1. What is your policy regarding submitting data?
We no longer accept maps for upload. The web site is maintained on a legacy basis without any guarantees.
2. Does emotion require multiple maps to predict polymorphism?
No. Our vibrational analysis is based on a single static model and assumes that the "energy landscape" of motion is approximately harmonic, i.e. centered around a minimum conformation. Clearly, this is a stark simplification, but it has been shown for decades in the atomic structure literature that normal mode analysis (NMA) has merits when describing the global motions of biomolecules. On the large scale, many proteins move as if they were elastic bodies. Hence, as a first approximation, it is sufficient to use a single deformable model starting from one known conformation.
3. How reliable is the amplitude of the animated motions?
It is important to understand that the amplitudes of the modes, as well as the spring constant used in our elastic model, are essentially arbitrary. The vibrational analysis returns infinitesimal displacements (much like a mathematical derivative measures infinitesimal changes in a function). To create a finite size displacement (corresponding to a tangent of a mathematical function in our analogy) we have to amplify the displacement by a finite size amplitude. This is necessary for the visualization of the modes. Imagine a swinging pendulum. The deviation of the pendulum from the resting positon must be reasonably large for the oscillation to be discernible. Likewise, we initialize our animations with a swinging amplitude that facilitates visualization of the modes. This amplitude is scaled based on the size of the molecule, but experimentally observed motions of molecules may differ in amplitude.
4. Does NMA adequately describe barrier-crossing transitions between multiple states?
This is a frequent misapprehension. It is clear that the elastic bending motions that can be simulated by our simple harmonic analysis involve very low energy barriers. More complex transitions across high energy barriers that involve a non-harmonic description of the energy landscape are beyond reach of our method. Our local predicitons can give a reasonable lead how the molecule behaves when deviating from the known conformation, but for large deformations the harmonic approximation will be less reliable.
5. Why are 12 modes shown for each EM map?
Researchers have shown that for opening and closing motions documented in the PDB one of the 12 lowest-frequency normal modes is typically closely related to the observed change. However, this cutoff is essentially arbitrary and is imposed only for practical reasons.
6. Does the ranking of the modes reflect their functional relevance?
The frequency-dependent ranking is a good indicator of the "relevance likelihood", but ultimately not stringent enough to predict whether such motions could be observed as polymorphism in EM or X-ray structures. Despite the well-documented successes of the method: We can not guarantee a priori that a particular low-frequency mode (or a linear combination of more modes) is relevant.
7. Why the option to annotate modes?
One way to validate the modes is to screen them against existing experimental data. This is where the user community can contribute, because they can rank the modes based on agreement with experiments (e.g. polymorphism in micrographs, FRET data, etc), and it is only such feedback that makes a public depository worthwhile.