Content of each directory : ==================================== - .pdb: bound structure - .analysis: a automatically generated report on the results of this complex - .pdb: unbound structures - .contactdis: the shortest heavy-atom distance between every residue in .pdb and the partner protein residues below 5A are considered interface residues - .zone: ProFit zone commands to calculate the ligand RMSD from the bound form - .izone: ProFit zone commands to calculate the interface RMSD from the bound form - (optional) .symzone, .symizone: ProFit zone commands to calculate RMSDs from the bound form by fitting to the other symmetric unit Directory : ------------------------ - .sur: List of all residues with NACCESS relative main chain or side chain accessibility >= 15 % - .: can be PIER, ProMate, WHISCY, PINUP, SPPIDER or cons-PPISP for every surface residue: the residue number, value and rank for the current predictor is given. If a residue is absent from the prediction, it is given a value of -999 - .bins: For every surface residue, the distance to the partner is given (from .contactdis) and for every predictor, the bin. For WHISCY, ProMate, PIER and PINUP, the bin is equal to the rank. For SPPIDER and PPISP, the bin is mapped from the value (see the mapping files in cport/). - .cport: List of all residues predicted by CPORT (threshold 3) - .dockpred--: List of residues predicted by analyzing the most abundant contacts (in the top 400, equal number as CPORT predictions, no surface accessibility filter) - .resdist: Intramolecular shortest heavy atom distances between residues Directory : The docking results ---------------- can be run1, run2 or run3 - Run1 and run2 were done using CPORT using threshold3, discarding 7/8 of the restraints at random (noecvpart = 8/7) run1: ntrials=1, structures_it0 = 10000 run2: ntrials=5, structures_it0 = 5000 - Run3 was done using center-of-mass restraints run3: ntrials=5, structures_it0 = 10000 Every run contains Directories it0, it1 and water (the three stages) Runs in which no structure in run1/it0 or run3/it0 was correct contain no other runs/iterations Directory it0: -------------- - complex_.pdb: top 400 structures from it0. is just an identifier - complex_.contacts: (only if at least one of the structures has CAPRI * quality) - file.compress: all 5000/10000 structures of it0 in compressed format. Use decompress in the tools directory with the unbound structures as reference structures to retrieve the PDBs - file.nam: the names of all structures sorted by HADDOCK score - file.list: the names of all structures and their HADDOCK scores - file.fnat: fraction of native contacts for all structures (only if at least one of the structures has CAPRI * quality) - i-RMSD.dat, l-RMSD.dat: interface and ligand RMSDs to the bound form (calculated on CA,C,O,N atoms) - (optional) sym-i-RMSD.dat, sym-l-RMSD.dat: interface and ligand RMSDs to the bound form, using the other symmetric unit - energies.stat: various energies for every structure Directory it1: -------------- - complex_.pdb: all structures from it1. is the rank after it0 - complex_.contacts: all contacts from complex_.pdb - file.nam, file.list, file.fnat, (sym-)(i-)RMSD.dat, energies.stat: see above Directory water: ---------------- - complex_w.pdb: all structures from water. is the rank after it0 - complex_w.contacts: all contacts from complex_w.pdb - file.nam, file.list, file.fnat, (sym-)(i-)RMSD.dat, energies.stat: see above - file.prmsd: pairwise ligand RMSD matrix between all water structures (note that this is a true ligand RMSD matrix unlike the default pairwise matrix generated by HADDOCK, which is an interface-ligand-RMSD matrix) The first two numbers indicate the rank of the structure in file.nam - cluster.out: clustering of the solutions with a ligand RMSD radius of 10 A and a minimal cluster size of 4. The numbers indicate the rank of the structure in file.nam. - file.cluster: For every structure, the cluster to which it belongs (cluster 1 is the largest, see above; 0 means that the structure did not cluster)