D2Check FAQ

  1. What is D2Check?
  2. What does D2Check describe at the protein level?
  3. What does D2Check describe at the residue level?
  4. What quantities are provided at this site?
  5. How is a checking function different than a scoring function?
  6. How is D2Check related to other checking functions, like ProCheck or WHAT_CHECK?
  7. Is D2Check useful for designing structures?
  8. Is the D2Check source code available?
  9. Are the distributions of the dihedral angles available?
  1. What is D2Check?
    • D2Check signals the relative correlation of the dihedral angles in a protein or at a particular residue relative to the PDB. A value of 0 suggests that such a correlation is typical, and subsessive integer increments from 0 indicated the decreased probability in standard deviations, respectively. More information is available in the about page.

  2. What does D2Check describe at the protein level?
      Overlall relative propensity of secondary structure in relation to PDB.

  3. What does D2Check describe at the residue level?
      Relative propensity of secondary structure at the residue level in relation to PDB.

  4. What quantities are provided at this site?
    • D2Check value of an overall protein
    • D2Strip visual represenation of the D2 values at the residue level
    • Phi-Psi (Ramachandran) Plot of a protein
    • Psi-Phi Plot of a protein
    • A file listing the dihedral angles of a protein. (optional)
    • A file listing the D2 values of all the residue positions, k. (optional)
    • Coming: D2 Strip Difference Plots between two protiens at the residue level.
    • Coming: A table of D2 Values for a list of requested proteins.

  5. How is a checking function different than a scoring function?
      Checking functions confirm a statistically relevant property of a given structure with the statistics of a reference set (e.g., the PDB). Scoring functions attempt to rank order a set according to some specified property, e.g., the binding affinity.

  6. How is D2Check related to other checking functions, like ProCheck or WHAT_CHECK?
      There exist several useful checking functions in the literature (and the web) that attempt to measure the accuracy of a given structure. ProCheck and WhatCheck are two popular (and succesful) such checking functions, whick like D2Check, use the residue dihedral angles distributions in their calculation in addition to other factors. ProCheck, for example, also investigate the Ch1-1 and Chi-2 angles, as well as some residue specific properties (i.e. angles for proline, Disulphide bonds).

      Although both ProCheck and WhatCheck provide a good evaluation of protein structures in terms of &Phi and &Psi angles, they do not discriminate the angles using the distributions of adjacent residues: &Psii-&Phii+1. The structural importance of this correlation between adjacent residues is shown in our previous work. (See references in the Conditions Link.)

      You can find additional information about Procheck and WhatChek by clicking following links. PROCHECK WHAT_CHECK

  7. Is D2Check useful for designing structures?
      No and yes. (1) Not directly since it isn't a scoring function. (2) But indirectly, it can provide a check on whether a particular structure exhibits a deviation away from the most likely dihedral angles to a degree that is typical of the reference set. (If it has no deviation, for example, then this would mean that none of the secondary structure is affected by tertiary contacts!)

  8. Is the D2Check source code available?
      Not yet. It will be made available in the fullness of time. We have thus far concentrated on making a useable package through this server. But the components are not yet seemlessly available for a general distribution.

  9. Are the distributions of the dihedral angles available?
      As with the code, they will be available in the fullness of time. Check out the Details page.