Short linear motifs – ex nihilo evolution of protein regulation

Computational identification and analysis of protein short linear motifs.

Short linear motifs (SLiMs) in proteins can act as targets for proteolytic cleavage, sites of post-translational modification, determinants of sub-cellular localization, and mediators of protein-protein interactions. Computational discovery of SLiMs involves assembling a group of proteins postulated to share a potential motif, masking out residues less likely to contain such a motif, down-weigh...

Evidence for the Concerted Evolution between Short Linear Protein Motifs and Their Flanking Regions

BACKGROUND Linear motifs are short modules of protein sequences that play a crucial role in mediating and regulating many protein-protein interactions. The function of linear motifs strongly depends on the context, e.g. functional instances mainly occur inside flexible regions that are accessible for interaction. Sometimes linear motifs appear as isolated islands of conservation in multiple seq...

Identifying Protein Short Linear Motifs by Position-Specific Scoring Matrix

Prediction of High-throughput Protein-Protein Interactions and Calmodulin Binding Using Short Linear Motifs

Prediction of protein-protein interactions (PPIs) is a difficult and important problem in biology. Although high-throughput technologies have made remarkable progress, the predictions are often inaccurate and include high rates of both false positives and false negatives. In addition, prediction of Calmodulin Binding Proteins (CaM-binding) is a problem that has been investigated deeply, though ...

Jon Perez Laraudogoitia Infinity Machines and Creation Ex Nihilo

In this paper a simple model in particle dynamics of a well-known supertask is constructed (the supertask was introduced by Max Black some years ago). As a consequence, a new and simple result about creation ex nihilo of particles can be proved compatible with classical dynamics. This result cannot be avoided by imposing boundary conditions at spatial infinity, and therefore is really new in th...