• Assign distance restraints: If you know what atom pairs should be in contact or in some distances, you can use this option to upload a text file including contact and/or distance information of atom pairs.

    This file can specify the atom-based distances between ith and jth residues in the format:
    "Res_No.i   Atom_type_i    Res_No.j   Atom_type_j   Distance_in_Angstroms   Weight   Restraint Function"

    12   CB    50   CB    8.1  1.0  HARMONIC
    14   CB    57   CA    6.2  2.0  HARMONIC
    21   CB    43   CA    4.0  0.5  RECIPROCAL
    124  CA    84   CB   17.4  10.0  RECIPROCAL
    36   CB   120   CB   17.4  0.25  HARMONIC

    The first and third positions in the file specify the residue indices for residue i and j, respectively, while the second and fourth positions specify the atom types from residues i and j, respectively, to enforce the distance restraint for. Here, distance restraints may be enforced between CA or CB atoms. The fifth position specifies the distance between the two atoms and the sixth position specifies the weight to apply to the restraint. The final position specifies the function that will be used to enforce the distance, either a harmonic restraint or a reciprocal squared restraint. Note, harmonic restraints will invoke a heavy penalty if the restraints are not satisfied, while the reciprocal squared function is less severe. If many distances are specified, it may be better to use the reciprocal squared function, while if only a handful of restraints are specified, it may be better to use harmonic restraints.

    The weight for each constraint can be set to increase the likilihood that it will be satisfied. If they are not specified, the weights will automatically be set to 1 by FoldDesign.

    Here is an example of the restaint file.