The University College Dublin hosts the Bioware server, which offers a collection of bioinformatics tools. These tools are designed for tasks such as discovering short linear motifs, characterizing peptides, and performing other such analyses of proteomics data. Three of these tools - PeptideLocator, SLiMPred, and Gopher - can be accessed programmatically via REST API.
The PeptideLocator service finds bioactive peptides in a given protein sequence. SLiMPred examines protein sequences to identify potential SLiMs (Shared Linear Motifs). Lastly, Gopher generates alignments of proteins that are orthologous (i.e. that fulfill similar roles in different species).