ProDA (Protein Design Assistant)
Replacement of protein segments with external peptide fragments is an efficient method. in the design of novel engineered protein, a researcher confronts with selection of appropriate peptide fragments. These peptides are used to alter protein properties and mimic protein structures in a manner that the overall fold of protein largely preserve. The peptide fragment proposer (PFpro) web server is a new service to propose a set of appropriate peptide using the structural and physicochemical characteristics of user's input pdb file. The output page provides a list of distinct fragments found by a search for best candidates in more than 600 million peptides.
Number of amino acids
Distance between two ends (Å) Minimum Maximum
Polarity e.g., PPNPN
Amino acid sequence e.g., K..SL
Secondary Structure e.g., SSSCC
Hydrophobicity e.g., EIEII
Number of results