Table 1.
Description of protein clusters in terms of RMSD.
Fig 1.
Relation between assignments based on RMSDA and RMSD.
A shows the percentage (Y-axis) of matching RMSDA- and RMSD assignments among all the RMSD assignments for a given cluster that lie within a certain distance (X-axis) from the cluster centre, i.e. the corresponding protein block (PB); B shows the reverse of A, namely, the percentage of matching RMSDA- and RMSD assignments among all the RMSDA assignments for a given cluster that lie within a certain RMSDA-distance (X-axis) from the centre; C shows the percentage of matching assignment for each RMSD-cluster among all fragments. The full set of fragments for this investigation is PDB30 (see Methods for details).
Fig 2.
Discrepancy examples between RMSDA and RMSD.
Structural alignment of a 5-residue protein fragments (green) against the standard alpha-helical structure (red) with dihedral angles ϕi = −57, ψi = −47, i = 1, …, 5. The examples (A)-(C) are chosen such that to highlight that one can find a (green) fragment with the same RMSDA distance value to the reference (red) fragment but varying RMSD. In (D), on the contrary, we show an example of a (green) fragment that has RMSDA of 0 to the reference (red), but a large RMSD. Dihedral angles of the fragment (A) are ϕi = −61.1, ψi = −42.8, i = 1, …, 5, its RMSDA to the standard helix is 14.1° and its RMSD to the standard helix is 0.09 Å; Dihedral angles of the fragment (B) are ϕi = −32.9, ψi = −42.9, i = 1, …, 5, its RMSDA to the standard helix is 14.1421 and its RMSD to the standard helix is 1.0065; Dihedral angles of the fragment (C) are all ϕi = −57, ψi = −47, except for ϕ3 = −17, its RMSDA to the standard helix is again 14.1421 and its RMSD to the standard helix is 0.74. Dihedral angles of the fragment (D) are all ϕi = −57, ψi = −47, except ω3 = 0 instead of the usual 180.
Table 2.
Predicted and actual angles.
Table 3.
Degrees of freedom.
Table 4.
Structural Words for RMSDA and RMSD assignments.
Fig 3.
Generation of predictors based on RMSD statistics between a protein fragment and the 16 basic protein blocks, schematic representation.
Fig 4.
Generation of predictors based on physico-chemical properties of amino acids comprising a protein fragment, schematic representation.