These are our current set of parameter and volume files for radii and volumes. They have been carefully optimized for packing calculations. We suggest you use these. They are derived from the following publication:
J Tsai, R Taylor, C Chothia & M Gerstein (1999). "The Packing Density in Proteins: Standard Radii and Volumes," J. Mol. Biol. 290: 253-266.
Parameters
ProtOr.atom-defs.dat Atom definition file with radii (description). ProtOr.resi-defs.dat Residue definition file (description). ProtOr.pdblist.dat List of 87 structures selected from SCOP (see above paper). Volumes
ProtOr.stdvol173.dat Final set of 173 volumes from atoms of 21 amino acids. ProtOr.atom-vols.dat Detailed volumes for the 18 basic atom types. ProtOr.residue-vols.dat Volumes for each residue. The volume files were calculated using Voronoi polyhedra with the run parameters:
- ProtOr radii set (ProtOr.atom-defs.dat & ProtOr.resi-defs.dat)
- SCOP set of 87 pdb structures (ProtOr.pdblist.dat)
- BL+ atom selection (help on this)
- simplified Method B to position the dividing plane
These are a provisional set of parameter and volume files for both proteins and nucleic acids. They were created by Neil Voss in the Fall 2000. They are currently under active development.
Parameters
| NucProt.atom-defs.dat | Atom definition file with radii (description). |
| NucProt.resi-defs.dat | Residue definition file (description). Please note that this set has more than 21 residues. This necessitates the using of a different routine to read this file (initial_residues_nt). |
| NucProt.pdblist.dat | List of 6 RNA structures (NDB codes). |
Volumes
| NucProt.stdvol258.dat | Provisional set of 258 volumes from atoms of 21 amino acids and 4 nucleotides. Please note that this set has more than 173 volumes. This necessitates the using of a different routine to read this file (read_standard_volumes_nt). |
| NucProt.atom-vols.dat | Detailed volumes for ~21 basic atom types (provisional). |
The volume files were calculated using Voronoi polyhedra with the run parameters:
The following conventions are used to give the parameters used and their resulting volumes if available. Note, the first portion of the name refers to atom radii typing scheme used (ie ProtOr) while the remainder outside of the identifiers below denote parameter values
*.atom-defs.* Atom definition file, with radii *.resi-defs.* Residue definition file *.pdblist.* List of structures *.vol173.* List of raw 173 output residue atom volumes *.atom-vols.* N atom volumes (& detail) *.residue-vols.* Residue volumes *.vol173predicted.* List of predicted 173 residue atom volumes, expaned from the *.atom-vols* file.
These are additional volumes using various atom selection methods. More details on the various atom selection codes -- e.g. B+, BD, &c.
Structure Lists :: These are additional pdb structure sets (they are explained in the above paper) and their resulting volumes (if available). All are arranged by atom selection method. In addition to the lists, we have the pdb files for each list tar'ed and gzip'ed here or you can get them by touching the "*" under the D heading
simple98.atom-defs.dat
Atom definition file with radii (description). simple98.resi-defs.dat Residue definition file (description).
M Gerstein, J Tsai & M Levitt (1995). "The volume of atoms on the protein surface: Calculated from simulation, using Voronoi polyhedra," Journal of Molecular Biology 249: 955-966.
mbg95.atom-defs.dat
Atom definition file with radii (description). mbg95.resi-defs.dat Residue definition file (description). mbg95.pdblist.dat
List of structures used. mbg95.vol173.dat
Final set of 173 volumes from atoms of 21 amino acids.
Chothia, C. (1975). Structural invariants in protein folding. Nature 254, 304-308.
chc75.atom-defs.dat
Atom definition file with radii (description). chc75.resi-defs.dat
Residue definition file (description). chc75.vol173.std.BL-.dat
Final set of 173 volumes from atoms of 21 amino acids. chc75.atom-vols.std.BL-.dat
Detailed volumes for the 18 basic atom types. chc75.residue-vols.std.BL-.dat
Volumes for each residue. Used the extra99.pdblist.std.dat and BL- atom selection.
Richards, F. M. (1974). The Interpretation of Protein Structures: Total Volume, Group Volume Distributions and Packing Density. J. Mol. Biol. 82, 1-14.
fmr74.atom-defs.dat
Atom definition file with radii (description). fmr74.resi-defs.dat Residue definition file (description). fmr74.vol173.std.BL-.dat
Final set of 173 volumes from atoms of 21 amino acids. fmr74.atom-vols.std.BL-.dat
Detailed volumes for the 18 basic atom types. fmr74.residue-vols.std.BL-.dat
Volumes for each residue. Used the extra99.pdblist.std.dat and BL- atom selection.
