Bioinformatics

Using AFPredictor, it was demonstrated that ‘ordered surface carbons’ (OSCs) are a distinguishing feature of AFPs and, more specifically, their ice-binding surfaces. AFPredictor identified AFPs from within a large set of structures with greater than 99% specificity. Furthermore, it was used to identify a novel ice-binding protein by screening a library of homology modeled structures based on cDNA sequences obtained from cold-acclimated winter rye (Secale cereale). - [Read A Computational Screening protocol for Antifreeze/Ice-Structuring Proteins]

Searches are not constrained for only tryptic peptides, and indexed databases (databases only containing tryptic peptides) are not used. In cases where there are very complex mixtures, such as cell lysates, nonspecific cleavages can occur. Therefore, nontryptic peptides would be missed in the database search. - [Read The Use of Mass Spectrometry in Proteomics: Database Searching]