FAQ

What can I do with the NMSim web server?

The NMSim web server allows performing normal mode-based geometric simulations for exploring biologically relevant conformational transitions in proteins. As a result, a trajectory of sampled protein conformations is obtained. The generated structures are of good stereochemical quality and can serve as input to docking approaches or as starting points for more sophisticated sampling techniques.

How does the NMSim approach work?

NMSim is a three-step multiscale approach that incorporates information about preferred directions of protein motions into a geometric simulation algorithm. The first step is a coarse-graining ("rigid cluster decomposition") of the protein structure using the FIRST approach based on rigidity theory. FIRST has been developed by M. Thorpe and coworkers and builds on ideas by D. Jacobs, L. Kuhn, and M. Thorpe. In the second step, a rigid cluster normal-mode analysis (RCNMA) provides low-frequency normal modes. The normal modes are used in the third step (NMSim) to extend the recently introduced idea of constrained geometric simulations of diffusive motions in proteins by biasing backbone motions of the protein, whereas side-chain motions are biased toward favorable rotamer states. The generated structures are iteratively corrected regarding steric clashes and stereochemical constraint violations. In total, when applied repetitively over all three steps, the procedure effciently generates a series of stereochemically allowed conformations that lie preferentially in the subspace spanned by low-frequency normal modes.

Where do I get more detailed information about the single steps?

FIRST and application for coarse-graining:

- Jacobs, D., Rader, A. J., Kuhn, L., Thorpe, M. F. Proteins 2001, 44, 150-165.
- Gohlke, H., Thorpe, M. F. Biophys. J. 2006, 91, 2115-2120.

RCNMA:

- Ahmed, A., Gohlke, H. Proteins 2006, 63, 1038-1051.
- Ahmed, A., Villinger, S., Gohlke, H. Proteins 2010, 78, 3341-3352.

NMSim:

- Ahmed, A., Rippmann, F., Barnickel, G., Gohlke, H. J. Chem. Inf. Model. 2011, 51, 1604-1622.
- Krüger, D.M., Ahmed, A., Gohlke, H. Nucleic Acids Res. 2012, 40, W310-W316, doi:10.1093/nar/gks478.

What do I need to perform an NMSim run?

You need one (or two, see below) PDB file(s) (*.pdb) in standard format or a PDB-ID. Please note that alternative sidechain conformations are not allowed.

How can I perform an NMSim run?

Upload one (or two) PDB files or type in a valid PDB-ID and choose the type of simulation (see below for a description). This will provide default parameters for the three steps, which have turned out to provide reasonable results on the systems tested. If you want to test the level of coarse-graining of the structure without starting a simulation, apply the "Preview RCD". To make a structure more floppy, lower the values for "E-cutoff for H-bonds" and/or "Hydrophobic cutoff ". Pressing the "Submit" button will start a simulation with the given level of coarse-graining. Note that you need to enter the given Capture Code in both cases. In the case of a simulation run, a link to the results page will appear immediately. The results page is updating itself every minute, the results will appear after completion of the calculations. Please note that this may take some hours (see estimated runtime in new window after job submission) depending on the load of the server and the size of your system. If you provide an (optional) email address, the link will be sent to you by email.

Which type of simulation to choose?

For an unbiased exploration of conformational space, choose either the "small scale motions" or "large scale motions" option. The former is suitable for exploring loop motions and generating ensembles for docking or distinct starting structures for more sophisticated simulation approaches. The latter is suitable for simulating domain movements. The "radius of gyration(ROG)-guided motions" option also moves the protein without any bias through conformational space; however, at each step, out of a few candidate conformations, the one with the lowest (or largest, depending on the parameter "ROG mode") ROG is chosen to continue the simulation. Over the course of the trajectory, this leads to more compact (extended) structures. Generating more compact structures has proven successful for simulating unbound to bound transitions in proteins. Finally, the "targeted simulation" option allows generating pathways between a starting and a target structure. Note that, because protein motions are preferentially performed in low-energy normal mode space, a perfect convergence to the target structure is not always achieved.

What is the meaning of the FIRST, RCNMA, and NMSim parameters?

Please see here for a detailed description of the parameters.

I got an error message when I try to submit a job. What can I do?

All error messages come along with a description that should help the user to fix the problem. Please also check that your PDB file fulfills the input conditions (see PLEASE NOTE). However, if a problem can not be solved, please do not hesitate to contact support[at]nmsim.de.

I got a logfile as a result. Where is the problem?

Please open the logfile and search for the keyword "ERROR". Here you will find a detailed description of the problem. Please also check that your PDB file fulfills the input conditions (see PLEASE NOTE). However, if a problem can not be solved, please do not hesitate to contact support[at]nmsim.de.

What cannot be done with the NMSim web server?

As is also true for other geometry-based simulation approaches, NMSim does not sample from a thermodynamic ensemble and, hence, does not provide a quantitative description of the distribution of the generated conformations, nor does it provide conformational energies. Still, such energies can be obtained by post-processing NMSim-generated conformations by molecular mechanics calculations. Another limitation arises from the fact that local structural rearrangements may not be well described by low-frequency modes that are used to guide backbone motions during the simulation. Finally, NMSim will fail if conformational changes require a substantial change in the constraint network underlying the steps of rigid cluster decomposition and geometric simulation. The latter precludes the use of NMSim in the current version for folding simulations.