Loop Modelling
Welcome to the help page of ProDA (Protein Design Assistant)

Our aim

ProDA is developed to returns suitable peptide fragments. Users can specify features to get desired peptide fragments. ProDA gives five different parameters as input. It search our database to find the best fragments. User can find peptide fragments based on 6 input criteria. The first two inputs are mandatory others are optional:

1. Number of amino acids
2. Distance between two ends
3. Amino acid compsition
4. Polarity
5. Surface location
6. Seconday structure


    Mandatory inputs


    1. Number of amino acids

    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.



    2. Distance between two ends

    It is the distance between N and C terminal of the loop. You can enter minimum and maximum amount of distance in Ã…ngstrom. 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).




    An example of input



    Optional inputs


    3. Amino acid compsition

    Each amino acid can be specified by its one letter name as follow:




    4. Polarity

    Each amino acid can be classified in two groups of Polar (P) and Non polar (N) as follow:




    5. Surface location

    Each amino acid is classified in three groups according to CASP Standard Exposed (E), Buried (B) and intermediated (I) as follow.



    6. Seconday structure

    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).





    You can use regular expression when you need to write more complex input.



    Example 1 : (abc)*



    Example 2 : de | abc



    Example 3 : a+



    Example 4 : a*



    Example 5 : a?