eBDIMS

Start a new simulation

This tutorial can be downloaded as a pdf-file.

Required input

A new eBDIMS simulation is initiated here. The minimal set of input data comprises:

• a job name (< 150 alphanumeric characters). The job name can be used to identify the submitted job in the public server queue.
• two distinct configurations of the same atomic protein strucutre (referred to as start and target end-states, respectively).

End-state structures

Start and target end-state structures can be either

• retrieved automatically from rcsb.org by providing structure PDB IDs, or
• manually uploaded as coordinate files in strict PDB format.

If start and target structures present different number of chains, only the number of chains in the shorter pdb structure will be accounted for

Curated and correctly formatted input files are available for each resolved example and can be used as template when preparing new end-state strucutres.

Type 1NQL or 1nql to fetch the entire PDB structure 1NQL.

One can specify chains of interest by indicating them immediately after the strucutre ID (separated by a colon). PDB IDs are case insensitive. Valid chain identifiers are A-Z (i.e. single characters). See examples below:

Uploaded PDB files should have file extension .pdb. The PDB header is optional.

Please double check for missing atoms, alternative conformations, etc that could potentially result in format errors. Use specialized software to check the integrity of the PDB files (Molprobity, Procheck, What if).

We recommend reconstructing small residue gaps (<5 residues) with specialized software such as Modeller.

Optional input

Job description

Each job can contain an elaborated description (< 500 characters).

Email address

It is possible to associate the job with an email address. When a new email address is entered into the system, a temporary password is sent to the email address which allows the user to log in to the dashboard page.

Ensemble structures

A key feature of the eBDIMS web application is to facilitate classification of protein structures by their projection onto the intrinsic normal mode (NM) and principal component (PC) motion-spaces. For that purpose, input end-state files can be accompanied by a third input file, the ensemble.

A detailed tutorial on how to prepare an ensemble file is available here.

Briefly, the ensemble file should contain at least three structures of the same protein in different conformations in a multi-pdb format with coordinate sets delimited by MODEL and ENDMDL labels (as in NMR pdb-entries. See example below).

  
    MODEL
      ( coordinate set 1 )
    ENDMDL
    MODEL
      ( ... )
    ENDMDL
    MODEL
      ( coordinate set n )
    ENDMDL
    
  

Note that:

• the ensemble should include both the start and target end-state structures,
• each coordinate set should be complete (i.e. no missing residues),
• all coordinate sets must have the same number of residues,
• 1000 models are considered at most,
• total file size is limited to 16 Mb.

For help with ensemble preparation, check the Bio3D tool or ProDy packages.

Submitted jobs

When a job is submitted to the eBDIMS server, the input structures are validated server-side against the criteria described above. Carbon-alpha residues are selected and any duplicates removed. The pdbParser script is used to select the common regions of end-state structures. Similarly, individual ensemble structures are checked for integrity and that all models have the same number of residues. Each model is assigned a model index (1–1000).

An error message will be thrown if any anomaly is detected (e.g. missing residues or inconsistent labelling), otherwise the new job will enter the server queue and the user will be automatically redirected to the associated and unique result page.

It is recommended to bookmark the result page if the job was submitted without an email address