CoNSEnsX with Django backend
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README.md

CoNSEnsX

Source code of the consensx.itk.ppke.hu site.

You can find the dockerized, ready-to-use version of the software here.

The server is specifically designed for structural ensembles that were generated to reflect the internal dynamics of proteins at a given time scale. Such ensembles are typically generated by restrained molecular dynamics methods or selection-based approaches. CoNSEnsX+ provides an ensemble-averaged analysis of all experimental parameters recognized in the input and offers a simple greedy selection approach to identify the sub-ensemble best reflecting the parameters chosen.

For detailed usage and description visit the CoNSEnsX description page.

NOE restraints

The following STR fields are needed for CoNSEnsX to identify NOE data:

  • in the save block:
    Gen_dist_constraint_list.Constraint_type      NOE
  • in the loop block:
    Gen_dist_constraint.ID
    Gen_dist_constraint.PDB_residue_no_1
    Gen_dist_constraint.PDB_residue_no_2
    Gen_dist_constraint.Comp_ID_1
    Gen_dist_constraint.Comp_ID_2
    Gen_dist_constraint.Atom_ID_1
    Gen_dist_constraint.Atom_ID_2

Note: The atomic naming convention must match the naming convention used in the input PDB file


Back-calculated parameters

RDC

The following STR fields are needed for CoNSEnsX to identify RDC data:

  • in the save block:
    RDC_list_[num]
  • in the loop block:
    RDC.Seq_ID_1        OR Atom_one_residue_seq_code
    RDC.Atom_type_1     OR Atom_one_atom_name
    RDC.Seq_ID_2        OR Atom_two_residue_seq_code
    RDC.Atom_type_2     OR Atom_two_atom_name
    RDC.Val             OR Residual_dipolar_coupling_value

Order parameters

The following STR fields are needed for CoNSEnsX to identify order parameter data:

  • in the save block:
    order_param
  • in the loop block:
    S2_value
    Residue_seq_code
    Atom_name

Scalar coupling

The following STR fields are needed for CoNSEnsX to identify scalar coupling data:

  • in the save block:
    coupling_constants
  • in the loop block:
    Atom_one_residue_seq_code
    Coupling_constant_code

Chemical shifts

The following STR fields are needed for CoNSEnsX to identify chemical shifts data:

  • in the save block:
    chem_shift_list_[num] OR assigned_chem_shift_list_[num]
  • in the loop block:
    Atom_chem_shift.Seq_ID        OR Residue_seq_code
    Atom_chem_shift.Comp_ID     OR Residue_label
    RDC.Seq_ID_2        OR Atom_name
    RDC.Atom_type_2     OR Chem_shift_value