It is the length of the loop. The defualt is 5 residues. You can choose the number of amino acids from 3 up to 20 residues.
It is the distance between N and C terminal of the loop. You can enter minimum and maximum amount of distance in Ångstrom. ProDa only look at the residues of the insterted loop so the distance is defined as a distance between two ends of the insterted loop (not the anchore residues). LoopFinder look at the residues just before and after the inserted loop (the anchore residues).
Each amino acid can be specified by its one letter name as follow:
Each amino acid can be classified in two groups of Polar (P) and Non polar (N) as follow:
Each amino acid is classified in three groups according to CASP Standard Exposed (E), Buried (B) and intermediated (I) as follow.
Each amino acid is classified in Coil (C), Helix (H) and Strand (E) as follow. At the output page the secondary structure is based on eigth state of DSSP (more detailed information).