Normal mode analysis TSD

The journal for this task can be found here.

Introduction

For this task 2gk1 is chosen as reference structure since it contains a ligand similar to the native one and therefore allows to easily observe the effect the presence of the ligand exerts on the normal modes. All HETATOMs but the one of this compound, NGT, were removed from the PDB structure.

ElNemo

wip

    What information do the different servers provide?
   How are the normal modes calculated, that is from which part of the structure? How many normal modes could in principle be calculated for your protein without any cutoff.
   Visualize the modes (provided by server or using for example PyMol or VMD) and describe what movements you observe: hinge-movement, “breathing”…
   Which regions of your protein are most flexible, most stable?
   Can you identify domains for your protein? Compare to the CATH, SCOP and Pfam domains of your protein.
   Can you observe notable differences between the normal modes calculated by the different servers?
   For WEBnm@ try the amplitude scaling and vectors option.
   Try the comparison/upload of second structure option, if: (i) you have PDB structures in different conformations or (ii) your protein has a bound ligand. Then either upload a structure with and one without the ligand, or delete the ligand in your structure. Note: Due to the force field that considers only C_alpha atoms, only changes in the backbone will give results. The model does not resolve changes in side-chain positions or SNPs.

Comparison to Molecular Dynamics

   When your MD simulations are finished, compare the lowest-frequency normal modes with your MD simulation using visualization software, e.g. PyMol or VMD. Can you observe different movements or similar dynamics? If possible, compare an overlay of the lowest-frequency modes to your MD simulation. You can superimpose the normal modes for example in VMD.
   What are the advantages and disadvantages of NMA compared to MD?