IntroductionPlease note that computations may take up to few days. Execution time depends not only on the size of the structure, but also on computational resources available. If you don't receive a response from the server within one week please inform us - we will check the status of your job. The solutions will be deleted one week after you receive the results.
We have limited computer resources. Please don't submit more than two jobs before receiving results from the server.
The average execution time for the Benchmark 4.0 (176 structures) was ca. 23 hours (the shortest: 3 hours, the longest: 6 days). The average execution time for a subset of 29 structures being executed in parallel was ca. 1 day 5 hours (the shortest: 20 hours, the longest: 1 day 13 hours).
Please send any comments or/and bug reports to the developers: SwarmDock [at] cancer.org.uk or Mieczyslaw.Torchala [at] cancer.org.uk.
ScopeThe web service is for the flexible modelling of protein-protein complexes using the SwarmDock algorithm which incorporates a normal modes approach [1,2]. Uploaded structures (in PDB format) of ligand and receptor must obey to only three simple rules:
- Files must have TER record after each chain (also after last one).
- Generally, only standard residues are allowed. However, our server recognises (as ATOM or HETATM) the following:
- HSE, HSP, HSD and changes them to HIS,
- MSE and changes to MET,
- PCA and changes to ALA,
- PTR and changes to TYR,
- ABA and changes to ALA,
- TYS and changes to TYR,
- SEC and changes to CYS,
- ASX and changes to ASP,
- GLX and changes to GLU,
- XLE and changes to LEU,
- CSD and changes to CYS,
- DLE and changes to LEU,
- DVA and changes to VAL,
- CGU and changes to GLU.
- Submitting files with missing residues is not encouraged. However, we will try to repair your files (by modelling loops with ALA) to make them ready for our server.
- Preprocessing (checking for structural correctness, modelling missing and non-standard residues, structure minimisation).
- Docking (point generation and running PSO).
- Postprocessing (structure minimisation, rescoring and clustering).
- Results returned, an archive with PDB formatted structures for members of each cluster. Additional files:
- clusters.txt (list of results in format: pdb file, number of members in the cluster, total number of contacts between receptor and ligand with cut-off at sum of van der Waals radii + 20%, number of contacts for receptor's residue list submitted by user, number of contacts for ligand's residue list submitted by user),
- contacts.txt (list of contacts with cut-off at sum of van der Waals radii + 20%, R-receptor, L-ligand, UR-user receptor, UL-user ligand),
- energies.txt (list of solutions with corresponding energies),
- best10.pdb (lowest energy structures of first ten clusters),
- ligand.pdb and receptor.pdb (files used as an input, may be different from these uploaded by the user because of repairs),
- uploaded_ligand.pdb and uploaded_receptor.pdb (files uploaded by the user),
- job.txt (details about submitted job).
If you wish to choose residues belonging to the binding site, we will provide you with information on the accessibility and conservation of the binding site residues. Residues are ordered due to the product of these two factors.
ExampleLet's assume that we want to dock a complex 2OUL. We have input files for both the receptor, TER_2OUL_r_u.pdb, and the ligand, TER_2OUL_l_u.pdb, with an added TER record after each chain. We submit it to the server as a full blind docking case (with default number of normal modes set equal to 5 for both receptor and ligand). Results for this submission are returned via the following link, allowing for some visualisation of the clustered solutions (Jmol ):