Proceedings of the National Academy of Sciences of the United States of America
Apr 9, 2015
Transmembrane β-barrels (TMBs) carry out major functions in substrate transport and protein biogenesis but experimental determination of their 3D structure is challenging. Encouraged by successful de novo 3D structure prediction of globular and α-hel...
Functional annotation of the gigantic metagenomic data is one of the major time-consuming and computationally demanding tasks, which is currently a bottleneck for the efficient analysis. The commonly used homology-based methods to functionally annota...
The discovery of peptides possessing high biological activity is very challenging due to the enormous diversity for which only a minority have the desired properties. To lower cost and reduce the time to obtain promising peptides, machine learning ap...
KeBABS provides a powerful, flexible and easy to use framework for KE: rnel- B: ased A: nalysis of B: iological S: equences in R. It includes efficient implementations of the most important sequence kernels, also including variants that allow for tak...
Many proteins are known to be associated with cancer diseases. It is quite often that their precise functional role in disease pathogenesis remains unclear. A strategy to gain a better understanding of the function of these proteins is to make use of...
Quorum sensing peptides (QSPs) are the signaling molecules used by the Gram-positive bacteria in orchestrating cell-to-cell communication. In spite of their enormous importance in signaling process, their detailed bioinformatics analysis is lacking. ...
BACKGROUND: DNA-binding proteins play a pivotal role in various intra- and extra-cellular activities ranging from DNA replication to gene expression control. Identification of DNA-binding proteins is one of the major challenges in the field of genome...
MOTIVATION: Machine learning may be the most popular computational tool in molecular biology. Providing sustained performance estimates is challenging. The standard cross-validation protocols usually fail in biology. Park and Marcotte found that even...
Improved understanding of the forces that determine drug specificity to their targets is important for drug design and discovery, as well as for gaining knowledge about molecular recognition. Here, we present a machine learning approach that includes...
MOTIVATION: Glycosylation is a ubiquitous type of protein post-translational modification (PTM) in eukaryotic cells, which plays vital roles in various biological processes (BPs) such as cellular communication, ligand recognition and subcellular reco...
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