Protein Structure Selection
Option 1: upload one or more PDB files
? Select one or more PDB files for upload. If multiple files are selected, they should already be aligned with each other. Selected files can be removed by clicking on the name to the right.
Option 2: automated retrieval via PDB ID
? Enter the ID of a single PDB file. The file is then automatically retrieved from RCSB.
load example
Structure Pre-Processing Options
Add hydrogen atoms with reduce
? Missing hydrogen atoms are added to the PDB file by the reduce tool.
Generate multimer with MakeMultimer
? Missing multimer copies are generated by the MakeMultimer tool using the transformation matrix provided by the PDB file.
Hydrogen atom processing
? This setting allows to fine-tune how hydrogen atoms should be dealt with when processing the input PDB, and can distinguish between hydrogen atoms in PDB protein atom records (ATOM) and hydrogen atoms in non-protein atom records (HETATM).
Hetero atom processing
? Hetero atoms are non-protein atoms listed under "HETATM" in a PDB file. Some PDB files also contain dummy atoms as HETATM records, for example membrane dummy atoms in PDBs from the OPM database. This settings can be used to specify how hetero atoms should be dealt with when processing PDB input.
Skip non-standard residues
? Protein atoms are listed under "ATOM" in a PDB file. If enabled, all "ATOM" records with other than standard residue names (ALA, ARG, ASN, ASP, CYS, GLN, GLU, GLY, HIS, ILE, LEU, LYS, MET, PHE, PRO, SER, THR, TRP, TYR, VAL) will be ignored when loading the PDB file. Atoms in "HETATM" records are not affected by this.
Load alternative locations of atoms
? Some atoms have multiple possible locations in the input protein file. By default, only the primary location is considered and the other locations are ignored. If enabled, all locations will be kept, which means that all alternative locations will be loaded as additional atoms.
PoreID Settings
What should be calculated
? By default, Pore ID generates results for pores and cavities. This can be restricted to only pores (accessible from the protein surface) or to only cavities (completely enclosed by the protein).
Probe radius (Å)
? After the solvent accessible surface (SAS) of the protein is computed (see above), PoreID "rolls" a probe across this surface and removes shallow surface regions that are not deeper than the probe. The higher this value, the deeper surface areas need to be before they are considered to be part of a pore. The default value is 4.0 Å.
Solvent radius (Å)
? To identify pores on the surface, Pore ID checks if enclosed areas in the protein are accessible for the surrounding solvent, i.e. water molecules with a radius of 1.4 Å. If the value is increased, hollow areas in the protein must also be accessible for these larger molecules to be classified as pores and not cavities. The default value is 1.2 Å.
Resolution (Å)
? PoreID places the protein on a 3D grid. The resolution specifies the length of a single grid box. The smaller the resolution value, the more fine-grained the computed pores, but also the potentially longer the required runtime. The default value is 3.0 Å.
Volume threshold (ų)
? Minimum volume (size) of pores and cavities. Smaller potential pores and cavities are not included in the results or further analysis steps. The default value is 50 ų.
AxisTrace Settings
Run AxisTrace
? Determines the axis of a pore or cavity and writes it into a pseudo PDB file for visualisation. Some pores have multiple axes, in which cases several output files are generated.
Minimum surface patch area (Ų)
? Minimum area of a pore surface patch in for it to count as a potential pore axis origin. The default value is 30 Ų.
GateOpen Settings
Run GateOpen
? Rotates the shared lining residues of two neighbouring pores in an effort to open the gate between them as much as possible. The result is a PDB file of the entire protein with the rotated residues.
Clash tolerance (Å)
? Allowed van der Waals radius overlap for rotamer generation. Lowering the clash tolerance can substantially speed up the GateOpen runtime, but too low values can also eliminate all potential rotamers. The default value is 0.75 Å.
Gate difficulty
? Some amino acids only have a small number of possible rotamers, while others have over 10,000. Depending on the number of residues in the gate and the number of possible rotamers of each gate residue, opening the gate can be very fast or take a long time. This setting allows to skip gates that are likely to take a long time to compute.