ProtNAff: protein-bound Nucleic Acid filters and fragment libraries.

Motivation: Atomistic models of nucleic acids (NA) fragments can be used to model the 3D structures of specific protein-NA interactions and address the problem of great NA flexibility, especially in their single-stranded regions. One way to obtain relevant NA fragments is to extract them from existing 3D structures corresponding to the targeted context (e.g.

HECTAR: a method to predict subcellular targeting in heterokonts.

Background: The heterokonts are a particularly interesting group of eukaryotic organisms; they include many key species of planktonic and coastal algae and several important pathogens. To understand the biology of these organisms, it is necessary to be able to predict the subcellular localisation of their proteins but this is not straightforward, particularly in photosynthetic heterokonts which possess a complex chloroplast, acquired as the result of a secondary endosymbiosis. This is because the bipartite target peptides that deliver proteins to these chloroplasts can be easily confused with the signal peptides of secreted proteins, causing currently available algorithms to make erroneous predictions.

Prediction of amphipathic in-plane membrane anchors in monotopic proteins using a SVM classifier.

Background: Membrane proteins are estimated to represent about 25% of open reading frames in fully sequenced genomes. However, the experimental study of proteins remains difficult. Considerable efforts have thus been made to develop prediction methods.