Loop Modelling


Protein Design Assistant searches for peptide fragments satisfying selection criteria related to residue polarity, secondary structure, residue type, and its location in the database protein (buried or solvent accessible).
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., HHHHH
Surface location e.g., EIEII
Number of results


ProDa searches for loops, regardless the structural environment. LoopFinder, on the other hand, searches for loops that superpose well on 2, 3, or 4 residues before and after the insert. LoopFinder will scan the entire PDB in minutes. It must run on your computer, so the code and databases are freely available.

Please use the following citation when referencing the results: