integration, retrieval and federated queries. In the past years, feature learning methods that are applicable to g...
In the era of big data, transformation of biomedical big data into valuable knowledge has been one of the most important challenges in bioinformatics. Deep learning has advanced rapidly since the early 2000s and now demonstrates state-of-the-art perf...
Characterizing the binding behaviors of RNA-binding proteins (RBPs) is important for understanding their functional roles in gene expression regulation. However, current high-throughput experimental methods for identifying RBP targets, such as CLIP-s...
MOTIVATION: The accurate ranking of predicted structural models and selecting the best model from a given candidate pool remain as open problems in the field of structural bioinformatics. The quality assessment (QA) methods used to address these prob...
MOTIVATION: Sources of variability in experimentally derived data include measurement error in addition to the physical phenomena of interest. This measurement error is a combination of systematic components, originating from the measuring instrument...
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