Format of the input structures and trajectories

General requirements for uploaded pdb files:

  • The non-amino acid residues found in the PDB structure of the protein will NOT be removed, but will be considered as cofactors in TRAPP-pocket simulations. Therefore, ligands must be removed from the binding site (in the reference structure and in the trajectories) before the PDB structure can be provided as an input.
  • Note that all input structures must have high sequence similarity in the binding site region to the sequence of the reference structure.
  • Non-standard residues of the binding site will not be taken into consideration for simulations or superimpositions, but will be present in the results .
  • If you would like to analyze several protein sub-units in one protein structure, you should remove the TER line between them, otherwise they will be considered as different snapshots.
  • Water molecules and ions should be removed from the reference file and from the trajectories, unless you want to keep crystallographic water molecules that occupy some pocket regions.
  • The L-RIP and RIPlig procedures remove all water molecules and ligands (including cofactors) automatically.

Input structures required:

  • Reference PDB structure of a protein:

The reference PDB structure is used for alignment or superimposition of snapshots from all trajectories, and as a reference structure for detection of transient pocket regions. If you are going to simulate protein conformational changes using MD, L-RIP, RIPlig or tCONCOORD, the structure must be complete (no missing residues) and residues must have standard names. However, it may contain some missing atoms (that can be generated using NAMD, see input parameters). For TRAPP-pocket and TRAPP-analysis, only the binding site must be complete.

  • The position of a binding pocket of interest relative to the reference structure can be defined in 2 alternative ways:
  1. Supply ligand coordinates in a PDB format for a ligand file placed at the center of the region of interest (the geometric center of the ligand atoms defines the pocket center of the grid over the binding site). Any small molecule or even one atom can be used as a reference ligand. The atomic coordinates of the reference ligand should be in the same frame to those of the protein reference structure.
  2. Supply the x, y, z coordinates of the center of the grid over the binding site relative to the reference protein structure.

Input trajectories:

The input of trajectories is optional and is used for running TRAPP-analysis and TRAPP-pocket only.

Trajectories or ensembles of protein conformations may be input in 2 alternative ways:

  • The trajectory or ensemble can be prepared as a set of concatenated PDB snapshots, each starting with MODEL (or at least the first snapshot should start with MODEL) and ending with either ENDMDL, END or TER lines.
  • The trajectory in DCD format (generated by NAMD) and the corresponding PDB file of a single snapshot.

In both cases the trajectory may be compressed by gzip (*gz file).