Computation of nDp for homo-oligomeric structures present in PDB
The pre-computed nDp metric is available for download here --- the tabulated file contains the following columns:
- code: code of the 'Biological assembly', in the form of xxxx_1, xxx_2 ... _1/_2 means that there can be multiple possible assemblies proposed by PDB.
- chain: chain identifier
- aa: residue name
- residue_number: residue number (renumbered from the SEQRES sequence)
- No subunits: Number of subunits in the homo-oligomer
- Symmetry: Internal symmetry of the homo-oligomer
- X: x-coordinate of the residue
- Y: y-coordinate of the residue
- Z: z-coordinate of the residue
- relative ASA: relative accessible surface area of the residue, calculated using AREAIMOL
- stickiness: stickiness of the patch surrounding the residue, as defined in Levy et al. PNAS 2012.
- d_plan: distance of the residue to the closest bounding plane.
- d_plan_symAxis: type of symmetry axis which the bounding plane is associated to (180 = 2-fold; 120 = 3-fold; etc.)
- d_plan_face : face-id of the homo-oligomer the axis is associated to
- h_100_repre : indicates whether the homo-oligomer is part of a set non-redundant at 100% sequence identity
- h_90_repre : indicates whether the homo-oligomer is part of a set non-redundant at 90% sequence identity
- h_80_repre : indicates whether the homo-oligomer is part of a set non-redundant at 80% sequence identity