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swanss / peptide_design

This repository contains code for the paper: "Tertiary motifs as building blocks for the design of protein-binding peptides"
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Add option to buildGreedyClusters #2

Closed swanss closed 2 years ago

swanss commented 2 years ago

Currently the greedy algorithm tries to cover seed windows. In some cases, this is not ideal, as it can result in clusters that are very similar (e.g. they have partial alignment to another cluster). One solution is to change the greedy algorithm so it tries to cover seed residues (instead of windows).